[{"_id":"9985","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-11T11:07:51Z","ddc":["612"],"file_date_updated":"2021-09-08T12:57:06Z","department":[{"_id":"PeJo"}],"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"08","intvolume":" 12","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"creator":"cchlebak","file_size":18310502,"date_updated":"2021-09-08T12:57:06Z","file_name":"2021_NatureCommunications_Watson.pdf","date_created":"2021-09-08T12:57:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9991","checksum":"1bf4f6a561f96bc426d754de9cb57710"}],"language":[{"iso":"eng"}],"issue":"1","volume":12,"article_number":"5083","citation":{"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.","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","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","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.","short":"J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Alexandra","last_name":"Pinggera","full_name":"Pinggera, Alexandra"},{"first_name":"Hinze","full_name":"Ho, Hinze","last_name":"Ho"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"article_processing_charge":"Yes","external_id":{"pmid":["34426577 "],"isi":["000687672000006"]},"title":"AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions","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).","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"23","publication":"Nature Communications","doi":"10.1038/s41467-021-25281-4","date_published":"2021-08-23T00:00:00Z","date_created":"2021-09-05T22:01:23Z"},{"oa_version":"Published Version","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."}],"intvolume":" 11","month":"09","language":[{"iso":"eng"}],"file":[{"date_created":"2021-09-02T14:05:43Z","file_name":"2021_SciPostPhys_DeNicola.pdf","date_updated":"2021-09-02T14:05:43Z","file_size":373833,"creator":"cchlebak","checksum":"e4ec69d893e31811efc6093cb6ea8eb7","file_id":"9984","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"eissn":["2666-9366"],"issn":["2542-4653"]},"ec_funded":1,"issue":"3","volume":11,"_id":"9981","keyword":["General Physics and Astronomy"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["519"],"date_updated":"2023-08-11T10:59:29Z","department":[{"_id":"MaSe"}],"file_date_updated":"2021-09-02T14:05:43Z","oa":1,"publisher":"SciPost","quality_controlled":"1","publication":"SciPost Physics","day":"02","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-09-02T11:49:47Z","doi":"10.21468/scipostphys.11.3.048","date_published":"2021-09-02T00:00:00Z","article_number":"048","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 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.","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","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","short":"S. De Nicola, SciPost Physics 11 (2021).","ieee":"S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” SciPost Physics, vol. 11, no. 3. SciPost, 2021.","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."},"title":"Importance sampling scheme for the stochastic simulation of quantum spin dynamics","article_processing_charge":"No","external_id":{"arxiv":["2103.16468"],"isi":["000692534200001"]},"author":[{"first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola"}]},{"_id":"9960","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-08-11T10:57:51Z","department":[{"_id":"MaSe"}],"oa_version":"Submitted Version","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."}],"month":"08","intvolume":" 127","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.13160"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","issue":"9","volume":127,"ec_funded":1,"article_number":"090602","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","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.","short":"N. Maskara, A. Michailidis, W.W. Ho, D. Bluvstein, S. Choi, M.D. Lukin, M. Serbyn, Physical Review Letters 127 (2021).","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.","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.","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."},"title":"Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving","author":[{"full_name":"Maskara, N.","last_name":"Maskara","first_name":"N."},{"last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"W. W.","last_name":"Ho","full_name":"Ho, W. W."},{"last_name":"Bluvstein","full_name":"Bluvstein, D.","first_name":"D."},{"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","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"external_id":{"arxiv":["2102.13160"],"isi":["000692200100002"]},"article_processing_charge":"No","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.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"27","publication":"Physical Review Letters","isi":1,"year":"2021","date_published":"2021-08-27T00:00:00Z","doi":"10.1103/PhysRevLett.127.090602","date_created":"2021-08-28T08:08:58Z"},{"year":"2021","isi":1,"publication":"Physical Review B","day":"15","date_created":"2021-08-28T16:44:55Z","date_published":"2021-08-15T00:00:00Z","doi":"10.1103/PhysRevB.104.L081112","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.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","citation":{"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.","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.","short":"M. Sonner, M. Serbyn, Z. Papić, D.A. Abanin, Physical Review B 104 (2021).","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000689734500009"],"arxiv":["2012.15676"]},"author":[{"last_name":"Sonner","full_name":"Sonner, Michael","first_name":"Michael"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."}],"title":"Thouless energy across the many-body localization transition in Floquet systems","article_number":"L081112","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":104,"issue":"8","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."}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.15676"}],"intvolume":" 104","month":"08","date_updated":"2023-08-11T10:57:09Z","department":[{"_id":"MaSe"}],"_id":"9961","article_type":"letter_note","type":"journal_article","status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","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."},"title":"Monocular reconstruction of neural face reflectance fields","article_processing_charge":"No","external_id":{"isi":["000739917304096"],"arxiv":["2008.10247"]},"author":[{"first_name":"Mallikarjun","full_name":"B R, Mallikarjun","last_name":"B R"},{"full_name":"Tewari, Ayush","last_name":"Tewari","first_name":"Ayush"},{"first_name":"Tae-Hyun","full_name":"Oh, Tae-Hyun","last_name":"Oh"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Hans-Peter","last_name":"Seidel","full_name":"Seidel, Hans-Peter"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"first_name":"Mohamed","last_name":"Elgharib","full_name":"Elgharib, Mohamed"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","day":"01","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-08-24T06:03:00Z","date_published":"2021-09-01T00:00:00Z","doi":"10.1109/CVPR46437.2021.00476","page":"4791-4800","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.","oa":1,"publisher":"IEEE","quality_controlled":"1","ddc":["000"],"date_updated":"2023-08-11T11:08:35Z","department":[{"_id":"BeBi"}],"file_date_updated":"2021-08-24T06:02:15Z","_id":"9957","status":"public","conference":{"start_date":"2021-06-20","end_date":"2021-06-25","location":"Nashville, TN, United States; Virtual","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"type":"conference","language":[{"iso":"eng"}],"file":[{"date_updated":"2021-08-24T06:02:15Z","file_size":4746649,"creator":"bbickel","date_created":"2021-08-24T06:02:15Z","file_name":"R_Monocular_Reconstruction_of_Neural_Face_Reflectance_Fields_CVPR_2021_paper[1].pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9958","checksum":"961db0bde76dd87cf833930080bb9f38"}],"publication_status":"published","publication_identifier":{"issn":["1063-6919"],"isbn":["978-166544509-2"]},"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"09","scopus_import":"1"},{"department":[{"_id":"JaMa"}],"file_date_updated":"2021-09-08T09:46:34Z","ddc":["621"],"date_updated":"2023-08-11T11:09:07Z","status":"public","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9973","volume":387,"ec_funded":1,"file":[{"creator":"cchlebak","date_updated":"2021-09-08T09:46:34Z","file_size":505971,"date_created":"2021-09-08T07:34:24Z","file_name":"2021_CommunMathPhys_Wirth.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8a602f916b1c2b0dc1159708b7cb204b","file_id":"9990"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publication_status":"published","month":"08","intvolume":" 387","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"title":"Complete gradient estimates of quantum Markov semigroups","author":[{"first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth"},{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2007.13506"],"isi":["000691214200001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.","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.","ista":"Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791."},"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"date_published":"2021-08-30T00:00:00Z","doi":"10.1007/s00220-021-04199-4","date_created":"2021-08-30T10:07:44Z","page":"761–791","day":"30","publication":"Communications in Mathematical Physics","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments."},{"_id":"10000","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2023-08-14T06:35:17Z","file_date_updated":"2022-05-13T07:40:15Z","department":[{"_id":"SaSi"}],"oa_version":"Published Version","pmid":1,"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."}],"intvolume":" 62","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2022-05-13T07:40:15Z","file_size":19707796,"creator":"dernst","date_created":"2022-05-13T07:40:15Z","file_name":"2021_IOVS_Schmitt.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c430967746f653aa1ae84ee617f62b73","file_id":"11369","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1552-5783"],"issn":["0146-0404"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":62,"issue":"10","article_number":"14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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.","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.","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."},"title":"Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression","external_id":{"isi":["000695230000014"],"pmid":["34398198"]},"article_processing_charge":"Yes","author":[{"last_name":"Schmitt","full_name":"Schmitt, Heather M.","first_name":"Heather M."},{"full_name":"Fehrman, Rachel L.","last_name":"Fehrman","first_name":"Rachel L."},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"first_name":"Huan","last_name":"Yang","full_name":"Yang, Huan"},{"last_name":"Guo","full_name":"Guo, Lian Wang","first_name":"Lian Wang"},{"full_name":"Schlamp, Cassandra L.","last_name":"Schlamp","first_name":"Cassandra L."},{"full_name":"Pelzel, Heather R.","last_name":"Pelzel","first_name":"Heather R."},{"first_name":"Robert W.","last_name":"Nickells","full_name":"Nickells, Robert W."}],"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). ","oa":1,"quality_controlled":"1","publisher":"Association for Research in Vision and Ophthalmology","publication":"Investigative Ophthalmology and Visual Science","day":"16","year":"2021","isi":1,"has_accepted_license":"1","date_created":"2021-09-12T22:01:23Z","date_published":"2021-08-16T00:00:00Z","doi":"10.1167/IOVS.62.10.14"},{"doi":"10.1007/s00029-021-00698-3","date_published":"2021-08-30T00:00:00Z","date_created":"2021-09-12T22:01:22Z","has_accepted_license":"1","isi":1,"year":"2021","day":"30","publication":"Selecta Mathematica","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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).","author":[{"first_name":"Peter","last_name":"Koroteev","full_name":"Koroteev, Peter"},{"id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","first_name":"Petr","full_name":"Pushkar, Petr","last_name":"Pushkar"},{"last_name":"Smirnov","full_name":"Smirnov, Andrey V.","first_name":"Andrey V."},{"first_name":"Anton M.","last_name":"Zeitlin","full_name":"Zeitlin, Anton M."}],"external_id":{"isi":["000692795200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Quantum K-theory of quiver varieties and many-body systems","citation":{"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.","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","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.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"87","issue":"5","volume":27,"publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"publication_status":"published","file":[{"date_created":"2021-09-13T11:31:34Z","file_name":"2021_SelectaMath_Koroteev.pdf","date_updated":"2021-09-13T11:31:34Z","file_size":584648,"creator":"cchlebak","checksum":"beadc5a722ffb48190e1e63ee2dbfee5","file_id":"10010","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 27","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"TaHa"}],"file_date_updated":"2021-09-13T11:31:34Z","date_updated":"2023-08-14T06:34:14Z","ddc":["530"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9998"},{"title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","author":[{"full_name":"Pulgar, Eduardo","last_name":"Pulgar","first_name":"Eduardo"},{"last_name":"Schwayer","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia"},{"first_name":"Néstor","full_name":"Guerrero, Néstor","last_name":"Guerrero"},{"first_name":"Loreto","full_name":"López, Loreto","last_name":"López"},{"full_name":"Márquez, Susana","last_name":"Márquez","first_name":"Susana"},{"full_name":"Härtel, Steffen","last_name":"Härtel","first_name":"Steffen"},{"first_name":"Rodrigo","full_name":"Soto, Rodrigo","last_name":"Soto"},{"full_name":"Heisenberg, Carl Philipp","last_name":"Heisenberg","first_name":"Carl Philipp"},{"full_name":"Concha, Miguel L.","last_name":"Concha","first_name":"Miguel L."}],"external_id":{"pmid":["34448451"],"isi":["000700428500001"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021)."},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e66483","doi":"10.7554/eLife.66483","date_published":"2021-08-27T00:00:00Z","date_created":"2021-09-12T22:01:23Z","day":"27","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2021","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"department":[{"_id":"CaHe"}],"file_date_updated":"2022-05-13T08:03:37Z","ddc":["570"],"date_updated":"2023-08-14T06:53:33Z","status":"public","keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9999","volume":10,"ec_funded":1,"file":[{"success":1,"file_id":"11371","checksum":"a3f82b0499cc822ac1eab48a01f3f57e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_eLife_Pulgar.pdf","date_created":"2022-05-13T08:03:37Z","file_size":9010446,"date_updated":"2022-05-13T08:03:37Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","month":"08","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}]},{"department":[{"_id":"KrCh"}],"date_updated":"2023-08-14T06:51:33Z","type":"conference","conference":{"end_date":"2021-07-02","location":"Rome, Italy","start_date":"2021-06-29","name":"LICS: Symposium on Logic in Computer Science"},"status":"public","keyword":["Computer science","Computational modeling","Markov processes","Probabilistic logic","Formal verification","Game Theory"],"_id":"10002","ec_funded":1,"publication_identifier":{"issn":["1043-6871"],"isbn":["978-1-6654-4896-3"],"eisbn":["978-1-6654-4895-6"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2104.07466","open_access":"1"}],"month":"07","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 ."}],"oa_version":"Preprint","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Dvorak, Wolfgang","last_name":"Dvorak","first_name":"Wolfgang"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"external_id":{"isi":["000947350400089"],"arxiv":["2104.07466"]},"article_processing_charge":"No","title":"Symbolic time and space tradeoffs for probabilistic verification","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"page":"1-13","date_published":"2021-07-07T00:00:00Z","doi":"10.1109/LICS52264.2021.9470739","date_created":"2021-09-12T22:01:24Z","isi":1,"year":"2021","day":"07","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"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."},{"citation":{"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.","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.","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","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","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.","short":"S. Floreani, F. Redig, F. Sau, Stochastic Processes and Their Applications 142 (2021) 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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Floreani, Simone","last_name":"Floreani","first_name":"Simone"},{"last_name":"Redig","full_name":"Redig, Frank","first_name":"Frank"},{"last_name":"Sau","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico"}],"external_id":{"arxiv":["1911.12564"],"isi":["000697748500005"]},"article_processing_charge":"Yes","title":"Hydrodynamics for the partial exclusion process in random environment","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"has_accepted_license":"1","isi":1,"year":"2021","day":"27","publication":"Stochastic Processes and their Applications","page":"124-158","date_published":"2021-08-27T00:00:00Z","doi":"10.1016/j.spa.2021.08.006","date_created":"2021-09-19T22:01:25Z","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.","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-08-14T06:52:43Z","ddc":["519"],"file_date_updated":"2022-05-13T07:55:50Z","department":[{"_id":"JaMa"}],"_id":"10024","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["hydrodynamic limit","random environment","random conductance model","arbitrary starting point quenched invariance principle","duality","mild solution"],"publication_identifier":{"issn":["0304-4149"]},"publication_status":"published","file":[{"file_id":"11370","checksum":"56768c553d7218ee5714902ffec90ec4","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-13T07:55:50Z","file_name":"2021_StochasticProcessesAppl_Floreani.pdf","creator":"dernst","date_updated":"2022-05-13T07:55:50Z","file_size":2115791}],"language":[{"iso":"eng"}],"volume":142,"ec_funded":1,"abstract":[{"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).","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 142"},{"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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"},"title":"Stochastic processes with expected stopping time","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"external_id":{"arxiv":["2104.07278"],"isi":["000947350400036"]},"article_processing_charge":"No","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).","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"day":"07","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","isi":1,"year":"2021","doi":"10.1109/LICS52264.2021.9470595","date_published":"2021-07-07T00:00:00Z","date_created":"2021-09-12T22:01:25Z","page":"1-13","_id":"10004","status":"public","keyword":["Computer science","Heuristic algorithms","Memory management","Automata","Markov processes","Probability distribution","Complexity theory"],"type":"conference","conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2021-06-29","location":"Rome, Italy","end_date":"2021-07-02"},"date_updated":"2023-08-14T06:52:07Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","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."}],"month":"07","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.07278"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-6654-4896-3"],"issn":["1043-6871"],"eisbn":["978-1-6654-4895-6"]},"publication_status":"published","ec_funded":1},{"date_published":"2021-09-01T00:00:00Z","doi":"10.1109/ISIT45174.2021.9518153","date_created":"2021-09-27T14:33:14Z","page":"2369-2374","day":"01","publication":"2021 IEEE International Symposium on Information Theory","isi":1,"year":"2021","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","oa":1,"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.","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","author":[{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Arman","full_name":"Fazeli, Arman","last_name":"Fazeli"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"last_name":"Goldsmith","full_name":"Goldsmith, Andrea","first_name":"Andrea"}],"external_id":{"arxiv":["2012.13378"],"isi":["000701502202078"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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."},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"related_material":{"record":[{"relation":"later_version","id":"10364","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-5386-8210-4"],"issn":["2157-8095"],"eisbn":["978-1-5386-8209-8"]},"publication_status":"published","month":"09","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.13378"}],"oa_version":"Preprint","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."}],"department":[{"_id":"MaMo"}],"date_updated":"2023-08-14T06:55:58Z","status":"public","type":"conference","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2021-07-20","location":"Melbourne, Australia","start_date":"2021-07-12"},"_id":"10053"},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","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.","date_created":"2021-09-21T15:58:59Z","date_published":"2021-09-21T00:00:00Z","doi":"10.1016/j.aim.2021.107992","publication":"Advances in Mathematics","day":"21","year":"2021","isi":1,"has_accepted_license":"1","project":[{"grant_number":"M02751","name":"Algebro-Geometric Applications of Factorization Homology","_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"107992","title":"The Atiyah-Bott formula and connectivity in chiral Koszul duality","external_id":{"arxiv":["1610.00212"],"isi":["000707040300031"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P","full_name":"Ho, Quoc P","orcid":"0000-0001-6889-1418","last_name":"Ho"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","short":"Q.P. Ho, Advances in Mathematics 392 (2021).","ieee":"Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,” Advances in Mathematics, vol. 392. Elsevier, 2021.","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.","ista":"Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 392, 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."},"intvolume":" 392","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"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].","lang":"eng"}],"volume":392,"language":[{"iso":"eng"}],"file":[{"file_size":840635,"date_updated":"2021-09-21T15:58:52Z","creator":"qho","file_name":"1-s2.0-S000187082100431X-main.pdf","date_created":"2021-09-21T15:58:52Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"10034","checksum":"f3c0086d41af11db31c00014efb38072"}],"publication_status":"published","publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"keyword":["Chiral algebras","Chiral homology","Factorization algebras","Koszul duality","Ran space"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10033","file_date_updated":"2021-09-21T15:58:52Z","department":[{"_id":"TaHa"}],"ddc":["514"],"date_updated":"2023-08-14T06:54:35Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto, C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767."},"title":"RIM-binding protein 2 organizes Ca21 channel topography and regulates release probability and vesicle replenishment at a fast central synapse","author":[{"full_name":"Butola, Tanvi","last_name":"Butola","first_name":"Tanvi"},{"last_name":"Alvanos","full_name":"Alvanos, Theocharis","first_name":"Theocharis"},{"last_name":"Hintze","full_name":"Hintze, Anika","first_name":"Anika"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948"},{"last_name":"Kleindienst","full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carolin","full_name":"Wichmann, Carolin","last_name":"Wichmann"},{"first_name":"Tobias","full_name":"Moser, Tobias","last_name":"Moser"}],"external_id":{"isi":["000752287700005"],"pmid":["34353898"]},"article_processing_charge":"No","day":"15","publication":"Journal of Neuroscience","isi":1,"has_accepted_license":"1","year":"2021","date_published":"2021-09-15T00:00:00Z","doi":"10.1523/JNEUROSCI.0586-21.2021","date_created":"2021-09-27T14:33:13Z","page":"7742-7767","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.","quality_controlled":"1","publisher":"Society for Neuroscience","oa":1,"ddc":["570"],"date_updated":"2023-08-14T06:56:30Z","file_date_updated":"2022-05-31T09:10:15Z","department":[{"_id":"RySh"}],"_id":"10051","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2022-05-31T09:10:15Z","file_size":11571961,"creator":"dernst","date_created":"2022-05-31T09:10:15Z","file_name":"2021_JourNeuroscience_Butola.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"769ab627c7355a50ccfd445e43a5f351","file_id":"11423","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2401"],"issn":["0270-6474"]},"publication_status":"published","issue":"37","volume":41,"oa_version":"Published Version","pmid":1,"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."}],"month":"09","intvolume":" 41","scopus_import":"1"},{"status":"public","conference":{"end_date":"2021-03-19","location":"Saarbrücken, Germany","start_date":"2021-03-16","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"10055","department":[{"_id":"KrCh"}],"file_date_updated":"2021-10-01T09:55:00Z","ddc":["000"],"date_updated":"2023-08-14T07:03:23Z","intvolume":" 187","month":"03","scopus_import":"1","alternative_title":["LIPIcs"],"oa_version":"Published Version","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 𝒟-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 𝒟-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 𝒟-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 𝒟-length of (n²+n+2)/2."}],"ec_funded":1,"volume":187,"language":[{"iso":"eng"}],"file":[{"date_created":"2021-10-01T09:55:00Z","file_name":"2021_LIPIcs_Jecker.pdf","creator":"cchlebak","date_updated":"2021-10-01T09:55:00Z","file_size":720250,"checksum":"17432a05733f408de300e17e390a90e4","file_id":"10063","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-9597-7180-1"],"issn":["1868-8969"]},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"44","title":"A Ramsey theorem for finite monoids","article_processing_charge":"No","external_id":{"isi":["000635691700044"]},"author":[{"last_name":"Jecker","full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","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","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."},"oa":1,"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","quality_controlled":"1","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.","date_created":"2021-09-27T14:33:15Z","doi":"10.4230/LIPIcs.STACS.2021.44","date_published":"2021-03-10T00:00:00Z","publication":"38th International Symposium on Theoretical Aspects of Computer Science","day":"10","year":"2021","has_accepted_license":"1","isi":1},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","doi":"10.1038/s41598-021-98411-z","date_published":"2021-09-28T00:00:00Z","date_created":"2021-10-03T22:01:21Z","day":"28","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2021","article_number":"19238","title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","author":[{"last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"full_name":"Stojanov, Miloš","last_name":"Stojanov","first_name":"Miloš"},{"last_name":"Blum","full_name":"Blum, Sabine","first_name":"Sabine"},{"last_name":"Baud","full_name":"Baud, David","first_name":"David"}],"article_processing_charge":"Yes","external_id":{"pmid":["34584125"],"isi":["000701575500083"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","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.","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.","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.","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."},"month":"09","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","pmid":1,"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."}],"volume":11,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10091","checksum":"f002ec22f609f58e1263b79e7f79601e","creator":"cchlebak","file_size":6970368,"date_updated":"2021-10-05T14:56:48Z","file_name":"2021_ScientificReports_Robinson.pdf","date_created":"2021-10-05T14:56:48Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10069","file_date_updated":"2021-10-05T14:56:48Z","department":[{"_id":"MaRo"}],"ddc":["618"],"date_updated":"2023-08-14T07:05:15Z"},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"citation":{"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.","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.","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).","ieee":"H. Zhou et al., “Half and quarter metals in rhombohedral trilayer graphene,” Nature. Springer Nature, 2021.","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","mla":"Zhou, Haoxin, et al. “Half and Quarter Metals in Rhombohedral Trilayer Graphene.” Nature, Springer Nature, 2021, doi:10.1038/s41586-021-03938-w."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000706977400002"],"arxiv":["2104.00653"]},"article_processing_charge":"No","author":[{"first_name":"Haoxin","last_name":"Zhou","full_name":"Zhou, Haoxin"},{"first_name":"Tian","last_name":"Xie","full_name":"Xie, Tian"},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"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.","last_name":"Spanton","full_name":"Spanton, Eric M."},{"last_name":"Taniguchi","full_name":"Taniguchi, Takashi","first_name":"Takashi"},{"first_name":"Kenji","last_name":"Watanabe","full_name":"Watanabe, Kenji"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Andrea F.","full_name":"Young, Andrea F.","last_name":"Young"}],"title":"Half and quarter metals in rhombohedral trilayer graphene","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","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2021","isi":1,"publication":"Nature","day":"01","date_created":"2021-09-19T22:01:25Z","doi":"10.1038/s41586-021-03938-w","date_published":"2021-09-01T00:00:00Z","_id":"10025","type":"journal_article","article_type":"original","keyword":["condensed matter - mesoscale and nanoscale physics","condensed matter - strongly correlated electrons","multidisciplinary"],"status":"public","date_updated":"2023-08-14T07:04:06Z","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.00653"}],"scopus_import":"1","month":"09","publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-021-04181-z","relation":"erratum"}]}},{"publication_identifier":{"eisbn":["978-3-662-63958-0"],"eissn":["1611-3349"],"isbn":["978-3-6626-3957-3"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":"12676 ","abstract":[{"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).","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/","open_access":"1"}],"month":"09","date_updated":"2023-08-14T07:06:16Z","department":[{"_id":"ElKo"}],"_id":"10076","type":"conference","conference":{"start_date":"2021-03-01","end_date":"2021-03-05","location":"Virtual","name":"FC: International Conference on Financial Cryptography and Data Security"},"status":"public","isi":1,"year":"2021","day":"17","publication":"FC 2021 Workshops","page":"431-450","doi":"10.1007/978-3-662-63958-0_34","date_published":"2021-09-17T00:00:00Z","date_created":"2021-10-03T22:01:24Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"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.","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","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","ieee":"S. Blackshear et al., “Reactive key-loss protection in blockchains,” in FC 2021 Workshops, Virtual, 2021, vol. 12676, pp. 431–450.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Sam","full_name":"Blackshear, Sam","last_name":"Blackshear"},{"last_name":"Chalkias","full_name":"Chalkias, Konstantinos","first_name":"Konstantinos"},{"first_name":"Panagiotis","full_name":"Chatzigiannis, Panagiotis","last_name":"Chatzigiannis"},{"first_name":"Riyaz","last_name":"Faizullabhoy","full_name":"Faizullabhoy, Riyaz"},{"first_name":"Irakliy","full_name":"Khaburzaniya, Irakliy","last_name":"Khaburzaniya"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Joshua","last_name":"Lind","full_name":"Lind, Joshua"},{"last_name":"Wong","full_name":"Wong, David","first_name":"David"},{"last_name":"Zakian","full_name":"Zakian, Tim","first_name":"Tim"}],"article_processing_charge":"No","external_id":{"isi":["000713005000034"]},"title":"Reactive key-loss protection in blockchains"},{"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"article_number":"109234","external_id":{"arxiv":["2008.01492"],"isi":["000703896600005"]},"article_processing_charge":"No","author":[{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo"},{"first_name":"Kohei","last_name":"Suzuki","full_name":"Suzuki, Kohei"}],"title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","citation":{"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.","short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Elsevier","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.","date_created":"2021-10-03T22:01:21Z","doi":"10.1016/j.jfa.2021.109234","date_published":"2021-09-15T00:00:00Z","year":"2021","isi":1,"publication":"Journal of Functional Analysis","day":"15","type":"journal_article","article_type":"original","status":"public","_id":"10070","department":[{"_id":"JaMa"}],"date_updated":"2023-08-14T07:05:44Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"scopus_import":"1","intvolume":" 281","month":"09","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."}],"oa_version":"Preprint","ec_funded":1,"issue":"11","volume":281,"publication_status":"published","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"language":[{"iso":"eng"}]},{"citation":{"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.","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.","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","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","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.","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"author":[{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Calcabrini","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano"},{"first_name":"Yuan","last_name":"Yu","full_name":"Yu, Yuan"},{"first_name":"Aziz","full_name":"Genç, Aziz","last_name":"Genç"},{"orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso"},{"last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"first_name":"Oana","full_name":"Cojocaru‐Mirédin, Oana","last_name":"Cojocaru‐Mirédin"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"}],"title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","article_number":"2106858","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"year":"2021","isi":1,"has_accepted_license":"1","publication":"Advanced Materials","day":"29","date_created":"2021-10-11T20:07:24Z","date_published":"2021-12-29T00:00:00Z","doi":"10.1002/adma.202106858","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.","oa":1,"quality_controlled":"1","publisher":"Wiley","date_updated":"2023-08-14T07:25:27Z","ddc":["620"],"department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"file_date_updated":"2022-02-03T13:16:14Z","_id":"10123","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["mechanical engineering","mechanics of materials","general materials science"],"status":"public","publication_status":"published","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10720","checksum":"990bccc527c64d85cf1c97885110b5f4","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-02-03T13:16:14Z","file_name":"2021_AdvancedMaterials_Liu.pdf","creator":"cchlebak","date_updated":"2022-02-03T13:16:14Z","file_size":5595666}],"ec_funded":1,"issue":"52","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12885"}]},"volume":33,"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"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 33","month":"12"},{"external_id":{"isi":["000706409200006"]},"article_processing_charge":"Yes","author":[{"first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat","last_name":"Artan"},{"first_name":"Stephen","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","full_name":"Barratt, Stephen","last_name":"Barratt"},{"first_name":"Sean M.","last_name":"Flynn","full_name":"Flynn, Sean M."},{"last_name":"Begum","full_name":"Begum, Farida","first_name":"Farida"},{"first_name":"Mark","full_name":"Skehel, Mark","last_name":"Skehel"},{"full_name":"Nicolas, Armel","last_name":"Nicolas","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono"}],"title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling","citation":{"short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"101094","date_created":"2021-10-10T22:01:23Z","date_published":"2021-09-01T00:00:00Z","doi":"10.1016/J.JBC.2021.101094","year":"2021","isi":1,"has_accepted_license":"1","publication":"Journal of Biological Chemistry","day":"01","oa":1,"quality_controlled":"1","publisher":"Elsevier","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).","file_date_updated":"2021-10-11T12:20:58Z","department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"date_updated":"2023-08-14T07:24:09Z","ddc":["612"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10117","ec_funded":1,"issue":"3","volume":297,"publication_status":"published","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","file_id":"10121","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_JBC_Artan.pdf","date_created":"2021-10-11T12:20:58Z","creator":"cchlebak","file_size":1680010,"date_updated":"2021-10-11T12:20:58Z"}],"scopus_import":"1","intvolume":" 297","month":"09","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"554c7fdb259eda703a8b6328a6dad55a","file_id":"10109","creator":"fmuehlbo","file_size":350632,"date_updated":"2021-10-07T23:32:18Z","file_name":"differentialmonitoring-cameraready-openaccess.pdf","date_created":"2021-10-07T23:32:18Z"}],"publication_status":"published","publication_identifier":{"eisbn":["978-3-030-88494-9"],"isbn":["978-3-030-88493-2"],"eissn":["1611-3349"],"issn":["0302-9743"]},"volume":12974,"related_material":{"record":[{"relation":"extended_version","id":"9946","status":"public"}]},"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"intvolume":" 12974","month":"10","place":"Cham","alternative_title":["LNCS"],"scopus_import":"1","ddc":["005"],"date_updated":"2023-08-14T07:20:30Z","department":[{"_id":"ToHe"}],"file_date_updated":"2021-10-07T23:32:18Z","_id":"10108","keyword":["run-time verification","software engineering","implicit specification"],"status":"public","conference":{"name":"RV: Runtime Verification","start_date":"2021-10-11","location":"Virtual","end_date":"2021-10-14"},"type":"conference","publication":"International Conference on Runtime Verification","day":"06","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-10-07T23:30:10Z","date_published":"2021-10-06T00:00:00Z","doi":"10.1007/978-3-030-88494-9_12","page":"231-243","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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243."},"title":"Differential monitoring","external_id":{"isi":["000719383800012"]},"article_processing_charge":"No","author":[{"last_name":"Mühlböck","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}]},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"e68238","author":[{"full_name":"Vuong-Brender, Thanh","last_name":"Vuong-Brender","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Thanh"},{"last_name":"Flynn","full_name":"Flynn, Sean","first_name":"Sean"},{"full_name":"Vallis, Yvonne","last_name":"Vallis","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E","first_name":"Yvonne"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"De Bono","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443"}],"external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"article_processing_charge":"No","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","citation":{"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.","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","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","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.","short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","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.","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"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).","doi":"10.7554/eLife.68238","date_published":"2021-09-17T00:00:00Z","date_created":"2021-10-10T22:01:22Z","has_accepted_license":"1","isi":1,"year":"2021","day":"17","publication":"eLife","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10116","file_date_updated":"2021-10-11T14:15:07Z","department":[{"_id":"MaDe"}],"date_updated":"2023-08-14T07:23:39Z","ddc":["610"],"scopus_import":"1","month":"09","intvolume":" 10","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."}],"oa_version":"Published Version","pmid":1,"volume":10,"ec_funded":1,"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","file":[{"success":1,"checksum":"b465e172d2b1f57aa26a2571a085d052","file_id":"10122","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2021_eLife_VuongBrender.pdf","date_created":"2021-10-11T14:15:07Z","file_size":1774624,"date_updated":"2021-10-11T14:15:07Z","creator":"cchlebak"}],"language":[{"iso":"eng"}]},{"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."}],"pmid":1,"oa_version":"Published Version","intvolume":" 13","month":"09","publication_status":"published","publication_identifier":{"issn":["1999-4915"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10115","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-08T10:38:15Z","file_name":"2021_Viruses_Obr.pdf","creator":"cchlebak","date_updated":"2021-10-08T10:38:15Z","file_size":4146796}],"volume":13,"issue":"9","_id":"10103","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["virology","infectious diseases"],"status":"public","date_updated":"2023-08-14T07:21:51Z","ddc":["616"],"file_date_updated":"2021-10-08T10:38:15Z","department":[{"_id":"FlSc"}],"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","oa":1,"quality_controlled":"1","publisher":"MDPI","year":"2021","isi":1,"has_accepted_license":"1","publication":"Viruses","day":"17","date_created":"2021-10-07T09:13:29Z","doi":"10.3390/v13091853","date_published":"2021-09-17T00:00:00Z","article_number":"1853","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}],"citation":{"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.","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","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","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["34578434"],"isi":["000699841100001"]},"article_processing_charge":"Yes","author":[{"last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."}],"title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly"},{"article_number":"104205","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from restricted Boltzmann machines. Physical Review B. 104(10), 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.","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","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","short":"R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).","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.","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."},"title":"Entanglement transitions from restricted Boltzmann machines","author":[{"last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"first_name":"Romain","full_name":"Vasseur, Romain","last_name":"Vasseur"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"external_id":{"isi":["000704414400002"],"arxiv":["2107.05735"]},"article_processing_charge":"No","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.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"30","publication":"Physical Review B","isi":1,"year":"2021","doi":"10.1103/physrevb.104.104205","date_published":"2021-09-30T00:00:00Z","date_created":"2021-10-02T09:03:42Z","_id":"10067","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-14T07:24:47Z","department":[{"_id":"MaSe"}],"oa_version":"Preprint","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."}],"month":"09","intvolume":" 104","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.05735"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","volume":104,"issue":"10","ec_funded":1},{"keyword":["run-time verification","software engineering","implicit specification"],"status":"public","type":"technical_report","_id":"9946","department":[{"_id":"ToHe"}],"file_date_updated":"2021-09-03T12:34:28Z","ddc":["005"],"date_updated":"2023-08-14T07:20:29Z","month":"09","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","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."}],"related_material":{"record":[{"status":"public","id":"9281","relation":"other"},{"relation":"shorter_version","status":"public","id":"10108"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"9948","checksum":"0f9aafd59444cb6bdca6925d163ab946","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"differentialmonitoring-techreport.pdf","date_created":"2021-08-20T19:59:44Z","creator":"fmuehlbo","file_size":"320453","date_updated":"2021-09-03T12:34:28Z"}],"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"title":"Differential monitoring","article_processing_charge":"No","author":[{"full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.","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.","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","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"},"oa":1,"publisher":"IST Austria","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.","date_created":"2021-08-20T20:00:37Z","date_published":"2021-09-01T00:00:00Z","doi":"10.15479/AT:ISTA:9946","page":"17","day":"01","year":"2021","has_accepted_license":"1"},{"issue":"18","volume":14,"publication_status":"published","publication_identifier":{"eissn":["1996-1944"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10140","checksum":"4929dfc673a3ae77c010b6174279cc1d","file_size":4404141,"date_updated":"2021-10-14T11:56:39Z","creator":"cchlebak","file_name":"2021_Materials_Chang.pdf","date_created":"2021-10-14T11:56:39Z"}],"scopus_import":"1","intvolume":" 14","month":"09","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"MaIb"}],"file_date_updated":"2021-10-14T11:56:39Z","date_updated":"2023-08-14T08:00:01Z","ddc":["540"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10073","date_created":"2021-10-03T22:01:23Z","doi":"10.3390/ma14185416","date_published":"2021-09-19T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Materials","day":"19","oa":1,"publisher":"MDPI","quality_controlled":"1","acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","article_processing_charge":"Yes","external_id":{"isi":["000700689400001"],"pmid":["34576640"]},"author":[{"last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","citation":{"ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","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.","short":"C. Chang, M. Ibáñez, Materials 14 (2021).","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"article_number":"5416"},{"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"last_name":"Moldovan","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A.","first_name":"Mikhail A.","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0"},{"last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"article_processing_charge":"No","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021).","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.","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.","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."},"project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1093/molbev/msab178","date_published":"2021-06-19T00:00:00Z","date_created":"2021-10-21T07:49:12Z","day":"19","publication":"Molecular Biology and Evolution","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Oxford University Press ","oa":1,"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.","department":[{"_id":"BeVi"}],"file_date_updated":"2022-05-06T09:47:18Z","ddc":["610"],"date_updated":"2023-08-14T08:03:06Z","status":"public","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10167","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"11352","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","success":1,"creator":"dernst","date_updated":"2022-05-06T09:47:18Z","file_size":1008594,"date_created":"2022-05-06T09:47:18Z","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication_status":"published","month":"06","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"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."}]},{"article_number":"6078","article_processing_charge":"No","external_id":{"isi":["000709050300001"]},"author":[{"first_name":"Lisa-Marie","last_name":"Appel","full_name":"Appel, Lisa-Marie"},{"first_name":"Vedran","full_name":"Franke, Vedran","last_name":"Franke"},{"first_name":"Melania","last_name":"Bruno","full_name":"Bruno, Melania"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"first_name":"Aiste","last_name":"Kasiliauskaite","full_name":"Kasiliauskaite, Aiste"},{"full_name":"Kaufmann, Tanja","last_name":"Kaufmann","first_name":"Tanja"},{"full_name":"Schoeberl, Ursula E.","last_name":"Schoeberl","first_name":"Ursula E."},{"first_name":"Martin G.","last_name":"Puchinger","full_name":"Puchinger, Martin G."},{"full_name":"Kostrhon, Sebastian","last_name":"Kostrhon","first_name":"Sebastian"},{"full_name":"Ebenwaldner, Carmen","last_name":"Ebenwaldner","first_name":"Carmen"},{"last_name":"Sebesta","full_name":"Sebesta, Marek","first_name":"Marek"},{"last_name":"Beltzung","full_name":"Beltzung, Etienne","first_name":"Etienne"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"last_name":"Lin","full_name":"Lin, Gen","first_name":"Gen"},{"last_name":"Vlasova","full_name":"Vlasova, Anna","first_name":"Anna"},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"},{"last_name":"Pavri","full_name":"Pavri, Rushad","first_name":"Rushad"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"last_name":"Stefl","full_name":"Stefl, Richard","first_name":"Richard"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"first_name":"Dea","full_name":"Slade, Dea","last_name":"Slade"}],"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","citation":{"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.","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","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.","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).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","date_created":"2021-10-20T14:40:32Z","date_published":"2021-10-19T00:00:00Z","doi":"10.1038/s41467-021-26360-2","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"19","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"status":"public","_id":"10163","department":[{"_id":"CaBe"}],"file_date_updated":"2021-10-21T13:51:49Z","date_updated":"2023-08-14T08:02:31Z","ddc":["610"],"intvolume":" 12","month":"10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":12,"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version","description":"Preprint "}]},"issue":"1","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_NatComm_Appel.pdf","date_created":"2021-10-21T13:51:49Z","creator":"cchlebak","file_size":5111706,"date_updated":"2021-10-21T13:51:49Z","success":1,"file_id":"10169","checksum":"d99fcd51aebde19c21314e3de0148007","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","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.","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.","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.","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.","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."},"title":"Neural acceleration of scattering-aware color 3D printing","article_processing_charge":"No","external_id":{"isi":["000657959600017"]},"author":[{"first_name":"Tobias","full_name":"Rittig, Tobias","last_name":"Rittig"},{"first_name":"Denis","last_name":"Sumin","full_name":"Sumin, Denis"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"first_name":"Alexey","full_name":"Voloboy, Alexey","last_name":"Voloboy"},{"first_name":"Alexander","last_name":"Wilkie","full_name":"Wilkie, Alexander"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"last_name":"Weyrich","full_name":"Weyrich, Tim","first_name":"Tim"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"}],"project":[{"grant_number":"642841","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Computer Graphics Forum","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-06-13T22:01:32Z","doi":"10.1111/cgf.142626","date_published":"2021-05-01T00:00:00Z","page":"205-219","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).","oa":1,"publisher":"Wiley","quality_controlled":"1","ddc":["004"],"date_updated":"2023-08-14T08:01:50Z","file_date_updated":"2021-10-11T12:06:50Z","department":[{"_id":"BeBi"}],"_id":"9547","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_size":26026501,"date_updated":"2021-10-11T12:06:50Z","creator":"bbickel","file_name":"ScatteringAwareColor3DPrinting_authorVersion.pdf","date_created":"2021-10-11T12:06:50Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10120","checksum":"33271724215f54a75c39d2ed40f2c502"}],"publication_status":"published","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"ec_funded":1,"volume":40,"issue":"2","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 40","month":"05","scopus_import":"1"},{"volume":7,"issue":"41","file":[{"file_id":"10189","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-27T14:16:06Z","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","date_updated":"2021-10-27T14:16:06Z","file_size":2441163,"creator":"cziletti"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"publication_status":"published","month":"10","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"NanoFab"}],"file_date_updated":"2021-10-27T14:16:06Z","ddc":["530"],"date_updated":"2023-08-14T08:04:42Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"10177","doi":"10.1126/sciadv.abj0127","date_published":"2021-10-08T00:00:00Z","date_created":"2021-10-24T22:01:33Z","day":"08","publication":"Science Advances","has_accepted_license":"1","isi":1,"year":"2021","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"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).","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","author":[{"full_name":"Martín-Sánchez, Javier","last_name":"Martín-Sánchez","first_name":"Javier"},{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Kirill V.","full_name":"Voronin, Kirill V.","last_name":"Voronin"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"full_name":"Ma, Weiliang","last_name":"Ma","first_name":"Weiliang"},{"full_name":"Bao, Qiaoliang","last_name":"Bao","first_name":"Qiaoliang"},{"first_name":"Valentyn S.","last_name":"Volkov","full_name":"Volkov, Valentyn S."},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"first_name":"Pablo","full_name":"Alonso-González, Pablo","last_name":"Alonso-González"}],"external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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.","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).","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.","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."},"article_number":"abj0127"},{"article_processing_charge":"No","external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"author":[{"full_name":"Runkel, Ingo","last_name":"Runkel","first_name":"Ingo"},{"first_name":"Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","last_name":"Szegedy","full_name":"Szegedy, Lorant","orcid":"0000-0003-2834-5054"}],"title":"Topological field theory on r-spin surfaces and the Arf-invariant","citation":{"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.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","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","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.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"102302","date_created":"2021-10-24T22:01:32Z","doi":"10.1063/5.0037826","date_published":"2021-10-01T00:00:00Z","year":"2021","isi":1,"publication":"Journal of Mathematical Physics","day":"01","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","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.”","department":[{"_id":"MiLe"}],"date_updated":"2023-08-14T08:04:12Z","article_type":"original","type":"journal_article","status":"public","_id":"10176","issue":"10","volume":62,"publication_status":"published","publication_identifier":{"issn":["00222488"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.09978"}],"scopus_import":"1","intvolume":" 62","month":"10","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 ℤ𝑟-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."}],"oa_version":"Preprint"},{"author":[{"full_name":"Bajaj, Sunanjay","last_name":"Bajaj","first_name":"Sunanjay"},{"full_name":"Bagley, Joshua A.","last_name":"Bagley","first_name":"Joshua A."},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M"},{"full_name":"Vertesy, Abel","last_name":"Vertesy","first_name":"Abel"},{"first_name":"Sakurako","last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako"},{"first_name":"Veronica","full_name":"Krenn, Veronica","last_name":"Krenn"},{"first_name":"Julie","last_name":"Lévi-Strauss","full_name":"Lévi-Strauss, Julie"},{"first_name":"Juergen A.","last_name":"Knoblich","full_name":"Knoblich, Juergen A."}],"external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"article_processing_charge":"Yes (in subscription journal)","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","citation":{"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.","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.","ieee":"S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021.","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).","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e108714","doi":"10.15252/embj.2021108714","date_published":"2021-10-18T00:00:00Z","date_created":"2021-10-24T22:01:34Z","has_accepted_license":"1","isi":1,"year":"2021","day":"18","publication":"EMBO Journal","publisher":"Embo Press","quality_controlled":"1","oa":1,"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).","department":[{"_id":"Bio"}],"file_date_updated":"2021-12-13T14:54:14Z","date_updated":"2023-08-14T08:05:23Z","ddc":["610"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10179","issue":"23","volume":40,"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"publication_status":"published","file":[{"file_size":7819881,"date_updated":"2021-12-13T14:54:14Z","creator":"alisjak","file_name":"2021_EMBO_Bajaj.pdf","date_created":"2021-12-13T14:54:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"78d2d02e775322297e774f72810a41a4","file_id":"10541"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 40","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."}],"pmid":1,"oa_version":"Published Version"},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","date_created":"2021-10-31T23:01:30Z","date_published":"2021-10-18T00:00:00Z","doi":"10.1038/s41467-021-26262-3","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"18","article_number":"6063","external_id":{"arxiv":["2103.16986"],"isi":["000708601800015"]},"article_processing_charge":"No","author":[{"first_name":"Luca","full_name":"Sortino, Luca","last_name":"Sortino"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"last_name":"Phillips","full_name":"Phillips, Catherine L.","first_name":"Catherine L."},{"full_name":"Brash, Alistair J.","last_name":"Brash","first_name":"Alistair J."},{"last_name":"Cambiasso","full_name":"Cambiasso, Javier","first_name":"Javier"},{"orcid":"0000-0001-7173-4923","full_name":"Marensi, Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena"},{"first_name":"A. Mark","last_name":"Fox","full_name":"Fox, A. Mark"},{"first_name":"Stefan A.","full_name":"Maier, Stefan A.","last_name":"Maier"},{"first_name":"Riccardo","last_name":"Sapienza","full_name":"Sapienza, Riccardo"},{"last_name":"Tartakovskii","full_name":"Tartakovskii, Alexander I.","first_name":"Alexander I."}],"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","citation":{"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.","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.","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","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","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","intvolume":" 12","month":"10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":12,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"8580d128389860f732028c521cd5949e","file_id":"10212","creator":"cchlebak","file_size":1434201,"date_updated":"2021-11-03T11:31:24Z","file_name":"2021_NatComm_Sortino.pdf","date_created":"2021-11-03T11:31:24Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10203","department":[{"_id":"BjHo"}],"file_date_updated":"2021-11-03T11:31:24Z","date_updated":"2023-08-14T08:12:12Z","ddc":["530"]},{"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."}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 23","publication_identifier":{"eissn":["13672630"]},"publication_status":"published","file":[{"file_id":"10193","checksum":"ace603e8f0962b3ba55f23fa34f57764","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-28T12:06:01Z","file_name":"2021_NewJPhys_Sahu.pdf","creator":"cziletti","date_updated":"2021-10-28T12:06:01Z","file_size":2215016}],"language":[{"iso":"eng"}],"volume":23,"issue":"9","_id":"10178","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-14T08:10:31Z","ddc":["570"],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-10-28T12:06:01Z","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","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"isi":1,"has_accepted_license":"1","year":"2021","day":"29","publication":"New Journal of Physics","date_published":"2021-09-29T00:00:00Z","doi":"10.1088/1367-2630/ac23f1","date_created":"2021-10-24T22:01:34Z","article_number":"093043","citation":{"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.","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","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","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.","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","last_name":"Sahu","full_name":"Sahu, Preeti"},{"full_name":"Schwarz, J. M.","last_name":"Schwarz","first_name":"J. M."},{"first_name":"M. Lisa","last_name":"Manning","full_name":"Manning, M. Lisa"}],"external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"article_processing_charge":"Yes","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue"},{"title":"Rectifiable curves in proximally smooth sets","external_id":{"arxiv":["2012.10691"],"isi":["000705774800001"]},"article_processing_charge":"No","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"first_name":"Mariana S.","full_name":"Lopushanski, Mariana S.","last_name":"Lopushanski"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis.","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.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","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","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."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","date_created":"2021-10-24T22:01:35Z","date_published":"2021-10-09T00:00:00Z","doi":"10.1007/s11228-021-00612-1","publication":"Set-Valued and Variational Analysis","day":"09","year":"2021","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"10181","department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T08:11:38Z","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1877-0541"],"issn":["0927-6947"]}},{"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).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"19","date_created":"2021-10-31T23:01:29Z","date_published":"2021-10-19T00:00:00Z","doi":"10.1038/s41467-021-26234-7","article_number":"6094","citation":{"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.","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.","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","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.","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).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"author":[{"full_name":"Pradhan, Saurabh J.","last_name":"Pradhan","first_name":"Saurabh J."},{"full_name":"Reddy, Puli Chandramouli","last_name":"Reddy","first_name":"Puli Chandramouli"},{"first_name":"Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny"},{"first_name":"Ankita","last_name":"Sharma","full_name":"Sharma, Ankita"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","last_name":"Sako","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075"},{"first_name":"Meghana S.","full_name":"Oak, Meghana S.","last_name":"Oak"},{"full_name":"Shah, Rini","last_name":"Shah","first_name":"Rini"},{"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"},{"full_name":"Tang, Yin","last_name":"Tang","first_name":"Yin"},{"full_name":"Mishra, Rakesh","last_name":"Mishra","first_name":"Rakesh"},{"last_name":"Deshpande","full_name":"Deshpande, Girish","first_name":"Girish"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"first_name":"Mahendra","full_name":"Sonawane, Mahendra","last_name":"Sonawane"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"}],"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"10","publication_status":"published","publication_identifier":{"eissn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"creator":"cziletti","file_size":7144437,"date_updated":"2021-11-09T13:59:26Z","file_name":"2021_NatureComm_Pradhan.pdf","date_created":"2021-11-09T13:59:26Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_id":"10262"}],"issue":"1","volume":12,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 ","description":"Preprint"}]},"_id":"10202","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-14T10:32:48Z","ddc":["570"],"file_date_updated":"2021-11-09T13:59:26Z","department":[{"_id":"CaHe"}]},{"publication_status":"published","publication_identifier":{"eissn":["1664-302X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"d41321748e9588dd3cf03e9a7222127f","file_id":"10272","file_size":2397203,"date_updated":"2021-11-11T10:54:40Z","creator":"cchlebak","file_name":"2021_FrontiersMicrob_Qi.pdf","date_created":"2021-11-11T10:54:40Z"}],"ec_funded":1,"volume":12,"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 12","month":"10","date_updated":"2023-08-14T11:43:23Z","ddc":["610"],"file_date_updated":"2021-11-11T10:54:40Z","_id":"10271","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["microbiology"],"status":"public","year":"2021","has_accepted_license":"1","isi":1,"publication":"Frontiers in Microbiology","day":"20","date_created":"2021-11-11T10:39:37Z","doi":"10.3389/fmicb.2021.760017","date_published":"2021-10-20T00:00:00Z","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.","oa":1,"publisher":"Frontiers","quality_controlled":"1","citation":{"short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34745067"],"isi":["000715997300001"]},"author":[{"id":"3B22D412-F248-11E8-B48F-1D18A9856A87","first_name":"Qin","last_name":"Qi","full_name":"Qi, Qin","orcid":"0000-0002-6148-2416"},{"first_name":"S. Andreas","last_name":"Angermayr","full_name":"Angermayr, S. Andreas"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","article_number":"760017","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}]},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"external_id":{"arxiv":["2012.13215"],"isi":["000712232700001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"title":"Eigenstate thermalization hypothesis for Wigner matrices","citation":{"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.","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.","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.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","page":"1005–1048","date_created":"2021-11-07T23:01:25Z","doi":"10.1007/s00220-021-04239-z","date_published":"2021-10-29T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"29","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10221","department":[{"_id":"LaEr"}],"file_date_updated":"2022-02-02T10:19:55Z","date_updated":"2023-08-14T10:29:49Z","ddc":["510"],"scopus_import":"1","intvolume":" 388","month":"10","abstract":[{"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).","lang":"eng"}],"oa_version":"Published Version","volume":388,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a2c7b6f5d23b5453cd70d1261272283b","file_id":"10715","creator":"cchlebak","file_size":841426,"date_updated":"2022-02-02T10:19:55Z","file_name":"2021_CommunMathPhys_Cipolloni.pdf","date_created":"2022-02-02T10:19:55Z"}]},{"publisher":"Springer Nature","quality_controlled":"1","oa":1,"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).","doi":"10.1007/s00205-021-01715-7","date_published":"2021-10-25T00:00:00Z","date_created":"2021-11-07T23:01:26Z","page":"1835–1906","day":"25","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","isi":1,"year":"2021","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","author":[{"last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2101.12566"],"isi":["000710850600001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","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.","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."},"month":"10","intvolume":" 242","scopus_import":"1","oa_version":"Published Version","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."}],"issue":"3","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9787"}]},"volume":242,"ec_funded":1,"file":[{"checksum":"672e9c21b20f1a50854b7c821edbb92f","file_id":"10544","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-14T08:35:42Z","file_name":"2021_Springer_Feliciangeli.pdf","date_updated":"2021-12-14T08:35:42Z","file_size":990529,"creator":"alisjak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10224","department":[{"_id":"RoSe"}],"file_date_updated":"2021-12-14T08:35:42Z","ddc":["530"],"date_updated":"2023-08-14T10:32:19Z"},{"external_id":{"isi":["000834044200002"]},"article_processing_charge":"No","author":[{"first_name":"Verica","last_name":"Vasic","full_name":"Vasic, Verica"},{"last_name":"Jones","full_name":"Jones, Mattson S.O.","first_name":"Mattson S.O."},{"last_name":"Haslinger","full_name":"Haslinger, Denise","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","first_name":"Denise"},{"last_name":"Knaus","full_name":"Knaus, Lisa","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael J.","full_name":"Schmeisser, Michael J.","last_name":"Schmeisser"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chiocchetti","full_name":"Chiocchetti, Andreas G.","first_name":"Andreas G."}],"title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","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","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.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"article_number":"1746","date_created":"2021-11-14T23:01:24Z","doi":"10.3390/genes12111746","date_published":"2021-10-30T00:00:00Z","year":"2021","has_accepted_license":"1","isi":1,"publication":"Genes","day":"30","oa":1,"publisher":"MDPI","quality_controlled":"1","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.","file_date_updated":"2022-05-16T07:02:27Z","department":[{"_id":"GaNo"}],"date_updated":"2023-08-14T11:46:12Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10281","ec_funded":1,"issue":"11","volume":12,"publication_status":"published","publication_identifier":{"eissn":["2073-4425"]},"language":[{"iso":"eng"}],"file":[{"file_id":"11380","checksum":"256cb832a9c3051c7dc741f6423b8cbd","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-16T07:02:27Z","file_name":"2021_Genes_Vasic.pdf","date_updated":"2022-05-16T07:02:27Z","file_size":1335308,"creator":"dernst"}],"alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"scopus_import":"1","intvolume":" 12","month":"10","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"}],"oa_version":"Published Version"},{"_id":"10282","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-14T11:46:43Z","department":[{"_id":"JiFr"}],"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."}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}],"scopus_import":"1","intvolume":" 233","month":"11","publication_status":"published","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"language":[{"iso":"eng"}],"volume":233,"citation":{"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.","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.","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.","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34637542"],"isi":["000714678100001"]},"author":[{"full_name":"Kashkan, Ivan","last_name":"Kashkan","first_name":"Ivan"},{"last_name":"Hrtyan","full_name":"Hrtyan, Mónika","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"first_name":"Aswathy","full_name":"Jayasree, Aswathy","last_name":"Jayasree"},{"first_name":"Roberta","full_name":"Filepová, Roberta","last_name":"Filepová"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"last_name":"Jacobs","full_name":"Jacobs, Thomas B.","first_name":"Thomas B."},{"last_name":"Frilander","full_name":"Frilander, Mikko J.","first_name":"Mikko J."},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Růžička, Kamil","last_name":"Růžička","first_name":"Kamil"}],"title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","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.","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2021","isi":1,"publication":"New Phytologist","day":"05","page":"329-343","date_created":"2021-11-14T23:01:24Z","doi":"10.1111/nph.17792","date_published":"2021-11-05T00:00:00Z"},{"status":"public","type":"journal_article","article_type":"original","_id":"10220","department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T11:43:55Z","intvolume":" 245","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":245,"related_material":{"record":[{"id":"8183","status":"public","relation":"earlier_version"},{"status":"public","id":"9308","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312"}],"title":"Eliminating higher-multiplicity intersections. III. Codimension 2","external_id":{"arxiv":["1511.03501"],"isi":["000712942100013"]},"article_processing_charge":"No","author":[{"first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"full_name":"Mabillard, Isaac","last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arkadiy B.","full_name":"Skopenkov, Arkadiy B.","last_name":"Skopenkov"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","date_created":"2021-11-07T23:01:24Z","doi":"10.1007/s11856-021-2216-z","date_published":"2021-10-30T00:00:00Z","page":"501–534 ","publication":"Israel Journal of Mathematics","day":"30","year":"2021","isi":1},{"day":"29","year":"2021","related_material":{"record":[{"id":"10284","status":"public","relation":"used_in_publication"}]},"date_published":"2021-10-29T00:00:00Z","doi":"10.5061/DRYAD.7PVMCVDTJ","date_created":"2023-05-23T16:14:35Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","ec_funded":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"10","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.7pvmcvdtj"}],"oa":1,"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021).","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","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."},"date_updated":"2023-08-14T11:45:28Z","department":[{"_id":"SyCr"}],"title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Naiser","full_name":"Naiser, Filip","first_name":"Filip"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","first_name":"Elisabeth"},{"first_name":"Jiri","full_name":"Matas, Jiri","last_name":"Matas"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","_id":"13061","status":"public","project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"type":"research_data_reference","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)"}},{"article_number":"e71575","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","external_id":{"isi":["000720945900001"]},"article_processing_charge":"No","author":[{"full_name":"Conde-Dusman, María J","last_name":"Conde-Dusman","first_name":"María J"},{"first_name":"Partha N","last_name":"Dey","full_name":"Dey, Partha N"},{"first_name":"Óscar","last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar"},{"id":"33D1B084-F248-11E8-B48F-1D18A9856A87","first_name":"Luis E","full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","full_name":"García-Lira, Carmen","last_name":"García-Lira"},{"full_name":"Grand, Teddy","last_name":"Grand","first_name":"Teddy"},{"first_name":"Victor","last_name":"Briz","full_name":"Briz, Victor"},{"full_name":"Velasco, Eric R","last_name":"Velasco","first_name":"Eric R"},{"last_name":"Andero Galí","full_name":"Andero Galí, Raül","first_name":"Raül"},{"full_name":"Niñerola, Sergio","last_name":"Niñerola","first_name":"Sergio"},{"first_name":"Angel","last_name":"Barco","full_name":"Barco, Angel"},{"first_name":"Pierre","last_name":"Paoletti","full_name":"Paoletti, Pierre"},{"full_name":"Wesseling, John F","last_name":"Wesseling","first_name":"John F"},{"first_name":"Fabrizio","full_name":"Gardoni, Fabrizio","last_name":"Gardoni"},{"full_name":"Tavalin, Steven J","last_name":"Tavalin","first_name":"Steven J"},{"first_name":"Isabel","full_name":"Perez-Otaño, Isabel","last_name":"Perez-Otaño"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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.","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","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.","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.","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."},"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","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).","date_created":"2021-11-18T06:59:45Z","date_published":"2021-11-17T00:00:00Z","doi":"10.7554/elife.71575","publication":"eLife","day":"17","year":"2021","has_accepted_license":"1","isi":1,"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10301","file_date_updated":"2021-11-18T07:02:02Z","department":[{"_id":"GaNo"}],"ddc":["570"],"date_updated":"2023-08-14T11:50:50Z","intvolume":" 10","month":"11","oa_version":"Published Version","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."}],"volume":10,"language":[{"iso":"eng"}],"file":[{"creator":"lgarciar","file_size":2477302,"date_updated":"2021-11-18T07:02:02Z","file_name":"elife-71575-v1.pdf","date_created":"2021-11-18T07:02:02Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"59318e9e41507cec83c2f4070e6ad540","file_id":"10302"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]}},{"publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"publication_status":"published","file":[{"checksum":"74743baa6ef431ef60c3de3bc4da045a","file_id":"11381","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-16T07:07:41Z","file_name":"2021_EmboReports_Restivo.pdf","date_updated":"2022-05-16T07:07:41Z","file_size":488583,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":22,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 22","date_updated":"2023-08-14T11:47:35Z","ddc":["570"],"department":[{"_id":"PreCl"}],"file_date_updated":"2022-05-16T07:07:41Z","_id":"10283","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","has_accepted_license":"1","isi":1,"year":"2021","day":"04","publication":"EMBO Reports","doi":"10.15252/embr.202153824","date_published":"2021-11-04T00:00:00Z","date_created":"2021-11-14T23:01:24Z","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.","quality_controlled":"1","publisher":"EMBO Press","oa":1,"citation":{"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","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","ieee":"L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.","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).","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Leonardo","full_name":"Restivo, Leonardo","last_name":"Restivo"},{"first_name":"Björn","last_name":"Gerlach","full_name":"Gerlach, Björn"},{"first_name":"Michael","last_name":"Tsoory","full_name":"Tsoory, Michael"},{"first_name":"Lior","full_name":"Bikovski, Lior","last_name":"Bikovski"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"first_name":"Claudia","last_name":"Pitzer","full_name":"Pitzer, Claudia"},{"first_name":"Isabelle C.","last_name":"Kos-Braun","full_name":"Kos-Braun, Isabelle C."},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"last_name":"Ward","full_name":"Ward, Jonathan","first_name":"Jonathan"},{"orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael","last_name":"Schunn","first_name":"Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Noldus","full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J."},{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"full_name":"Voikar, Vootele","last_name":"Voikar","first_name":"Vootele"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000714350000001"]},"title":"Towards best practices in research: Role of academic core facilities","article_number":"e53824"},{"article_number":"304","title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","author":[{"first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","orcid":"0000-0002-3219-2022","full_name":"Çoruh, Mehmet Orkun"},{"last_name":"Frank","full_name":"Frank, Anna","first_name":"Anna"},{"last_name":"Tanaka","full_name":"Tanaka, Hideaki","first_name":"Hideaki"},{"first_name":"Akihiro","full_name":"Kawamoto, Akihiro","last_name":"Kawamoto"},{"last_name":"El-Mohsnawy","full_name":"El-Mohsnawy, Eithar","first_name":"Eithar"},{"first_name":"Takayuki","last_name":"Kato","full_name":"Kato, Takayuki"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"first_name":"Christoph","last_name":"Gerle","full_name":"Gerle, Christoph"},{"first_name":"Marc M.","last_name":"Nowaczyk","full_name":"Nowaczyk, Marc M."},{"first_name":"Genji","full_name":"Kurisu, Genji","last_name":"Kurisu"}],"external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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.","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","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","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.","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.","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."},"quality_controlled":"1","publisher":"Springer ","oa":1,"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.","doi":"10.1038/s42003-021-01808-9","date_published":"2021-03-08T00:00:00Z","date_created":"2021-11-19T11:37:29Z","day":"08","publication":"Communications Biology","has_accepted_license":"1","isi":1,"year":"2021","status":"public","keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10310","department":[{"_id":"LeSa"}],"file_date_updated":"2021-11-19T15:09:18Z","ddc":["570"],"date_updated":"2023-08-14T11:51:19Z","month":"03","intvolume":" 4","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"volume":4,"issue":"1","file":[{"creator":"cchlebak","date_updated":"2021-11-19T15:09:18Z","file_size":6030261,"date_created":"2021-11-19T15:09:18Z","file_name":"2021_CommBio_Çoruh.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10318","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2399-3642"]},"publication_status":"published"},{"year":"2021","has_accepted_license":"1","isi":1,"publication":"eLife","day":"01","date_created":"2021-11-11T10:05:18Z","doi":"10.7554/elife.72132","date_published":"2021-11-01T00:00:00Z","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).","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","citation":{"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.","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.","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.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"author":[{"last_name":"Marconi","full_name":"Marconi, Marco","first_name":"Marco"},{"first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","last_name":"Gallemi"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof","full_name":"Wabnik, Krzysztof","last_name":"Wabnik"}],"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","article_number":"72132","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_eLife_Marconi.pdf","date_created":"2022-05-13T09:00:29Z","file_size":14137503,"date_updated":"2022-05-13T09:00:29Z","creator":"dernst","success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","file_id":"11372","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":10,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 10","month":"11","date_updated":"2023-08-14T11:49:23Z","ddc":["570"],"department":[{"_id":"EvBe"}],"file_date_updated":"2022-05-13T09:00:29Z","_id":"10270","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"article_number":"e2102350118","project":[{"grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021).","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.","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.","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."},"title":"Experimental observation of the origin and structure of elastoinertial turbulence","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H","full_name":"Choueiri, George H","last_name":"Choueiri"},{"full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M"},{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"first_name":"Sarath","last_name":"Sankar","full_name":"Sankar, Sarath"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"No","external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]},"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.","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"day":"03","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2021","date_published":"2021-11-03T00:00:00Z","doi":"10.1073/pnas.2102350118","date_created":"2021-11-17T13:24:24Z","_id":"10299","status":"public","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"type":"journal_article","article_type":"original","date_updated":"2023-08-14T11:50:10Z","department":[{"_id":"BjHo"}],"pmid":1,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"11","intvolume":" 118","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.00023"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","volume":118,"issue":"45"},{"scopus_import":"1","month":"11","intvolume":" 12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":12,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"success":1,"checksum":"1c392b12b9b7b615d422d9fabe19cdb9","file_id":"10292","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_NatComm_Aubret.pdf","date_created":"2021-11-15T13:25:52Z","creator":"cchlebak","file_size":6282703,"date_updated":"2021-11-15T13:25:52Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10280","file_date_updated":"2021-11-15T13:25:52Z","department":[{"_id":"JePa"}],"date_updated":"2023-08-14T11:48:37Z","ddc":["530"],"quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","date_published":"2021-11-04T00:00:00Z","doi":"10.1038/s41467-021-26699-6","date_created":"2021-11-14T23:01:23Z","has_accepted_license":"1","isi":1,"year":"2021","day":"04","publication":"Nature Communications","article_number":"6398","author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"first_name":"Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","last_name":"Martinet","orcid":"0000-0002-2916-6632","full_name":"Martinet, Quentin"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"article_processing_charge":"Yes","external_id":{"pmid":["34737315"],"isi":["000714754400010"]},"title":"Metamachines of pluripotent colloids","citation":{"ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","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.","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","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"scopus_import":"1","intvolume":" 19","month":"11","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."}],"pmid":1,"oa_version":"Published Version","related_material":{"record":[{"id":"13069","status":"public","relation":"research_data"}]},"issue":"11","volume":19,"publication_status":"published","publication_identifier":{"eissn":["1545-7885"],"issn":["1544-9173"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2021-11-22T09:34:03Z","file_size":4069215,"date_created":"2021-11-22T09:34:03Z","file_name":"2021_PLoSBio_Chauve.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10330","checksum":"0c61b667f814fd9435b3ac42036fc36d","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"10322","file_date_updated":"2021-11-22T09:34:03Z","department":[{"_id":"MaDe"}],"date_updated":"2023-08-14T11:53:27Z","ddc":["570"],"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","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.","date_created":"2021-11-21T23:01:28Z","date_published":"2021-11-01T00:00:00Z","doi":"10.1371/journal.pbio.3001431","year":"2021","has_accepted_license":"1","isi":1,"publication":"PLoS Biology","day":"01","article_number":"e3001431","article_processing_charge":"No","external_id":{"pmid":["34723964"],"isi":["000715818400001"]},"author":[{"first_name":"Laetitia","last_name":"Chauve","full_name":"Chauve, Laetitia"},{"last_name":"Hodge","full_name":"Hodge, Francesca","first_name":"Francesca"},{"first_name":"Sharlene","full_name":"Murdoch, Sharlene","last_name":"Murdoch"},{"last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah","first_name":"Fatemah"},{"last_name":"Mann","full_name":"Mann, Harry Jack","first_name":"Harry Jack"},{"first_name":"Andrea","full_name":"Lopez-Clavijo, Andrea","last_name":"Lopez-Clavijo"},{"first_name":"Hanneke","last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke"},{"last_name":"West","full_name":"West, Greg","first_name":"Greg"},{"full_name":"Sousa, Bebiana C.","last_name":"Sousa","first_name":"Bebiana C."},{"first_name":"Anne","last_name":"Segonds-Pichon","full_name":"Segonds-Pichon, Anne"},{"first_name":"Cheryl","full_name":"Li, Cheryl","last_name":"Li"},{"last_name":"Wingett","full_name":"Wingett, Steven","first_name":"Steven"},{"last_name":"Kienberger","full_name":"Kienberger, Hermine","first_name":"Hermine"},{"last_name":"Kleigrewe","full_name":"Kleigrewe, Karin","first_name":"Karin"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"De Bono"},{"full_name":"Wakelam, Michael","last_name":"Wakelam","first_name":"Michael"},{"last_name":"Casanueva","full_name":"Casanueva, Olivia","first_name":"Olivia"}],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","citation":{"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.","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.","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).","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"ec_funded":1,"file":[{"date_created":"2023-08-14T11:55:10Z","file_name":"2023_ExperimentalMath_Akopyan.pdf","date_updated":"2023-08-14T11:55:10Z","file_size":1966019,"creator":"dernst","checksum":"3514382e3a1eb87fa6c61ad622874415","file_id":"14053","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1944-950X"],"issn":["1058-6458"]},"publication_status":"published","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2023-08-14T11:55:10Z","department":[{"_id":"HeEd"}],"ddc":["510"],"date_updated":"2023-08-14T11:57:07Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10222","date_published":"2021-10-25T00:00:00Z","doi":"10.1080/10586458.2021.1980459","date_created":"2021-11-07T23:01:25Z","page":"1-15","day":"25","publication":"Experimental Mathematics","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Taylor and Francis","oa":1,"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.","title":"The beauty of random polytopes inscribed in the 2-sphere","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000710893500001"],"arxiv":["2007.07783"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","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.","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.","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","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."},"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Discretization in Geometry and Dynamics"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}]},{"ddc":["547"],"date_updated":"2023-08-14T11:55:04Z","department":[{"_id":"PaSc"}],"file_date_updated":"2021-11-23T15:06:58Z","_id":"10323","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a5c9dbf80dc2c5aaa737f456c941d964","file_id":"10333","file_size":4700798,"date_updated":"2021-11-23T15:06:58Z","creator":"cchlebak","file_name":"2021_FrontiersMolBioSc_Sučec.pdf","date_created":"2021-11-23T15:06:58Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2296-889X"]},"publication_status":"published","volume":8,"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"10","intvolume":" 8","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","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.","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005."},"title":"How do chaperones bind (partly) unfolded client proteins?","author":[{"last_name":"Sučec","full_name":"Sučec, Iva","first_name":"Iva"},{"last_name":"Bersch","full_name":"Bersch, Beate","first_name":"Beate"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"external_id":{"pmid":["34760928"],"isi":["000717241700001"]},"article_processing_charge":"Yes (via OA deal)","article_number":"762005","day":"25","publication":"Frontiers in Molecular Biosciences","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.3389/fmolb.2021.762005","date_published":"2021-10-25T00:00:00Z","date_created":"2021-11-21T23:01:29Z","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).","publisher":"Frontiers","quality_controlled":"1","oa":1},{"_id":"13069","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","citation":{"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.","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.","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","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.","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).","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."},"date_updated":"2023-08-14T11:53:26Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Laetitia","full_name":"Chauve, Laetitia","last_name":"Chauve"},{"last_name":"Hodge","full_name":"Hodge, Francesca","first_name":"Francesca"},{"first_name":"Sharlene","last_name":"Murdoch","full_name":"Murdoch, Sharlene"},{"first_name":"Fatemah","last_name":"Masoudzadeh","full_name":"Masoudzadeh, Fatemah"},{"first_name":"Harry-Jack","last_name":"Mann","full_name":"Mann, Harry-Jack"},{"last_name":"Lopez-Clavijo","full_name":"Lopez-Clavijo, Andrea","first_name":"Andrea"},{"last_name":"Okkenhaug","full_name":"Okkenhaug, Hanneke","first_name":"Hanneke"},{"full_name":"West, Greg","last_name":"West","first_name":"Greg"},{"first_name":"Bebiana C.","last_name":"Sousa","full_name":"Sousa, Bebiana C."},{"full_name":"Segonds-Pichon, Anne","last_name":"Segonds-Pichon","first_name":"Anne"},{"full_name":"Li, Cheryl","last_name":"Li","first_name":"Cheryl"},{"full_name":"Wingett, Steven","last_name":"Wingett","first_name":"Steven"},{"full_name":"Kienberger, Hermine","last_name":"Kienberger","first_name":"Hermine"},{"first_name":"Karin","full_name":"Kleigrewe, Karin","last_name":"Kleigrewe"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"},{"first_name":"Michael","full_name":"Wakelam, Michael","last_name":"Wakelam"},{"full_name":"Casanueva, Olivia","last_name":"Casanueva","first_name":"Olivia"}],"article_processing_charge":"No","department":[{"_id":"MaDe"}],"title":"Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5547464"}],"oa":1,"month":"12","year":"2021","day":"25","date_published":"2021-12-25T00:00:00Z","doi":"10.5281/ZENODO.5519410","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10322"}]},"date_created":"2023-05-23T16:40:56Z"},{"_id":"10325","status":"public","type":"conference","conference":{"name":"FC: Financial Cryptography","location":"Virtual","end_date":"2021-03-05","start_date":"2021-03-01"},"date_updated":"2023-08-14T12:59:26Z","department":[{"_id":"ElKo"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"10","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://eprint.iacr.org/2019/1128","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"],"eisbn":["978-3-662-64331-0"]},"publication_status":"published","volume":"12675 ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","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","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","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."},"title":"SoK: Communication across distributed ledgers","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"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro","first_name":"Pedro"},{"first_name":"Aggelos","full_name":"Kiayias, Aggelos","last_name":"Kiayias"},{"full_name":"Knottenbelt, William J.","last_name":"Knottenbelt","first_name":"William J."}],"article_processing_charge":"No","external_id":{"isi":["000712016200001"]},"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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"23","publication":"25th International Conference on Financial Cryptography and Data Security","isi":1,"year":"2021","doi":"10.1007/978-3-662-64331-0_1","date_published":"2021-10-23T00:00:00Z","date_created":"2021-11-21T23:01:29Z","page":"3-36"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work.","page":"209-230","date_created":"2021-11-21T23:01:29Z","date_published":"2021-10-23T00:00:00Z","doi":"10.1007/978-3-662-64331-0_11","year":"2021","isi":1,"publication":"25th International Conference on Financial Cryptography and Data Security","day":"23","article_processing_charge":"No","external_id":{"arxiv":["1905.11360"],"isi":["000712016200011"]},"author":[{"full_name":"Avarikioti, Zeta","last_name":"Avarikioti","first_name":"Zeta"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Roger","last_name":"Wattenhofer","full_name":"Wattenhofer, Roger"},{"last_name":"Zindros","full_name":"Zindros, Dionysis","first_name":"Dionysis"}],"title":"Brick: Asynchronous incentive-compatible payment channels","citation":{"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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"10","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","volume":"12675 ","publication_status":"published","publication_identifier":{"eisbn":["978-3-662-64331-0"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-6626-4330-3"]},"language":[{"iso":"eng"}],"conference":{"location":"Virtual","end_date":"2021-03-05","start_date":"2021-03-01","name":"FC: Financial Cryptography"},"type":"conference","status":"public","_id":"10324","department":[{"_id":"ElKo"}],"date_updated":"2023-08-14T12:59:58Z"},{"_id":"10363","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-14T13:01:38Z","department":[{"_id":"CaGu"}],"pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"11","intvolume":" 34","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/protein/gzab025"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"publication_status":"published","volume":34,"article_number":"gzab025","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","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).","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.","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.","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.","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."},"title":"Rational engineering of an erythropoietin fusion protein to treat hypoxia","author":[{"first_name":"Jungmin","last_name":"Lee","full_name":"Lee, Jungmin"},{"full_name":"Vernet, Andyna","last_name":"Vernet","first_name":"Andyna"},{"last_name":"Gruber","full_name":"Gruber, Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","first_name":"Nathalie"},{"first_name":"Kasia M.","last_name":"Kready","full_name":"Kready, Kasia M."},{"first_name":"Devin R.","full_name":"Burrill, Devin R.","last_name":"Burrill"},{"last_name":"Way","full_name":"Way, Jeffrey C.","first_name":"Jeffrey C."},{"full_name":"Silver, Pamela A.","last_name":"Silver","first_name":"Pamela A."}],"external_id":{"pmid":["34725710"],"isi":["000746596900001"]},"article_processing_charge":"No","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.","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"01","publication":"Protein Engineering, Design and Selection","isi":1,"year":"2021","doi":"10.1093/protein/gzab025","date_published":"2021-11-01T00:00:00Z","date_created":"2021-11-28T23:01:28Z"},{"isi":1,"year":"2021","day":"17","publication":"Cells and Development","date_published":"2021-11-17T00:00:00Z","doi":"10.1016/j.cdev.2021.203758","date_created":"2021-11-28T23:01:30Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"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.","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.","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.","short":"C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lennon, Ana Maria","last_name":"Lennon","first_name":"Ana Maria"},{"full_name":"Mayor, Roberto","last_name":"Mayor","first_name":"Roberto"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"}],"external_id":{"pmid":["34800748"],"isi":["000974771600028"]},"article_processing_charge":"No","title":"Special rebranding issue: “Quantitative cell and developmental biology”","article_number":"203758","publication_identifier":{"issn":["2667-2901"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":168,"issue":"12","oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cdev.2021.203758"}],"month":"11","intvolume":" 168","date_updated":"2023-08-14T13:02:40Z","department":[{"_id":"CaHe"}],"_id":"10366","article_type":"letter_note","type":"journal_article","status":"public"},{"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 12","month":"11","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_size":2303405,"date_updated":"2021-12-10T08:54:09Z","creator":"cchlebak","file_name":"2021_NatComm_Ucar.pdf","date_created":"2021-12-10T08:54:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10529","checksum":"63c56ec75314a71e63e7dd2920b3c5b5"}],"ec_funded":1,"related_material":{"record":[{"id":"13058","status":"public","relation":"research_data"}]},"volume":12,"_id":"10402","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-14T13:18:46Z","ddc":["573"],"department":[{"_id":"EdHa"}],"file_date_updated":"2021-12-10T08:54:09Z","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.).","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2021","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"24","date_created":"2021-12-05T23:01:40Z","date_published":"2021-11-24T00:00:00Z","doi":"10.1038/s41467-021-27135-5","article_number":"6830","project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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.","ieee":"M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["34819507"],"isi":["000722322900020"]},"author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"last_name":"Kamenev","full_name":"Kamenev, Dmitrii","first_name":"Dmitrii"},{"last_name":"Sunadome","full_name":"Sunadome, Kazunori","first_name":"Kazunori"},{"id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C","full_name":"Fachet, Dominik C","last_name":"Fachet"},{"full_name":"Lallemend, Francois","last_name":"Lallemend","first_name":"Francois"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"full_name":"Hadjab, Saida","last_name":"Hadjab","first_name":"Saida"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"title":"Theory of branching morphogenesis by local interactions and global guidance"},{"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","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","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","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.","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."},"title":"Trojan-resilience without cryptography","author":[{"id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip","last_name":"Chakraborty","full_name":"Chakraborty, Suvradip"},{"first_name":"Stefan","full_name":"Dziembowski, Stefan","last_name":"Dziembowski"},{"full_name":"Gałązka, Małgorzata","last_name":"Gałązka","first_name":"Małgorzata"},{"full_name":"Lizurej, Tomasz","last_name":"Lizurej","first_name":"Tomasz"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"external_id":{"isi":["000728364000014"]},"article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"04","isi":1,"year":"2021","doi":"10.1007/978-3-030-90453-1_14","date_published":"2021-11-04T00:00:00Z","date_created":"2021-12-05T23:01:42Z","page":"397-428","_id":"10407","status":"public","type":"conference","conference":{"start_date":"2021-11-08","end_date":"2021-11-11","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography Conference"},"date_updated":"2023-08-14T13:07:46Z","department":[{"_id":"KrPi"}],"oa_version":"Preprint","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."}],"month":"11","intvolume":" 13043","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1224"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9-783-0309-0452-4"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","volume":13043,"ec_funded":1},{"month":"11","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":10,"file":[{"date_created":"2021-12-10T08:31:41Z","file_name":"2021_eLife_Biane.pdf","creator":"cchlebak","date_updated":"2021-12-10T08:31:41Z","file_size":13131322,"checksum":"c7c33c3319428d56e332e22349c50ed3","file_id":"10528","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10403","file_date_updated":"2021-12-10T08:31:41Z","department":[{"_id":"RySh"}],"ddc":["570"],"date_updated":"2023-08-14T13:12:07Z","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"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.","date_published":"2021-11-03T00:00:00Z","doi":"10.7554/eLife.65954","date_created":"2021-12-05T23:01:40Z","day":"03","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2021","article_number":"e65954","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","author":[{"full_name":"Biane, Celia","last_name":"Biane","first_name":"Celia"},{"first_name":"Florian","last_name":"Rückerl","full_name":"Rückerl, Florian"},{"first_name":"Therese","last_name":"Abrahamsson","full_name":"Abrahamsson, Therese"},{"last_name":"Saint-Cloment","full_name":"Saint-Cloment, Cécile","first_name":"Cécile"},{"last_name":"Mariani","full_name":"Mariani, Jean","first_name":"Jean"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"first_name":"David A.","full_name":"Digregorio, David A.","last_name":"Digregorio"},{"full_name":"Sherrard, Rachel M.","last_name":"Sherrard","first_name":"Rachel M."},{"first_name":"Laurence","last_name":"Cathala","full_name":"Cathala, Laurence"}],"external_id":{"isi":["000715789500001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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).","ieee":"C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021."}},{"doi":"10.1038/s42005-021-00753-7","date_published":"2021-11-26T00:00:00Z","date_created":"2021-12-05T23:01:39Z","day":"26","publication":"Communications Physics","has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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).","title":"Generation of spin currents by a temperature gradient in a two-terminal device","author":[{"full_name":"Barfknecht, Rafael E.","last_name":"Barfknecht","first_name":"Rafael E."},{"last_name":"Foerster","full_name":"Foerster, Angela","first_name":"Angela"},{"first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T.","last_name":"Zinner"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"external_id":{"arxiv":["2101.02020"],"isi":["10.1038/s42005-021-00753-7"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","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"},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"252","volume":4,"issue":"1","ec_funded":1,"file":[{"file_id":"10420","checksum":"9097319952cb9a3d96e7fd3aa9813a03","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-06T14:53:41Z","file_name":"2021_NatComm_Barfknecht.pdf","date_updated":"2021-12-06T14:53:41Z","file_size":1068984,"creator":"alisjak"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23993650"]},"publication_status":"published","month":"11","intvolume":" 4","scopus_import":"1","oa_version":"Published Version","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."}],"department":[{"_id":"MiLe"}],"file_date_updated":"2021-12-06T14:53:41Z","ddc":["530"],"date_updated":"2023-08-14T13:04:34Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10401"},{"oa":1,"publisher":"Wiley","quality_controlled":"1","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","date_created":"2021-12-05T23:01:40Z","doi":"10.1111/cgf.14418","date_published":"2021-11-27T00:00:00Z","page":"253-264","publication":"Computer Graphics Forum","day":"27","year":"2021","isi":1,"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"title":"Interactive analysis of CNN robustness","external_id":{"isi":["000722952000024"],"arxiv":["2110.07667"]},"article_processing_charge":"No","author":[{"last_name":"Sietzen","full_name":"Sietzen, Stefan","first_name":"Stefan"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Judy","full_name":"Borowski, Judy","last_name":"Borowski"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"full_name":"Waldner, Manuela","last_name":"Waldner","first_name":"Manuela"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","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.","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","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","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.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 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."},"intvolume":" 40","month":"11","main_file_link":[{"url":"https://arxiv.org/abs/2110.07667","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"issue":"7","volume":40,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"status":"public","article_type":"original","type":"journal_article","_id":"10404","department":[{"_id":"ToHe"}],"date_updated":"2023-08-14T13:11:42Z"},{"year":"2021","day":"25","date_published":"2021-08-25T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10402"}]},"doi":"10.5281/ZENODO.5257160","date_created":"2023-05-23T13:46:34Z","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5257161","open_access":"1"}],"month":"08","date_updated":"2023-08-14T13:18:46Z","citation":{"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.","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).","ieee":"M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021.","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar"}],"article_processing_charge":"No","title":"Source data for the manuscript \"Theory of branching morphogenesis by local interactions and global guidance\"","department":[{"_id":"EdHa"}],"_id":"13058","type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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.","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.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","last_name":"Auerbach","first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"full_name":"Baig, Mirza Ahad","last_name":"Baig","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","first_name":"Mirza Ahad"},{"full_name":"Cueto Noval, Miguel","last_name":"Cueto Noval","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000728363700008"]},"article_processing_charge":"No","title":"Grafting key trees: Efficient key management for overlapping groups","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).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"year":"2021","day":"04","publication":"19th International Conference","page":"222-253","doi":"10.1007/978-3-030-90456-2_8","date_published":"2021-11-04T00:00:00Z","date_created":"2021-12-05T23:01:42Z","_id":"10408","type":"conference","conference":{"start_date":"2021-11-08","end_date":"2021-11-11","location":"Raleigh, NC, United States","name":"TCC: Theory of Cryptography"},"status":"public","date_updated":"2023-08-14T13:19:39Z","department":[{"_id":"KrPi"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2021/1158","open_access":"1"}],"month":"11","intvolume":" 13044","publication_identifier":{"isbn":["9-783-0309-0455-5"],"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["978-3-030-90456-2"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":13044,"ec_funded":1},{"article_type":"original","type":"journal_article","keyword":["general physics and astronomy"],"status":"public","_id":"10527","department":[{"_id":"MaSe"}],"date_updated":"2023-08-14T13:19:13Z","main_file_link":[{"url":"https://arxiv.org/abs/2109.00011","open_access":"1"}],"scopus_import":"1","intvolume":" 127","month":"12","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."}],"oa_version":"Preprint","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","description":"News on IST Webpage"}]},"volume":127,"issue":"24","publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"247001","external_id":{"isi":["000923819400004"],"arxiv":["2109.00011"]},"article_processing_charge":"No","author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","full_name":"Holder, Tobias","last_name":"Holder"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"}],"title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","citation":{"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.","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.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"American Physical Society","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.","date_created":"2021-12-10T07:51:33Z","doi":"10.1103/physrevlett.127.247001","date_published":"2021-12-09T00:00:00Z","year":"2021","isi":1,"publication":"Physical Review Letters","day":"09"},{"issue":"45","volume":9,"publication_status":"published","publication_identifier":{"issn":["2050-7534"],"eissn":["2050-7526"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2021-12-13T09:24:42Z","file_size":4979390,"date_created":"2021-12-13T09:24:42Z","file_name":"2021_JMaterChemC_Dong.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10538","checksum":"6b73c214ce54a6894a5854b4364413d7","success":1}],"scopus_import":"1","intvolume":" 9","month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"MaIb"}],"file_date_updated":"2021-12-13T09:24:42Z","date_updated":"2023-08-17T06:18:44Z","ddc":["540"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10534","page":"16217-16225","date_created":"2021-12-12T23:01:27Z","date_published":"2021-12-07T00:00:00Z","doi":"10.1039/d1tc02753k","year":"2021","has_accepted_license":"1","isi":1,"publication":"Journal of Materials Chemistry C","day":"07","oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","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","external_id":{"isi":["000688135700001"]},"author":[{"first_name":"Jingjin","full_name":"Dong, Jingjin","last_name":"Dong"},{"full_name":"Sami, Selim","last_name":"Sami","first_name":"Selim"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs"},{"full_name":"Alessandri, Riccardo","last_name":"Alessandri","first_name":"Riccardo"},{"first_name":"Fatimeh","last_name":"Jahani","full_name":"Jahani, Fatimeh"},{"last_name":"Qiu","full_name":"Qiu, Li","first_name":"Li"},{"last_name":"Marrink","full_name":"Marrink, Siewert J.","first_name":"Siewert J."},{"first_name":"Remco W.A.","last_name":"Havenith","full_name":"Havenith, Remco W.A."},{"first_name":"Jan C.","full_name":"Hummelen, Jan C.","last_name":"Hummelen"},{"last_name":"Loi","full_name":"Loi, Maria A.","first_name":"Maria A."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"}],"title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","citation":{"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.","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_number":"e72676","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020","grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","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.","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","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","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.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","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."},"title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","external_id":{"isi":["000754832000001"],"pmid":["34850679"]},"article_processing_charge":"No","author":[{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"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.","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","day":"01","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-12-10T13:12:08Z","date_published":"2021-12-01T00:00:00Z","doi":"10.7554/elife.72676","_id":"10533","keyword":["genetics and molecular biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-08-17T06:21:08Z","department":[{"_id":"DaZi"}],"file_date_updated":"2022-05-16T10:42:22Z","pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 10","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_id":"11384","checksum":"22ed4c55fb550f6da02ae55c359be651","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-05-16T10:42:22Z","file_name":"2021_eLife_Choi.pdf","date_updated":"2022-05-16T10:42:22Z","file_size":2715200,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"ec_funded":1,"volume":10},{"volume":11,"file":[{"checksum":"56cbac80e6891ce750511a30161b7792","file_id":"10539","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-12-13T13:32:37Z","file_name":"2021_Frontiers_Stefanescu.pdf","creator":"alisjak","date_updated":"2021-12-13T13:32:37Z","file_size":9245199}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2234-943X"]},"publication_status":"published","month":"11","intvolume":" 11","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2021-12-13T13:32:37Z","department":[{"_id":"DaSi"}],"ddc":["610"],"date_updated":"2023-08-17T06:20:32Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10536","date_published":"2021-11-18T00:00:00Z","doi":"10.3389/fonc.2021.765151","date_created":"2021-12-12T23:01:27Z","day":"18","publication":"Frontiers in Oncology","has_accepted_license":"1","isi":1,"year":"2021","quality_controlled":"1","publisher":"Frontiers","oa":1,"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.","title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","author":[{"full_name":"Stefanescu, Cristina","last_name":"Stefanescu","first_name":"Cristina"},{"first_name":"Merel","last_name":"Van Gogh","full_name":"Van Gogh, Merel"},{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","first_name":"Marko","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","last_name":"Roblek"},{"last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias","first_name":"Mathias"},{"full_name":"Borsig, Lubor","last_name":"Borsig","first_name":"Lubor"}],"external_id":{"isi":["000726603400001"],"pmid":["34868988"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","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.","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."},"article_number":"765151"},{"type":"journal_article","article_type":"original","status":"public","_id":"10537","department":[{"_id":"RoSe"}],"date_updated":"2023-08-17T06:19:14Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08224"}],"scopus_import":"1","month":"12","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."}],"oa_version":"Preprint","ec_funded":1,"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"article_processing_charge":"No","external_id":{"isi":["000725405700001"],"arxiv":["2103.08224"]},"author":[{"last_name":"Benedikter","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"full_name":"Porta, Marcello","last_name":"Porta","first_name":"Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"title":"Bosonization of fermionic many-body dynamics","citation":{"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.","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.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021).","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.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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).","date_created":"2021-12-12T23:01:28Z","doi":"10.1007/s00023-021-01136-y","date_published":"2021-12-02T00:00:00Z","year":"2021","isi":1,"publication":"Annales Henri Poincaré","day":"02"},{"page":"343-452","date_published":"2021-06-30T00:00:00Z","doi":"10.1007/s00205-021-01686-9","date_created":"2021-12-16T12:12:33Z","isi":1,"has_accepted_license":"1","year":"2021","day":"30","publication":"Archive for Rational Mechanics and Analysis","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"first_name":"Stefan","full_name":"Neukamm, Stefan","last_name":"Neukamm"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000668431200001"],"arxiv":["1908.02273"]},"title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","citation":{"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.","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","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","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":242,"issue":"1","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"cc830b739aed83ca2e32c4e0ce266a4c","file_id":"10558","success":1,"creator":"cchlebak","date_updated":"2021-12-16T14:58:08Z","file_size":1640121,"date_created":"2021-12-16T14:58:08Z","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 242","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."}],"oa_version":"Published Version","file_date_updated":"2021-12-16T14:58:08Z","department":[{"_id":"JuFi"}],"date_updated":"2023-08-17T06:23:21Z","ddc":["530"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"_id":"10549"},{"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_processing_charge":"No","external_id":{"isi":["000728364000017"]},"author":[{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"title":"On treewidth, separators and Yao’s garbling","citation":{"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.","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","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","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.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.","page":"486-517","date_created":"2021-12-05T23:01:43Z","date_published":"2021-11-04T00:00:00Z","doi":"10.1007/978-3-030-90453-1_17","year":"2021","isi":1,"publication":"19th International Conference","day":"04","conference":{"name":"TCC: Theory of Cryptography","start_date":"2021-11-08","end_date":"2021-11-11","location":"Raleigh, NC, United States"},"type":"conference","status":"public","_id":"10409","department":[{"_id":"KrPi"}],"date_updated":"2023-08-17T06:21:38Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/926"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"11","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."}],"oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10044"}]},"volume":"13043 ","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"],"issn":["0302-9743"]},"language":[{"iso":"eng"}]},{"ec_funded":1,"issue":"6","volume":104,"publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2106.06344","open_access":"1"}],"intvolume":" 104","month":"12","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."}],"oa_version":"Preprint","department":[{"_id":"MaSe"}],"date_updated":"2023-08-17T06:22:49Z","type":"journal_article","article_type":"original","status":"public","_id":"10545","date_created":"2021-12-14T20:46:07Z","doi":"10.1103/physreva.104.062423","date_published":"2021-12-14T00:00:00Z","year":"2021","isi":1,"publication":"Physical Review A","day":"14","oa":1,"publisher":"American Physical Society","quality_controlled":"1","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.","external_id":{"arxiv":["2106.06344"],"isi":["000753659200004"]},"article_processing_charge":"No","author":[{"first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","citation":{"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.","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.","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","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.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"article_number":"062423"},{"department":[{"_id":"ElKo"}],"date_updated":"2023-08-17T06:24:44Z","type":"conference","conference":{"name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy","end_date":"2021-07-30","start_date":"2021-07-26"},"status":"public","_id":"10554","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08325"}],"month":"07","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."}],"oa_version":"Preprint","author":[{"first_name":"Idit","full_name":"Keidar, Idit","last_name":"Keidar"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Naor, Oded","last_name":"Naor","first_name":"Oded"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"}],"article_processing_charge":"No","external_id":{"arxiv":["2102.08325"],"isi":["000744439800016"]},"title":"All You Need is DAG","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"165-175","date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467905","date_created":"2021-12-16T13:21:13Z","isi":1,"year":"2021","day":"21","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"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"},{"day":"25","publication":"Frontiers in Ecology and Evolution","isi":1,"has_accepted_license":"1","year":"2021","doi":"10.3389/fevo.2021.626442","date_published":"2021-03-25T00:00:00Z","date_created":"2021-12-20T07:53:19Z","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.","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","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.","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.","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.","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."},"title":"Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels","author":[{"first_name":"Henry","full_name":"Goehlich, Henry","last_name":"Goehlich"},{"first_name":"Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87","last_name":"Sartoris","full_name":"Sartoris, Linda"},{"first_name":"Kim-Sara","last_name":"Wagner","full_name":"Wagner, Kim-Sara"},{"full_name":"Wendling, Carolin C.","last_name":"Wendling","first_name":"Carolin C."},{"first_name":"Olivia","last_name":"Roth","full_name":"Roth, Olivia"}],"external_id":{"isi":["000637736300001"]},"article_processing_charge":"No","article_number":"626442","file":[{"creator":"alisjak","file_size":3175085,"date_updated":"2021-12-20T10:44:20Z","file_name":"2021_Frontiers_Goehlich.pdf","date_created":"2021-12-20T10:44:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10572","checksum":"8d6e2b767bb0240a9b5a3a3555be51fd"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2296-701X"]},"publication_status":"published","volume":9,"oa_version":"Published Version","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."}],"month":"03","intvolume":" 9","scopus_import":"1","ddc":["597"],"date_updated":"2023-08-17T06:27:22Z","department":[{"_id":"SyCr"}],"file_date_updated":"2021-12-20T10:44:20Z","_id":"10568","status":"public","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"issue":"12","volume":11,"publication_status":"published","publication_identifier":{"eissn":["2073-4352"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2021_Crystals_Yuzheng.pdf","date_created":"2022-01-03T09:46:53Z","creator":"alisjak","file_size":4569639,"date_updated":"2022-01-03T09:46:53Z","success":1,"checksum":"668e9d777608ce0a3bc2e305133bd06b","file_id":"10591","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","alternative_title":["Hybrid and Composite Crystalline Materials"],"intvolume":" 11","month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2022-01-03T09:46:53Z","department":[{"_id":"KiMo"}],"date_updated":"2023-08-17T06:31:20Z","ddc":["620"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"10586","date_created":"2022-01-02T23:01:34Z","doi":"10.3390/cryst11121509","date_published":"2021-12-03T00:00:00Z","year":"2021","isi":1,"has_accepted_license":"1","publication":"Crystals","day":"03","oa":1,"publisher":"MDPI","quality_controlled":"1","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.","article_processing_charge":"No","external_id":{"isi":["000736602200001"]},"author":[{"first_name":"Yuzheng","full_name":"Lu, Yuzheng","last_name":"Lu"},{"full_name":"Arshad, Naila","last_name":"Arshad","first_name":"Naila"},{"first_name":"Muhammad Sultan","last_name":"Irshad","full_name":"Irshad, Muhammad Sultan"},{"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"},{"full_name":"Yousaf, Muhammad","last_name":"Yousaf","first_name":"Muhammad"},{"first_name":"Abdelaty Edrees","last_name":"Sayed","full_name":"Sayed, Abdelaty Edrees"},{"first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846"}],"title":"Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination","citation":{"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","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","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).","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1509"},{"file_date_updated":"2021-12-20T10:14:14Z","department":[{"_id":"SyCr"}],"date_updated":"2023-08-17T06:26:15Z","ddc":["573"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10569","issue":"24","volume":224,"publication_identifier":{"issn":["0022-0949"],"eissn":["1477-9145"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10571","checksum":"75d13a5ec8e3b90e3bc02bd8a9c17eef","success":1,"creator":"cchlebak","date_updated":"2021-12-20T10:14:14Z","file_size":607096,"date_created":"2021-12-20T10:14:14Z","file_name":"2021_JExpBio_Szabo.pdf"}],"language":[{"iso":"eng"}],"month":"12","intvolume":" 224","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."}],"pmid":1,"oa_version":"Published Version","author":[{"last_name":"Szabo","full_name":"Szabo, B","first_name":"B"},{"last_name":"Mangione","full_name":"Mangione, R","first_name":"R"},{"first_name":"M","last_name":"Rath","full_name":"Rath, M"},{"last_name":"Pašukonis","full_name":"Pašukonis, A","first_name":"A"},{"first_name":"SA","last_name":"Reber","full_name":"Reber, SA"},{"id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook","full_name":"Oh, Jinook","orcid":"0000-0001-7425-2372","last_name":"Oh"},{"first_name":"M","last_name":"Ringler","full_name":"Ringler, M"},{"full_name":"Ringler, E","last_name":"Ringler","first_name":"E"}],"article_processing_charge":"No","external_id":{"pmid":["34845497"],"isi":["000738259300013"]},"title":"Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles","citation":{"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.","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","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","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.","short":"B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (2021).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"jeb243647","doi":"10.1242/jeb.243647","date_published":"2021-12-16T00:00:00Z","date_created":"2021-12-20T07:54:22Z","has_accepted_license":"1","isi":1,"year":"2021","day":"16","publication":"Journal of Experimental Biology","quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"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."},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods in Applied Sciences 31 (2021) 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."},"title":"On the dynamic slip boundary condition for Navier-Stokes-like problems","external_id":{"arxiv":["2009.09057"],"isi":["000722309400001"]},"article_processing_charge":"No","author":[{"full_name":"Abbatiello, Anna","last_name":"Abbatiello","first_name":"Anna"},{"first_name":"Miroslav","last_name":"Bulíček","full_name":"Bulíček, Miroslav"},{"first_name":"Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","full_name":"Maringová, Erika","last_name":"Maringová"}],"project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"publication":"Mathematical Models and Methods in Applied Sciences","day":"13","year":"2021","has_accepted_license":"1","isi":1,"date_created":"2021-12-26T23:01:27Z","date_published":"2021-10-13T00:00:00Z","doi":"10.1142/S0218202521500470","page":"2165-2212","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.","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","ddc":["510"],"date_updated":"2023-08-17T06:29:01Z","file_date_updated":"2022-05-16T10:55:45Z","department":[{"_id":"JuFi"}],"_id":"10575","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":795483,"date_updated":"2022-05-16T10:55:45Z","file_name":"2021_MathModelsMethods_Abbatiello.pdf","date_created":"2022-05-16T10:55:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11385","checksum":"8c0a9396335f0b70e1f5cbfe450a987a"}],"publication_status":"published","publication_identifier":{"eissn":["1793-6314"],"issn":["0218-2025"]},"volume":31,"issue":"11","oa_version":"Published Version","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."}],"intvolume":" 31","month":"10","scopus_import":"1"},{"issue":"12","volume":37,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10578","checksum":"244cfcac0479ca6e3444c098ab2860a1","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2021_VisComput_Chen.pdf","date_created":"2021-12-27T13:51:08Z","creator":"cchlebak","file_size":5741094,"date_updated":"2021-12-27T13:51:08Z"}],"publication_status":"published","publication_identifier":{"issn":["0178-2789"],"eissn":["1432-2315"]},"intvolume":" 37","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2021-12-27T13:51:08Z","department":[{"_id":"BeBi"}],"ddc":["000"],"date_updated":"2023-08-17T06:29:34Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"10574","date_created":"2021-12-26T23:01:26Z","date_published":"2021-12-01T00:00:00Z","doi":"10.1007/s00371-021-02227-x","page":"2975-2987","publication":"Visual Computer","day":"01","year":"2021","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","title":"The effect of geometry and illumination on appearance perception of different material categories","external_id":{"isi":["000673536600003"]},"article_processing_charge":"Yes","author":[{"first_name":"Bin","last_name":"Chen","full_name":"Chen, Bin"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","last_name":"Piovarci"},{"last_name":"Seidel","full_name":"Seidel, Hans Peter","first_name":"Hans Peter"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"},{"first_name":"Ana","full_name":"Serrano, Ana","last_name":"Serrano"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","short":"B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987.","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","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"}},{"issue":"26","volume":184,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"intvolume":" 184","month":"12","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"EdHa"}],"date_updated":"2023-08-17T06:28:25Z","status":"public","article_type":"original","type":"journal_article","_id":"10573","date_created":"2021-12-26T23:01:26Z","date_published":"2021-12-22T00:00:00Z","doi":"10.1016/j.cell.2021.11.025","page":"6313-6325.e18","publication":"Cell","day":"22","year":"2021","isi":1,"oa":1,"quality_controlled":"1","publisher":"Elsevier ; Cell Press","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.","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","article_processing_charge":"No","external_id":{"isi":["000735387500002"]},"author":[{"first_name":"Akankshi","full_name":"Munjal, Akankshi","last_name":"Munjal"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Tsai, Tony Y.C.","last_name":"Tsai","first_name":"Tony Y.C."},{"last_name":"Mitchison","full_name":"Mitchison, Timothy J.","first_name":"Timothy J."},{"last_name":"Megason","full_name":"Megason, Sean G.","first_name":"Sean G."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","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.","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 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."}},{"_id":"10674","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["computer science","computer science and game theory","logic in computer science"],"date_updated":"2023-08-17T06:56:42Z","ddc":["510"],"file_date_updated":"2022-01-26T08:04:50Z","department":[{"_id":"ToHe"}],"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."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 17","publication_identifier":{"eissn":["1860-5974"]},"publication_status":"published","file":[{"creator":"alisjak","date_updated":"2022-01-26T08:04:50Z","file_size":819878,"date_created":"2022-01-26T08:04:50Z","file_name":"2021_LMCS_AGHAJOHAR.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10690","checksum":"b35586a50ed1ca8f44767de116d18d81","success":1}],"language":[{"iso":"eng"}],"issue":"1","volume":17,"project":[{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"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","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","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.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Milad","last_name":"Aghajohari","full_name":"Aghajohari, Milad"},{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"external_id":{"isi":["000658724600010"],"arxiv":["1905.03588"]},"article_processing_charge":"No","title":"Determinacy in discrete-bidding infinite-duration games","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","quality_controlled":"1","publisher":"International Federation for Computational Logic","oa":1,"has_accepted_license":"1","isi":1,"year":"2021","day":"03","publication":"Logical Methods in Computer Science","page":"10:1-10:23","doi":"10.23638/LMCS-17(1:10)2021","date_published":"2021-02-03T00:00:00Z","date_created":"2022-01-25T16:32:13Z"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-030-92074-6"],"issn":["0302-9743"],"eisbn":["978-3-030-92075-3"]},"ec_funded":1,"volume":13091,"oa_version":"Preprint","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."}],"intvolume":" 13091","month":"12","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1262"}],"alternative_title":["LNCS"],"scopus_import":"1","date_updated":"2023-08-17T06:34:41Z","department":[{"_id":"KrPi"}],"_id":"10609","status":"public","conference":{"name":"ASIACRYPT: International Conference on Cryptology in Asia","end_date":"2021-12-10","location":"Virtual, Singapore","start_date":"2021-12-06"},"type":"conference","publication":"27th International Conference on the Theory and Application of Cryptology and Information Security","day":"01","year":"2021","isi":1,"date_created":"2022-01-09T23:01:27Z","doi":"10.1007/978-3-030-92075-3_12","date_published":"2021-12-01T00:00:00Z","page":"335-364","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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."},"title":"Reverse firewalls for adaptively secure MPC without setup","external_id":{"isi":["000927876200012"]},"article_processing_charge":"No","author":[{"full_name":"Chakraborty, Suvradip","last_name":"Chakraborty","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"first_name":"Chaya","full_name":"Ganesh, Chaya","last_name":"Ganesh"},{"first_name":"Mahak","last_name":"Pancholi","full_name":"Pancholi, Mahak"},{"first_name":"Pratik","last_name":"Sarkar","full_name":"Sarkar, Pratik"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}]},{"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"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)."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"12","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"10611","checksum":"759c7a873d554c48a6639e6350746ca6","file_size":7769934,"date_updated":"2022-01-10T09:40:37Z","creator":"alisjak","file_name":"2021_eLife_Godard.pdf","date_created":"2022-01-10T09:40:37Z"}],"volume":10,"_id":"10606","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-17T06:32:44Z","ddc":["570"],"department":[{"_id":"CaHe"}],"file_date_updated":"2022-01-10T09:40:37Z","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).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2021","isi":1,"has_accepted_license":"1","publication":"eLife","day":"21","date_created":"2022-01-09T23:01:26Z","date_published":"2021-12-21T00:00:00Z","doi":"10.7554/eLife.75639","article_number":"e75639","project":[{"_id":"2646861A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03601","name":"Control of embryonic cleavage pattern"}],"citation":{"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.","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.","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","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","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.","short":"B.G. Godard, R. Dumollard, C.-P.J. Heisenberg, A. Mcdougall, ELife 10 (2021).","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000733610100001"]},"article_processing_charge":"No","author":[{"full_name":"Godard, Benoit G","last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"full_name":"Dumollard, Remi","last_name":"Dumollard","first_name":"Remi"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"last_name":"Mcdougall","full_name":"Mcdougall, Alex","first_name":"Alex"}],"title":"Combined effect of cell geometry and polarity domains determines the orientation of unequal division"},{"month":"10","intvolume":" 91","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"volume":91,"file":[{"file_id":"10612","checksum":"360681585acb51e80d17c6b213c56b55","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-01-10T13:41:40Z","file_name":"2021_Parkinsonism_Venezia.pdf","date_updated":"2022-01-10T13:41:40Z","file_size":6848513,"creator":"alisjak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1353-8020"],"eissn":["1873-5126"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10607","file_date_updated":"2022-01-10T13:41:40Z","department":[{"_id":"EM-Fac"}],"ddc":["610"],"date_updated":"2023-08-17T06:36:01Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"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.","doi":"10.1016/j.parkreldis.2021.09.007","date_published":"2021-10-01T00:00:00Z","date_created":"2022-01-09T23:01:26Z","page":"59-65","day":"01","publication":"Parkinsonism & Related Disorders","has_accepted_license":"1","isi":1,"year":"2021","title":"Toll-like receptor 4 deficiency facilitates α-synuclein propagation and neurodegeneration in a mouse model of prodromal Parkinson's disease","author":[{"first_name":"Serena","full_name":"Venezia, Serena","last_name":"Venezia"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann"},{"first_name":"Gregor K.","last_name":"Wenning","full_name":"Wenning, Gregor K."},{"first_name":"Nadia","full_name":"Stefanova, Nadia","last_name":"Stefanova"}],"article_processing_charge":"No","external_id":{"pmid":["34530328"],"isi":["000701142900012"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","short":"S. Venezia, W. Kaufmann, G.K. Wenning, N. Stefanova, Parkinsonism & Related Disorders 91 (2021) 59–65.","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"}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"A. Ghazaryan, E.M. Nica, O. Erten, P. Ghaemi, New Journal of Physics 23 (2021).","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","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","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.","ista":"Ghazaryan A, Nica EM, Erten O, Ghaemi P. 2021. Shadow surface states in topological Kondo insulators. New Journal of Physics. 23(12), 123042.","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."},"title":"Shadow surface states in topological Kondo insulators","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"first_name":"Emilian M.","full_name":"Nica, Emilian M.","last_name":"Nica"},{"first_name":"Onur","full_name":"Erten, Onur","last_name":"Erten"},{"full_name":"Ghaemi, Pouyan","last_name":"Ghaemi","first_name":"Pouyan"}],"article_processing_charge":"No","external_id":{"arxiv":["2012.11625"],"isi":["000734063700001"]},"article_number":"123042","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"23","publication":"New Journal of Physics","has_accepted_license":"1","isi":1,"year":"2021","date_published":"2021-12-23T00:00:00Z","doi":"10.1088/1367-2630/ac4124","date_created":"2022-01-16T23:01:28Z","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.","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-08-17T06:54:54Z","department":[{"_id":"MiLe"}],"file_date_updated":"2022-01-17T10:01:58Z","_id":"10628","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"10632","checksum":"0c3cb6816242fa8afd1cc87a5fe77821","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-01-17T10:01:58Z","file_name":"2021_NewJourPhys_Ghazaryan.pdf","date_updated":"2022-01-17T10:01:58Z","file_size":2533102,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1367-2630"]},"publication_status":"published","issue":"12","volume":23,"ec_funded":1,"oa_version":"Published Version","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."}],"month":"12","intvolume":" 23","scopus_import":"1"},{"ec_funded":1,"volume":104,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"intvolume":" 104","month":"12","main_file_link":[{"url":"http://128.84.4.18/abs/2107.00468","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"MiLe"}],"date_updated":"2023-08-17T06:52:17Z","status":"public","type":"journal_article","article_type":"original","_id":"10631","date_created":"2022-01-16T23:01:29Z","date_published":"2021-12-30T00:00:00Z","doi":"10.1103/PhysRevA.104.L061303","publication":"Physical Review A","day":"30","year":"2021","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","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.","title":"Excited rotational states of molecules in a superfluid","external_id":{"isi":["000739618300001"],"arxiv":["2107.00468"]},"article_processing_charge":"No","author":[{"full_name":"Cherepanov, Igor","last_name":"Cherepanov","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","first_name":"Igor"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"full_name":"Schouder, Constant A.","last_name":"Schouder","first_name":"Constant A."},{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"first_name":"Simon H.","full_name":"Albrechtsen, Simon H.","last_name":"Albrechtsen"},{"full_name":"Muñoz, Alberto Viñas","last_name":"Muñoz","first_name":"Alberto Viñas"},{"last_name":"Christiansen","full_name":"Christiansen, Lars","first_name":"Lars"},{"full_name":"Stapelfeldt, Henrik","last_name":"Stapelfeldt","first_name":"Henrik"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","ieee":"I. Cherepanov et al., “Excited rotational states of molecules in a superfluid,” Physical Review A, vol. 104, no. 6. American Physical Society, 2021.","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","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.","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.","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."},"project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"A path-integral approach to composite impurities","grant_number":"M02641","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425"}],"article_number":"L061303"},{"_id":"10597","status":"public","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2021-07-12","location":"Virtual, Melbourne, Australia","end_date":"2021-07-20"},"type":"conference","date_updated":"2023-08-17T06:32:06Z","department":[{"_id":"MaMo"}],"oa_version":"Preprint","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."}],"month":"09","main_file_link":[{"url":"https://arxiv.org/abs/2011.12882","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["978-1-5386-8209-8"],"isbn":["978-1-5386-8210-4"]},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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.","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."},"title":"Sparse multi-decoder recursive projection aggregation for Reed-Muller codes","article_processing_charge":"No","external_id":{"arxiv":["2011.12882"],"isi":["000701502201029"]},"author":[{"full_name":"Fathollahi, Dorsa","last_name":"Fathollahi","first_name":"Dorsa"},{"first_name":"Nariman","last_name":"Farsad","full_name":"Farsad, Nariman"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"oa":1,"publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","publication":"2021 IEEE International Symposium on Information Theory","day":"01","year":"2021","isi":1,"date_created":"2022-01-03T11:31:26Z","date_published":"2021-09-01T00:00:00Z","doi":"10.1109/isit45174.2021.9517887","page":"1082-1087"},{"series_title":"ICRA","_id":"10666","status":"public","type":"conference","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"conference":{"name":"ICRA: International Conference on Robotics and Automation","location":"Xi'an, China","end_date":"2021-06-05","start_date":"2021-05-30"},"ddc":["000"],"date_updated":"2023-08-17T06:58:38Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"oa_version":"None","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."}],"main_file_link":[{"url":"https://arxiv.org/abs/2103.08187","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-1-7281-9077-8"],"isbn":["978-1-7281-9078-5"],"eissn":["2577-087X"],"issn":["1050-4729"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"11362","status":"public"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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."},"title":"Adversarial training is not ready for robot learning","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000765738803040"],"arxiv":["2103.08187"]},"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).","quality_controlled":"1","oa":1,"publication":"2021 IEEE International Conference on Robotics and Automation","has_accepted_license":"1","isi":1,"year":"2021","doi":"10.1109/ICRA48506.2021.9561036","date_published":"2021-01-01T00:00:00Z","date_created":"2022-01-25T15:44:54Z","page":"4140-4147"},{"intvolume":" 157","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1909.03266","open_access":"1"}],"oa_version":"Preprint","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."}],"issue":"7","volume":157,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0010-437X"],"eissn":["1570-5846"]},"keyword":["Algebra and Number Theory"],"status":"public","article_type":"original","type":"journal_article","_id":"10711","department":[{"_id":"TiBr"}],"date_updated":"2023-08-17T06:59:16Z","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","acknowledgement":"We would like to thank the anonymous referees for carefully reading the paper and for their remarks and suggestions.","date_created":"2022-02-01T08:10:43Z","date_published":"2021-06-28T00:00:00Z","doi":"10.1112/s0010437x21007351","page":"1610-1651","publication":"Compositio Mathematica","day":"28","year":"2021","isi":1,"title":"The distribution of the maximum of partial sums of Kloosterman sums and other trace functions","article_processing_charge":"No","external_id":{"isi":["000667289300001"],"arxiv":["1909.03266"]},"author":[{"first_name":"Pascal","last_name":"Autissier","full_name":"Autissier, Pascal"},{"last_name":"Bonolis","full_name":"Bonolis, Dante","id":"6A459894-5FDD-11E9-AF35-BB24E6697425","first_name":"Dante"},{"full_name":"Lamzouri, Youness","last_name":"Lamzouri","first_name":"Youness"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"P. Autissier, D. Bonolis, Y. Lamzouri, Compositio Mathematica 157 (2021) 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."}},{"month":"07","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"volume":11,"issue":"7","ec_funded":1,"file":[{"date_created":"2022-03-18T09:53:15Z","file_name":"2021_Nanomaterials_Li.pdf","creator":"dernst","date_updated":"2022-03-18T09:53:15Z","file_size":4867547,"file_id":"10859","checksum":"f28a8b5cf80f5605828359bb398463b0","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2079-4991"]},"publication_status":"published","status":"public","keyword":["General Materials Science","General Chemical Engineering"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10858","file_date_updated":"2022-03-18T09:53:15Z","department":[{"_id":"MaIb"}],"ddc":["540"],"date_updated":"2023-08-17T07:08:30Z","quality_controlled":"1","publisher":"MDPI","oa":1,"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.","date_published":"2021-07-14T00:00:00Z","doi":"10.3390/nano11071827","date_created":"2022-03-18T09:45:02Z","day":"14","publication":"Nanomaterials","has_accepted_license":"1","isi":1,"year":"2021","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"1827","title":"Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping","author":[{"first_name":"Mengyao","full_name":"Li, Mengyao","last_name":"Li"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"first_name":"Ting","full_name":"Zhang, Ting","last_name":"Zhang"},{"last_name":"Zuo","full_name":"Zuo, Yong","first_name":"Yong"},{"first_name":"Ke","full_name":"Xiao, Ke","last_name":"Xiao"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Llorca","full_name":"Llorca, Jordi","first_name":"Jordi"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"external_id":{"isi":["000676570000001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","short":"M. Li, Y. Zhang, T. Zhang, Y. Zuo, K. Xiao, J. Arbiol, J. Llorca, Y. Liu, A. Cabot, Nanomaterials 11 (2021).","ieee":"M. Li et al., “Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping,” Nanomaterials, vol. 11, no. 7. MDPI, 2021."}},{"page":"2051-2064.e8","date_created":"2022-03-08T07:51:04Z","date_published":"2021-05-24T00:00:00Z","doi":"10.1016/j.cub.2021.02.043","year":"2021","isi":1,"publication":"Current Biology","day":"24","oa":1,"quality_controlled":"1","publisher":"Elsevier","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 ).","external_id":{"pmid":["33711252"],"isi":["000654652200002"]},"article_processing_charge":"No","author":[{"first_name":"Stephanie","full_name":"Stahnke, Stephanie","last_name":"Stahnke"},{"first_name":"Hermann","full_name":"Döring, Hermann","last_name":"Döring"},{"full_name":"Kusch, Charly","last_name":"Kusch","first_name":"Charly"},{"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"},{"last_name":"Guledani","full_name":"Guledani, Aleks","first_name":"Aleks"},{"full_name":"Pleines, Irina","last_name":"Pleines","first_name":"Irina"},{"first_name":"Michael","last_name":"Schnoor","full_name":"Schnoor, Michael"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Robert","full_name":"Geffers, Robert","last_name":"Geffers"},{"first_name":"Manfred","last_name":"Rohde","full_name":"Rohde, Manfred"},{"first_name":"Mathias","full_name":"Müsken, Mathias","last_name":"Müsken"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"first_name":"Anika","last_name":"Steffen","full_name":"Steffen, Anika"},{"last_name":"Faix","full_name":"Faix, Jan","first_name":"Jan"},{"last_name":"Nieswandt","full_name":"Nieswandt, Bernhard","first_name":"Bernhard"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Stradal","full_name":"Stradal, Theresia E.B.","first_name":"Theresia E.B."}],"title":"Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion","citation":{"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.","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.","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","volume":31,"publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.03.24.005835"}],"scopus_import":"1","intvolume":" 31","month":"05","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."}],"oa_version":"Preprint","pmid":1,"department":[{"_id":"MiSi"}],"date_updated":"2023-08-17T07:01:14Z","article_type":"original","type":"journal_article","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"status":"public","_id":"10834"},{"ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-8548-0"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/153753"}],"month":"07","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."}],"oa_version":"Submitted Version","department":[{"_id":"DaAl"}],"date_updated":"2023-08-17T07:11:03Z","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","location":"Virtual, Italy","end_date":"2021-07-30","start_date":"2021-07-26"},"type":"conference","status":"public","_id":"9935","page":"469–479","date_created":"2021-08-17T18:14:15Z","doi":"10.1145/3465084.3467937","date_published":"2021-07-21T00:00:00Z","year":"2021","isi":1,"publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","day":"21","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","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","external_id":{"isi":["000744439800048"]},"author":[{"full_name":"Czumaj, Artur","last_name":"Czumaj","first_name":"Artur"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","last_name":"Davies","full_name":"Davies, Peter","orcid":"0000-0002-5646-9524"},{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"title":"Improved deterministic (Δ+1) coloring in low-space MPC","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","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.","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}]},{"status":"public","keyword":["Applied Mathematics","Geometry and Topology","Analysis"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10856","department":[{"_id":"UlWa"}],"file_date_updated":"2022-03-18T09:31:59Z","ddc":["510"],"date_updated":"2023-08-17T07:07:58Z","month":"01","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","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 \u001cnd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2."}],"issue":"1","volume":9,"file":[{"date_created":"2022-03-18T09:31:59Z","file_name":"2021_AnalysisMetricSpaces_Ivanov.pdf","creator":"dernst","date_updated":"2022-03-18T09:31:59Z","file_size":789801,"checksum":"7e615ac8489f5eae580b6517debfdc53","file_id":"10857","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2299-3274"]},"publication_status":"published","title":"On the volume of sections of the cube","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"first_name":"Igor","last_name":"Tsiutsiurupa","full_name":"Tsiutsiurupa, Igor"}],"external_id":{"isi":["000734286800001"],"arxiv":["2004.02674"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","short":"G. Ivanov, I. Tsiutsiurupa, Analysis and Geometry in Metric Spaces 9 (2021) 1–18.","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.","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.","ista":"Ivanov G, Tsiutsiurupa I. 2021. On the volume of sections of the cube. Analysis and Geometry in Metric Spaces. 9(1), 1–18."},"quality_controlled":"1","publisher":"De Gruyter","oa":1,"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.","date_published":"2021-01-29T00:00:00Z","doi":"10.1515/agms-2020-0103","date_created":"2022-03-18T09:25:14Z","page":"1-18","day":"29","publication":"Analysis and Geometry in Metric Spaces","isi":1,"has_accepted_license":"1","year":"2021"},{"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Component Stability in Low-Space Massively Parallel Computation.” In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, 481–491. Association for Computing Machinery, 2021. https://doi.org/10.1145/3465084.3467903.","ista":"Czumaj A, Davies P, Parter M. 2021. Component stability in low-space massively parallel computation. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 481–491.","mla":"Czumaj, Artur, et al. “Component Stability in Low-Space Massively Parallel Computation.” Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 481–491, doi:10.1145/3465084.3467903.","ama":"Czumaj A, Davies P, Parter M. Component stability in low-space massively parallel computation. In: Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2021:481–491. doi:10.1145/3465084.3467903","apa":"Czumaj, A., Davies, P., & Parter, M. (2021). Component stability in low-space massively parallel computation. In Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing (pp. 481–491). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3465084.3467903","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. 481–491.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Component stability in low-space massively parallel computation,” in Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Virtual, Italy, 2021, pp. 481–491."},"title":"Component stability in low-space massively parallel computation","article_processing_charge":"No","external_id":{"arxiv":["2106.01880"],"isi":["000744439800049"]},"author":[{"full_name":"Czumaj, Artur","last_name":"Czumaj","first_name":"Artur"},{"full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"first_name":"Merav","full_name":"Parter, Merav","last_name":"Parter"}],"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.","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","day":"21","year":"2021","isi":1,"date_created":"2021-08-17T18:11:16Z","date_published":"2021-07-21T00:00:00Z","doi":"10.1145/3465084.3467903","page":"481–491","_id":"9933","status":"public","conference":{"start_date":"2021-07-26","end_date":"2021-07-30","location":"Virtual, Italy","name":"PODC: Principles of Distributed Computing"},"type":"conference","date_updated":"2023-08-17T07:11:32Z","department":[{"_id":"DaAl"}],"oa_version":"Submitted Version","abstract":[{"text":"In this paper, we study the power and limitations of component-stable algorithms in the low-space model of Massively Parallel Computation (MPC). Recently Ghaffari, Kuhn and Uitto (FOCS 2019) introduced the class of component-stable low-space MPC algorithms, which are, informally, defined as algorithms for which the outputs reported by the nodes in different connected components are required to be independent. This very natural notion was introduced to capture most (if not all) of the known efficient MPC algorithms to date, and it was the first general class of MPC algorithms for which one can show non-trivial conditional lower bounds. In this paper we enhance the framework of component-stable algorithms and investigate its effect on the complexity of randomized and deterministic low-space MPC. Our key contributions include: 1) We revise and formalize the lifting approach of Ghaffari, Kuhn and Uitto. This requires a very delicate amendment of the notion of component stability, which allows us to fill in gaps in the earlier arguments. 2) We also extend the framework to obtain conditional lower bounds for deterministic algorithms and fine-grained lower bounds that depend on the maximum degree Δ. 3) We demonstrate a collection of natural graph problems for which non-component-stable algorithms break the conditional lower bound obtained for component-stable algorithms. This implies that, for both deterministic and randomized algorithms, component-stable algorithms are conditionally weaker than the non-component-stable ones.\r\n\r\nAltogether our results imply that component-stability might limit the computational power of the low-space MPC model, paving the way for improved upper bounds that escape the conditional lower bound setting of Ghaffari, Kuhn, and Uitto.","lang":"eng"}],"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/2106.01880","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450385480"]},"ec_funded":1},{"issue":"3","volume":64,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0013-0915"],"eissn":["1464-3839"]},"publication_status":"published","month":"08","intvolume":" 64","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1017/S0013091521000080","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum.","lang":"eng"}],"department":[{"_id":"JaMa"}],"date_updated":"2023-08-17T07:12:05Z","status":"public","type":"journal_article","article_type":"original","_id":"9627","date_published":"2021-08-01T00:00:00Z","doi":"10.1017/S0013091521000080","date_created":"2021-07-04T22:01:24Z","page":"443-447","day":"01","publication":"Proceedings of the Edinburgh Mathematical Society","isi":1,"year":"2021","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","title":"Self-adjoint extensions of bipartite Hamiltonians","author":[{"first_name":"Daniel","last_name":"Lenz","full_name":"Lenz, Daniel"},{"first_name":"Timon","full_name":"Weinmann, Timon","last_name":"Weinmann"},{"first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.03670"],"isi":["000721363700003"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:10.1017/S0013091521000080.","short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” Proceedings of the Edinburgh Mathematical Society, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021.","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 2021;64(3):443-447. doi:10.1017/S0013091521000080","apa":"Lenz, D., Weinmann, T., & Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. Cambridge University Press. https://doi.org/10.1017/S0013091521000080","chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” Proceedings of the Edinburgh Mathematical Society. Cambridge University Press, 2021. https://doi.org/10.1017/S0013091521000080.","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447."}},{"department":[{"_id":"RoSe"}],"file_date_updated":"2022-05-16T12:23:40Z","ddc":["510"],"date_updated":"2023-08-21T06:30:30Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7901","ec_funded":1,"volume":225,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"11386","checksum":"f38c79dfd828cdc7f49a34b37b83d376","creator":"dernst","file_size":1089319,"date_updated":"2022-05-16T12:23:40Z","file_name":"2021_InventMath_Benedikter.pdf","date_created":"2022-05-16T12:23:40Z"}],"publication_status":"published","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"intvolume":" 225","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy."}],"title":"Correlation energy of a weakly interacting Fermi gas","external_id":{"isi":["000646573600001"],"arxiv":["2005.08933"]},"article_processing_charge":"Yes (via OA deal)","author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter"},{"first_name":"Phan Thành","last_name":"Nam","full_name":"Nam, Phan Thành"},{"last_name":"Porta","full_name":"Porta, Marcello","first_name":"Marcello"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 225, 885–979.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas.” Inventiones Mathematicae. Springer, 2021. https://doi.org/10.1007/s00222-021-01041-5.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Inventiones Mathematicae 225 (2021) 885–979.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas,” Inventiones Mathematicae, vol. 225. Springer, pp. 885–979, 2021.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. Springer. https://doi.org/10.1007/s00222-021-01041-5","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 2021;225:885-979. doi:10.1007/s00222-021-01041-5","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas.” Inventiones Mathematicae, vol. 225, Springer, 2021, pp. 885–979, doi:10.1007/s00222-021-01041-5."},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"date_created":"2020-05-28T16:48:20Z","date_published":"2021-05-03T00:00:00Z","doi":"10.1007/s00222-021-01041-5","page":"885-979","publication":"Inventiones Mathematicae","day":"03","year":"2021","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"We thank Christian Hainzl for helpful discussions and a referee for very careful reading of the paper and many helpful suggestions. NB and RS were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 694227). Part of the research of NB was conducted on the RZD18 Nice–Milan–Vienna–Moscow. NB thanks Elliott H. Lieb and Peter Otte for explanations about the Luttinger model. PTN has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP acknowledges financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, grant agreement No. 802901). BS gratefully acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS (grant agreement No. 834782). All authors acknowledge support for workshop participation from Mathematisches Forschungsinstitut Oberwolfach (Leibniz Association). NB, PTN, BS, and RS acknowledge support for workshop participation from Fondation des Treilles."},{"abstract":[{"text":"While most simulations of the epoch of reionization have focused on single-stellar populations in star-forming dwarf galaxies, products of binary evolution are expected to significantly contribute to emissions of hydrogen-ionizing photons. Among these products are stripped stars (or helium stars), which have their envelopes stripped from interactions with binary companions, leaving an exposed helium core. Previous work has suggested these stripped stars can dominate the Lyman Continuum (LyC) photon output of high-redshift, low-luminosity galaxies post-starburst. Other sources of hard radiation in the early universe include zero-metallicity Population iii stars, which may have similar spectral energy distribution (SED) properties to galaxies with radiation dominated by stripped-star emissions. Here, we use four metrics (the power-law exponent over wavelength intervals 240–500 Å, 600–900 Å, and 1200–2000 Å, and the ratio of total luminosity in FUV wavelengths to LyC wavelengths) to compare the SEDs of simulated galaxies with only single-stellar evolution, galaxies containing stripped stars, and galaxies containing Population iii stars, with four different initial mass functions (IMFs). We find that stripped stars significantly alter SEDs in the LyC range of galaxies at the epoch of reionization. SEDs in galaxies with stripped stars have lower power-law indices in the LyC range and lower FUV to LyC luminosity ratios. These differences in SEDs are present at all considered luminosities (${M}_{\\mathrm{UV}}\\gt -15$, AB system), and are most pronounced for lower-luminosity galaxies. Intrinsic SEDs as well as those with interstellar medium absorption of galaxies with stripped stars and Population iii stars are found to be distinct for all tested Population iii IMFs.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3847/1538-4357/ac0af6","open_access":"1"}],"scopus_import":"1","intvolume":" 918","month":"08","publication_status":"published","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"language":[{"iso":"eng"}],"issue":"1","volume":918,"_id":"13456","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","date_updated":"2023-08-21T11:44:50Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"American Astronomical Society","year":"2021","publication":"The Astrophysical Journal","day":"27","date_created":"2023-08-03T10:11:24Z","date_published":"2021-08-27T00:00:00Z","doi":"10.3847/1538-4357/ac0af6","article_number":"5","citation":{"ista":"Berzin E, Secunda A, Cen R, Menegas A, Götberg YLL. 2021. Spectral signatures of population III and envelope-stripped stars in galaxies at the epoch of reionization. The Astrophysical Journal. 918(1), 5.","chicago":"Berzin, Elizabeth, Amy Secunda, Renyue Cen, Alexander Menegas, and Ylva Louise Linsdotter Götberg. “Spectral Signatures of Population III and Envelope-Stripped Stars in Galaxies at the Epoch of Reionization.” The Astrophysical Journal. American Astronomical Society, 2021. https://doi.org/10.3847/1538-4357/ac0af6.","short":"E. Berzin, A. Secunda, R. Cen, A. Menegas, Y.L.L. Götberg, The Astrophysical Journal 918 (2021).","ieee":"E. Berzin, A. Secunda, R. Cen, A. Menegas, and Y. L. L. Götberg, “Spectral signatures of population III and envelope-stripped stars in galaxies at the epoch of reionization,” The Astrophysical Journal, vol. 918, no. 1. American Astronomical Society, 2021.","ama":"Berzin E, Secunda A, Cen R, Menegas A, Götberg YLL. Spectral signatures of population III and envelope-stripped stars in galaxies at the epoch of reionization. The Astrophysical Journal. 2021;918(1). doi:10.3847/1538-4357/ac0af6","apa":"Berzin, E., Secunda, A., Cen, R., Menegas, A., & Götberg, Y. L. L. (2021). Spectral signatures of population III and envelope-stripped stars in galaxies at the epoch of reionization. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ac0af6","mla":"Berzin, Elizabeth, et al. “Spectral Signatures of Population III and Envelope-Stripped Stars in Galaxies at the Epoch of Reionization.” The Astrophysical Journal, vol. 918, no. 1, 5, American Astronomical Society, 2021, doi:10.3847/1538-4357/ac0af6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2102.08408"]},"author":[{"last_name":"Berzin","full_name":"Berzin, Elizabeth","first_name":"Elizabeth"},{"last_name":"Secunda","full_name":"Secunda, Amy","first_name":"Amy"},{"first_name":"Renyue","last_name":"Cen","full_name":"Cen, Renyue"},{"last_name":"Menegas","full_name":"Menegas, Alexander","first_name":"Alexander"},{"id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg"}],"title":"Spectral signatures of population III and envelope-stripped stars in galaxies at the epoch of reionization"},{"publisher":"American Astronomical Society","quality_controlled":"1","oa":1,"doi":"10.3847/2041-8213/ac0b42","date_published":"2021-07-23T00:00:00Z","date_created":"2023-08-03T10:11:45Z","day":"23","publication":"The Astrophysical Journal Letters","year":"2021","article_number":"L5","title":"Binary-stripped stars as core-collapse supernovae progenitors","author":[{"full_name":"Vartanyan, David","last_name":"Vartanyan","first_name":"David"},{"first_name":"Eva","last_name":"Laplace","full_name":"Laplace, Eva"},{"full_name":"Renzo, Mathieu","last_name":"Renzo","first_name":"Mathieu"},{"last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Burrows, Adam","last_name":"Burrows","first_name":"Adam"},{"first_name":"Selma E.","full_name":"de Mink, Selma E.","last_name":"de Mink"}],"article_processing_charge":"No","external_id":{"arxiv":["2104.03317"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Vartanyan, David, et al. “Binary-Stripped Stars as Core-Collapse Supernovae Progenitors.” The Astrophysical Journal Letters, vol. 916, no. 1, L5, American Astronomical Society, 2021, doi:10.3847/2041-8213/ac0b42.","ieee":"D. Vartanyan, E. Laplace, M. Renzo, Y. L. L. Götberg, A. Burrows, and S. E. de Mink, “Binary-stripped stars as core-collapse supernovae progenitors,” The Astrophysical Journal Letters, vol. 916, no. 1. American Astronomical Society, 2021.","short":"D. Vartanyan, E. Laplace, M. Renzo, Y.L.L. Götberg, A. Burrows, S.E. de Mink, The Astrophysical Journal Letters 916 (2021).","ama":"Vartanyan D, Laplace E, Renzo M, Götberg YLL, Burrows A, de Mink SE. Binary-stripped stars as core-collapse supernovae progenitors. The Astrophysical Journal Letters. 2021;916(1). doi:10.3847/2041-8213/ac0b42","apa":"Vartanyan, D., Laplace, E., Renzo, M., Götberg, Y. L. L., Burrows, A., & de Mink, S. E. (2021). Binary-stripped stars as core-collapse supernovae progenitors. The Astrophysical Journal Letters. American Astronomical Society. https://doi.org/10.3847/2041-8213/ac0b42","chicago":"Vartanyan, David, Eva Laplace, Mathieu Renzo, Ylva Louise Linsdotter Götberg, Adam Burrows, and Selma E. de Mink. “Binary-Stripped Stars as Core-Collapse Supernovae Progenitors.” The Astrophysical Journal Letters. American Astronomical Society, 2021. https://doi.org/10.3847/2041-8213/ac0b42.","ista":"Vartanyan D, Laplace E, Renzo M, Götberg YLL, Burrows A, de Mink SE. 2021. Binary-stripped stars as core-collapse supernovae progenitors. The Astrophysical Journal Letters. 916(1), L5."},"month":"07","intvolume":" 916","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2104.03317","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Most massive stars experience binary interactions in their lifetimes that can alter both the surface and core structure of the stripped star with significant effects on their ultimate fate as core-collapse supernovae. However, core-collapse supernovae simulations to date have focused almost exclusively on the evolution of single stars. We present a systematic simulation study of single and binary-stripped stars with the same initial mass as candidates for core-collapse supernovae (11–21 M⊙). Generally, we find that binary-stripped stars core tend to have a smaller compactness parameter, with a more prominent, deeper silicon/oxygen interface, and explode preferentially to the corresponding single stars of the same initial mass. Such a dichotomy of behavior between these two modes of evolution would have important implications for supernovae statistics, including the final neutron star masses, explosion energies, and nucleosynthetic yields. Binary-stripped remnants are also well poised to populate the possible mass gap between the heaviest neutron stars and the lightest black holes. Our work presents an improvement along two fronts, as we self-consistently account for the pre-collapse stellar evolution and the subsequent explosion outcome. Even so, our results emphasize the need for more detailed stellar evolutionary models to capture the sensitive nature of explosion outcome."}],"issue":"1","volume":916,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-8213"],"issn":["2041-8205"]},"publication_status":"published","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_type":"original","type":"journal_article","_id":"13458","extern":"1","date_updated":"2023-08-21T11:37:48Z"},{"article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"13459","date_updated":"2023-08-21T11:35:50Z","extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/2103.13642","open_access":"1"}],"scopus_import":"1","intvolume":" 161","month":"05","abstract":[{"lang":"eng","text":"The B emission-line stars are rapid rotators that were probably spun up by mass and angular momentum accretion through mass transfer in an interacting binary. Mass transfer will strip the donor star of its envelope to create a small and hot subdwarf remnant. Here we report on Hubble Space Telescope/STIS far-ultraviolet spectroscopy of a sample of Be stars that reveals the presence of the hot sdO companion through the calculation of cross-correlation functions of the observed and model spectra. We clearly detect the spectral signature of the sdO star in 10 of the 13 stars in the sample, and the spectral signals indicate that the sdO stars are hot, relatively faint, and slowly rotating as predicted by models. A comparison of their temperatures and radii with evolutionary tracks indicates that the sdO stars occupy the relatively long-lived, He-core burning stage. Only 1 of the 10 detections was a known binary prior to this investigation, which emphasizes the difficulty of finding such Be+sdO binaries through optical spectroscopy. However, these results and others indicate that many Be stars probably host hot subdwarf companions."}],"oa_version":"Preprint","volume":161,"issue":"5","publication_status":"published","publication_identifier":{"eissn":["1538-3881"],"issn":["0004-6256"]},"language":[{"iso":"eng"}],"article_number":"248","external_id":{"arxiv":["2103.13642"]},"article_processing_charge":"No","author":[{"last_name":"Wang","full_name":"Wang, Luqian","first_name":"Luqian"},{"full_name":"Gies, Douglas R.","last_name":"Gies","first_name":"Douglas R."},{"full_name":"Peters, Geraldine J.","last_name":"Peters","first_name":"Geraldine J."},{"orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter"},{"full_name":"Chojnowski, S. Drew","last_name":"Chojnowski","first_name":"S. Drew"},{"full_name":"Lester, Kathryn V.","last_name":"Lester","first_name":"Kathryn V."},{"last_name":"Howell","full_name":"Howell, Steve B.","first_name":"Steve B."}],"title":"The detection and characterization of Be+sdO binaries from HST/STIS FUV spectroscopy","citation":{"mla":"Wang, Luqian, et al. “The Detection and Characterization of Be+sdO Binaries from HST/STIS FUV Spectroscopy.” The Astronomical Journal, vol. 161, no. 5, 248, American Astronomical Society, 2021, doi:10.3847/1538-3881/abf144.","ieee":"L. Wang et al., “The detection and characterization of Be+sdO binaries from HST/STIS FUV spectroscopy,” The Astronomical Journal, vol. 161, no. 5. American Astronomical Society, 2021.","short":"L. Wang, D.R. Gies, G.J. Peters, Y.L.L. Götberg, S.D. Chojnowski, K.V. Lester, S.B. Howell, The Astronomical Journal 161 (2021).","ama":"Wang L, Gies DR, Peters GJ, et al. The detection and characterization of Be+sdO binaries from HST/STIS FUV spectroscopy. The Astronomical Journal. 2021;161(5). doi:10.3847/1538-3881/abf144","apa":"Wang, L., Gies, D. R., Peters, G. J., Götberg, Y. L. L., Chojnowski, S. D., Lester, K. V., & Howell, S. B. (2021). The detection and characterization of Be+sdO binaries from HST/STIS FUV spectroscopy. The Astronomical Journal. American Astronomical Society. https://doi.org/10.3847/1538-3881/abf144","chicago":"Wang, Luqian, Douglas R. Gies, Geraldine J. Peters, Ylva Louise Linsdotter Götberg, S. Drew Chojnowski, Kathryn V. Lester, and Steve B. Howell. “The Detection and Characterization of Be+sdO Binaries from HST/STIS FUV Spectroscopy.” The Astronomical Journal. American Astronomical Society, 2021. https://doi.org/10.3847/1538-3881/abf144.","ista":"Wang L, Gies DR, Peters GJ, Götberg YLL, Chojnowski SD, Lester KV, Howell SB. 2021. The detection and characterization of Be+sdO binaries from HST/STIS FUV spectroscopy. The Astronomical Journal. 161(5), 248."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"American Astronomical Society","quality_controlled":"1","date_created":"2023-08-03T10:11:57Z","date_published":"2021-05-04T00:00:00Z","doi":"10.3847/1538-3881/abf144","year":"2021","publication":"The Astronomical Journal","day":"04"}]