[{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model."}],"_id":"7637","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 33","status":"public","title":"From weakly interacting particles to a regularised Dean-Kawasaki model","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"10","citation":{"ama":"Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 2020;33(2):864-891. doi:10.1088/1361-6544/ab5174","apa":"Cornalba, F., Shardlow, T., & Zimmer, J. (2020). From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab5174","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles to a regularised Dean-Kawasaki model,” Nonlinearity, vol. 33, no. 2. IOP Publishing, pp. 864–891, 2020.","ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.","short":"F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.","mla":"Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity, vol. 33, no. 2, IOP Publishing, 2020, pp. 864–91, doi:10.1088/1361-6544/ab5174.","chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab5174."},"publication":"Nonlinearity","page":"864-891","article_type":"original","date_published":"2020-01-10T00:00:00Z","year":"2020","department":[{"_id":"JuFi"}],"publisher":"IOP Publishing","publication_status":"published","author":[{"full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","id":"2CEB641C-A400-11E9-A717-D712E6697425","last_name":"Cornalba","first_name":"Federico"},{"full_name":"Shardlow, Tony","first_name":"Tony","last_name":"Shardlow"},{"full_name":"Zimmer, Johannes","first_name":"Johannes","last_name":"Zimmer"}],"volume":33,"date_created":"2020-04-05T22:00:49Z","date_updated":"2023-08-18T10:26:07Z","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"month":"01","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.06448","open_access":"1"}],"external_id":{"arxiv":["1811.06448"],"isi":["000508175400001"]},"isi":1,"quality_controlled":"1","doi":"10.1088/1361-6544/ab5174","language":[{"iso":"eng"}]},{"article_number":"2459","file_date_updated":"2020-07-14T12:48:01Z","license":"https://creativecommons.org/licenses/by/4.0/","pmid":1,"year":"2020","publisher":"MDPI","department":[{"_id":"RySh"}],"publication_status":"published","author":[{"first_name":"Alejandro","last_name":"Martín-Belmonte","full_name":"Martín-Belmonte, Alejandro"},{"full_name":"Aguado, Carolina","last_name":"Aguado","first_name":"Carolina"},{"last_name":"Alfaro-Ruíz","first_name":"Rocío","full_name":"Alfaro-Ruíz, Rocío"},{"last_name":"Moreno-Martínez","first_name":"Ana Esther","full_name":"Moreno-Martínez, Ana Esther"},{"first_name":"Luis","last_name":"De La Ossa","full_name":"De La Ossa, Luis"},{"full_name":"Martínez-Hernández, José","last_name":"Martínez-Hernández","first_name":"José"},{"last_name":"Buisson","first_name":"Alain","full_name":"Buisson, Alain"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"}],"volume":21,"date_updated":"2023-08-21T06:13:19Z","date_created":"2020-04-19T22:00:55Z","publication_identifier":{"eissn":["14220067"]},"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000535574200201"],"pmid":["32252271"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.3390/ijms21072459","language":[{"iso":"eng"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7664","intvolume":" 21","ddc":["570"],"title":"Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease","status":"public","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2941197,"content_type":"application/pdf","file_name":"2020_JournMolecSciences_Martin_Belmonte.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T11:43:18Z","checksum":"b9d2f1657d8c4a74b01a62b474d009b0","file_id":"7669","relation":"main_file"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"02","citation":{"ieee":"A. Martín-Belmonte et al., “Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” International journal of molecular sciences, vol. 21, no. 7. MDPI, 2020.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21072459","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459.","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s disease. International journal of molecular sciences. 2020;21(7). doi:10.3390/ijms21072459","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459.","short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján, International Journal of Molecular Sciences 21 (2020).","mla":"Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International Journal of Molecular Sciences, vol. 21, no. 7, 2459, MDPI, 2020, doi:10.3390/ijms21072459."},"publication":"International journal of molecular sciences","article_type":"original","date_published":"2020-04-02T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"19","scopus_import":"1","date_published":"2020-03-19T00:00:00Z","citation":{"mla":"Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience, vol. 14, 63, Frontiers Media, 2020, doi:10.3389/fncel.2020.00063.","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","chicago":"Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular Neuroscience. Frontiers Media, 2020. https://doi.org/10.3389/fncel.2020.00063.","ama":"Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 2020;14. doi:10.3389/fncel.2020.00063","ista":"Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63.","apa":"Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., & Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2020.00063","ieee":"K. Eguchi et al., “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” Frontiers in Cellular Neuroscience, vol. 14. Frontiers Media, 2020."},"publication":"Frontiers in Cellular Neuroscience","article_type":"original","abstract":[{"lang":"eng","text":"Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions."}],"type":"journal_article","file":[{"file_id":"7668","relation":"main_file","date_created":"2020-04-20T10:59:49Z","date_updated":"2020-07-14T12:48:01Z","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9227283}],"oa_version":"Published Version","_id":"7665","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","status":"public","title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","ddc":["570"],"publication_identifier":{"issn":["16625102"]},"month":"03","doi":"10.3389/fncel.2020.00063","language":[{"iso":"eng"}],"external_id":{"isi":["000525582200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482","_id":"2659CC84-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:48:01Z","article_number":"63","author":[{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"},{"id":"3C054040-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"volume":14,"date_updated":"2023-08-21T06:12:48Z","date_created":"2020-04-19T22:00:55Z","year":"2020","publisher":"Frontiers Media","department":[{"_id":"JoDa"},{"_id":"RySh"}],"publication_status":"published"},{"day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-04-08T00:00:00Z","article_type":"original","page":"2647-2653","publication":"Nano Letters","citation":{"chicago":"Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c00205.","mla":"Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” Nano Letters, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:10.1021/acs.nanolett.0c00205.","short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","ista":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653.","apa":"Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., & Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c00205","ieee":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” Nano Letters, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020.","ama":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 2020;20(4):2647-2653. doi:10.1021/acs.nanolett.0c00205"},"abstract":[{"lang":"eng","text":"Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization."}],"issue":"4","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_NanoLetters_Felhofer.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7108014,"creator":"dernst","relation":"main_file","file_id":"7667","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-20T10:43:36Z","checksum":"fe46146a9c4c620592a1932a8599069e"}],"ddc":["530"],"status":"public","title":"Wood deformation leads to rearrangement of molecules at the nanoscale","intvolume":" 20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7663","month":"04","publication_identifier":{"eissn":["15306992"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.0c00205","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32196350"],"isi":["000526413400055"]},"file_date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-19T22:00:54Z","date_updated":"2023-08-21T06:12:09Z","volume":20,"author":[{"full_name":"Felhofer, Martin","first_name":"Martin","last_name":"Felhofer"},{"first_name":"Peter","last_name":"Bock","full_name":"Bock, Peter"},{"first_name":"Adya","last_name":"Singh","full_name":"Singh, Adya"},{"first_name":"Batirtze","last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze"},{"first_name":"Ronald","last_name":"Zirbs","full_name":"Zirbs, Ronald"},{"full_name":"Gierlinger, Notburga","last_name":"Gierlinger","first_name":"Notburga"}],"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"American Chemical Society","year":"2020","pmid":1},{"file":[{"file_id":"8786","relation":"main_file","success":1,"checksum":"f8cc96e497f00c38340b5dafe0cb91d7","date_updated":"2020-11-20T13:22:21Z","date_created":"2020-11-20T13:22:21Z","access_level":"open_access","file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf","creator":"dernst","file_size":701673,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 64","title":"Tri-partitions and bases of an ordered complex","ddc":["510"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7666","abstract":[{"lang":"eng","text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups."}],"type":"journal_article","date_published":"2020-03-20T00:00:00Z","page":"759-775","article_type":"original","citation":{"ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","apa":"Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00188-x","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775, 2020.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x.","short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775.","chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00188-x."},"publication":"Discrete and Computational Geometry","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"20","scopus_import":"1","volume":64,"date_created":"2020-04-19T22:00:56Z","date_updated":"2023-08-21T06:13:48Z","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Ölsböck, Katharina","first_name":"Katharina","last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297"}],"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","ec_funded":1,"file_date_updated":"2020-11-20T13:22:21Z","language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00188-x","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000520918800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"03"},{"author":[{"full_name":"Minets, Sasha","orcid":"0000-0003-3883-1806","id":"3E7C5304-F248-11E8-B48F-1D18A9856A87","last_name":"Minets","first_name":"Sasha"}],"date_created":"2020-04-26T22:00:44Z","date_updated":"2023-08-21T06:14:58Z","volume":26,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:48:02Z","article_number":"30","doi":"10.1007/s00029-020-00553-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1801.01429"],"isi":["000526036400001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"month":"04","publication_identifier":{"issn":["10221824"],"eissn":["14209020"]},"oa_version":"Published Version","file":[{"file_id":"7690","relation":"main_file","date_updated":"2020-07-14T12:48:02Z","date_created":"2020-04-28T10:57:58Z","checksum":"2368c4662629b4759295eb365323b2ad","file_name":"2020_SelectaMathematica_Minets.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":792469}],"_id":"7683","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["510"],"title":"Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces","intvolume":" 26","abstract":[{"text":"For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2020-04-15T00:00:00Z","publication":"Selecta Mathematica, New Series","citation":{"mla":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series, vol. 26, no. 2, 30, Springer Nature, 2020, doi:10.1007/s00029-020-00553-x.","short":"S. Minets, Selecta Mathematica, New Series 26 (2020).","chicago":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” Selecta Mathematica, New Series. Springer Nature, 2020. https://doi.org/10.1007/s00029-020-00553-x.","ama":"Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 2020;26(2). doi:10.1007/s00029-020-00553-x","ista":"Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30.","apa":"Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. Springer Nature. https://doi.org/10.1007/s00029-020-00553-x","ieee":"S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” Selecta Mathematica, New Series, vol. 26, no. 2. Springer Nature, 2020."},"article_type":"original","day":"15","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"file_date_updated":"2020-10-01T13:20:45Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_number":"137175","author":[{"last_name":"Samojlov","first_name":"Aleksej","full_name":"Samojlov, Aleksej"},{"first_name":"David","last_name":"Schuster","full_name":"Schuster, David"},{"full_name":"Kahr, Jürgen","first_name":"Jürgen","last_name":"Kahr"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"}],"date_updated":"2023-08-21T06:14:21Z","date_created":"2020-04-20T19:29:31Z","volume":362,"year":"2020","acknowledgement":"S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"StFr"}],"month":"12","doi":"10.1016/j.electacta.2020.137175","language":[{"iso":"eng"}],"oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000582869700060"]},"quality_controlled":"1","isi":1,"abstract":[{"text":"Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.","lang":"eng"}],"issue":"12","type":"journal_article","file":[{"file_id":"8593","relation":"main_file","date_updated":"2020-10-01T13:20:45Z","date_created":"2020-10-01T13:20:45Z","success":1,"checksum":"1ab1aa2024d431e2a089ea336bc08298","file_name":"2020_ElectrochimicaActa_Samojlov.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1404030}],"oa_version":"Published Version","_id":"7672","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","status":"public","ddc":["540"],"intvolume":" 362","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-12-01T00:00:00Z","publication":"Electrochimica Acta","citation":{"mla":"Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta, vol. 362, no. 12, 137175, Elsevier, 2020, doi:10.1016/j.electacta.2020.137175.","short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020).","chicago":"Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica Acta. Elsevier, 2020. https://doi.org/10.1016/j.electacta.2020.137175.","ama":"Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 2020;362(12). doi:10.1016/j.electacta.2020.137175","ista":"Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175.","ieee":"A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” Electrochimica Acta, vol. 362, no. 12. Elsevier, 2020.","apa":"Samojlov, A., Schuster, D., Kahr, J., & Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2020.137175"},"article_type":"original"},{"ec_funded":1,"author":[{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Schönenberger","full_name":"Schönenberger, Philipp"},{"full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/librarian-of-memory/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2020-04-26T22:00:45Z","date_updated":"2023-08-21T06:15:31Z","volume":106,"year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}],"month":"04","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"doi":"10.1016/j.neuron.2020.01.021","language":[{"iso":"eng"}],"external_id":{"isi":["000528268200013"],"pmid":["32070475"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2020.01.021"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"}],"issue":"2","type":"journal_article","oa_version":"Published Version","_id":"7684","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Assembly-specific disruption of hippocampal replay leads to selective memory deficit","intvolume":" 106","day":"22","article_processing_charge":"No","scopus_import":"1","date_published":"2020-04-22T00:00:00Z","publication":"Neuron","citation":{"chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.01.021.","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, Neuron 106 (2020) 291–300.e6.","mla":"Gridchyn, Igor, et al. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” Neuron, vol. 106, no. 2, Elsevier, 2020, p. 291–300.e6, doi:10.1016/j.neuron.2020.01.021.","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Assembly-specific disruption of hippocampal replay leads to selective memory deficit,” Neuron, vol. 106, no. 2. Elsevier, p. 291–300.e6, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.01.021","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 106(2), 291–300.e6.","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 2020;106(2):291-300.e6. doi:10.1016/j.neuron.2020.01.021"},"article_type":"original","page":"291-300.e6"},{"abstract":[{"lang":"eng","text":"Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids."}],"issue":"8","type":"journal_article","file":[{"file_id":"7798","relation":"main_file","checksum":"a9b152381307cf45fe266a8dc5640388","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-04T12:25:19Z","access_level":"open_access","file_name":"2020_BBA_Adjobo_Hermans.pdf","creator":"dernst","content_type":"application/pdf","file_size":3826792}],"oa_version":"Published Version","ddc":["570"],"title":"NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2","status":"public","intvolume":" 1861","_id":"7788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-08-01T00:00:00Z","article_type":"original","publication":"Biochimica et Biophysica Acta - Bioenergetics","citation":{"ama":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, et al. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 2020;1861(8). doi:10.1016/j.bbabio.2020.148213","ista":"Adjobo-Hermans MJW, De Haas R, Willems PHGM, Wojtala A, Van Emst-De Vries SE, Wagenaars JA, Van Den Brand M, Rodenburg RJ, Smeitink JAM, Nijtmans LG, Sazanov LA, Wieckowski MR, Koopman WJH. 2020. NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. 1861(8), 148213.","apa":"Adjobo-Hermans, M. J. W., De Haas, R., Willems, P. H. G. M., Wojtala, A., Van Emst-De Vries, S. E., Wagenaars, J. A., … Koopman, W. J. H. (2020). NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2020.148213","ieee":"M. J. W. Adjobo-Hermans et al., “NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8. Elsevier, 2020.","mla":"Adjobo-Hermans, Merel J. W., et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1861, no. 8, 148213, Elsevier, 2020, doi:10.1016/j.bbabio.2020.148213.","short":"M.J.W. Adjobo-Hermans, R. De Haas, P.H.G.M. Willems, A. Wojtala, S.E. Van Emst-De Vries, J.A. Wagenaars, M. Van Den Brand, R.J. Rodenburg, J.A.M. Smeitink, L.G. Nijtmans, L.A. Sazanov, M.R. Wieckowski, W.J.H. Koopman, Biochimica et Biophysica Acta - Bioenergetics 1861 (2020).","chicago":"Adjobo-Hermans, Merel J.W., Ria De Haas, Peter H.G.M. Willems, Aleksandra Wojtala, Sjenet E. Van Emst-De Vries, Jori A. Wagenaars, Mariel Van Den Brand, et al. “NDUFS4 Deletion Triggers Loss of NDUFA12 in Ndufs4−/− Mice and Leigh Syndrome Patients: A Stabilizing Role for NDUFAF2.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2020. https://doi.org/10.1016/j.bbabio.2020.148213."},"file_date_updated":"2020-07-14T12:48:03Z","article_number":"148213","date_updated":"2023-08-21T06:19:18Z","date_created":"2020-05-03T22:00:47Z","volume":1861,"author":[{"last_name":"Adjobo-Hermans","first_name":"Merel J.W.","full_name":"Adjobo-Hermans, Merel J.W."},{"full_name":"De Haas, Ria","last_name":"De Haas","first_name":"Ria"},{"first_name":"Peter H.G.M.","last_name":"Willems","full_name":"Willems, Peter H.G.M."},{"last_name":"Wojtala","first_name":"Aleksandra","full_name":"Wojtala, Aleksandra"},{"first_name":"Sjenet E.","last_name":"Van Emst-De Vries","full_name":"Van Emst-De Vries, Sjenet E."},{"first_name":"Jori A.","last_name":"Wagenaars","full_name":"Wagenaars, Jori A."},{"last_name":"Van Den Brand","first_name":"Mariel","full_name":"Van Den Brand, Mariel"},{"full_name":"Rodenburg, Richard J.","last_name":"Rodenburg","first_name":"Richard J."},{"last_name":"Smeitink","first_name":"Jan A.M.","full_name":"Smeitink, Jan A.M."},{"full_name":"Nijtmans, Leo G.","last_name":"Nijtmans","first_name":"Leo G."},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"},{"full_name":"Wieckowski, Mariusz R.","last_name":"Wieckowski","first_name":"Mariusz R."},{"full_name":"Koopman, Werner J.H.","first_name":"Werner J.H.","last_name":"Koopman"}],"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Elsevier","year":"2020","pmid":1,"month":"08","publication_identifier":{"eissn":["18792650"],"issn":["00052728"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.bbabio.2020.148213","isi":1,"quality_controlled":"1","external_id":{"isi":["000540842000012"],"pmid":["32335026"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"citation":{"short":"S. Dekoninck, E.B. Hannezo, A. Sifrim, Y.A. Miroshnikova, M. Aragona, M. Malfait, S. Gargouri, C. De Neunheuser, C. Dubois, T. Voet, S.A. Wickström, B.D. Simons, C. Blanpain, Cell 181 (2020) 604–620.e22.","mla":"Dekoninck, Sophie, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell, vol. 181, no. 3, Elsevier, 2020, p. 604–620.e22, doi:10.1016/j.cell.2020.03.015.","chicago":"Dekoninck, Sophie, Edouard B Hannezo, Alejandro Sifrim, Yekaterina A. Miroshnikova, Mariaceleste Aragona, Milan Malfait, Souhir Gargouri, et al. “Defining the Design Principles of Skin Epidermis Postnatal Growth.” Cell. Elsevier, 2020. https://doi.org/10.1016/j.cell.2020.03.015.","ama":"Dekoninck S, Hannezo EB, Sifrim A, et al. Defining the design principles of skin epidermis postnatal growth. Cell. 2020;181(3):604-620.e22. doi:10.1016/j.cell.2020.03.015","ieee":"S. Dekoninck et al., “Defining the design principles of skin epidermis postnatal growth,” Cell, vol. 181, no. 3. Elsevier, p. 604–620.e22, 2020.","apa":"Dekoninck, S., Hannezo, E. B., Sifrim, A., Miroshnikova, Y. A., Aragona, M., Malfait, M., … Blanpain, C. (2020). Defining the design principles of skin epidermis postnatal growth. Cell. Elsevier. https://doi.org/10.1016/j.cell.2020.03.015","ista":"Dekoninck S, Hannezo EB, Sifrim A, Miroshnikova YA, Aragona M, Malfait M, Gargouri S, De Neunheuser C, Dubois C, Voet T, Wickström SA, Simons BD, Blanpain C. 2020. Defining the design principles of skin epidermis postnatal growth. Cell. 181(3), 604–620.e22."},"publication":"Cell","page":"604-620.e22","article_type":"original","date_published":"2020-04-30T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7789","intvolume":" 181","status":"public","ddc":["570"],"title":"Defining the design principles of skin epidermis postnatal growth","file":[{"access_level":"open_access","file_name":"2020_Cell_Dekoninck.pdf","file_size":17992888,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7795","checksum":"e2114902f4e9d75a752e9efb5ae06011","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-04T10:20:55Z"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues.","lang":"eng"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000530708400016"],"pmid":["32259486"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.cell.2020.03.015","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"month":"04","pmid":1,"year":"2020","department":[{"_id":"EdHa"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Sophie","last_name":"Dekoninck","full_name":"Dekoninck, Sophie"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"last_name":"Sifrim","first_name":"Alejandro","full_name":"Sifrim, Alejandro"},{"full_name":"Miroshnikova, Yekaterina A.","first_name":"Yekaterina A.","last_name":"Miroshnikova"},{"first_name":"Mariaceleste","last_name":"Aragona","full_name":"Aragona, Mariaceleste"},{"last_name":"Malfait","first_name":"Milan","full_name":"Malfait, Milan"},{"last_name":"Gargouri","first_name":"Souhir","full_name":"Gargouri, Souhir"},{"full_name":"De Neunheuser, Charlotte","first_name":"Charlotte","last_name":"De Neunheuser"},{"last_name":"Dubois","first_name":"Christine","full_name":"Dubois, Christine"},{"full_name":"Voet, Thierry","first_name":"Thierry","last_name":"Voet"},{"full_name":"Wickström, Sara A.","last_name":"Wickström","first_name":"Sara A."},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"full_name":"Blanpain, Cédric","first_name":"Cédric","last_name":"Blanpain"}],"volume":181,"date_updated":"2023-08-21T06:17:43Z","date_created":"2020-05-03T22:00:48Z","file_date_updated":"2020-07-14T12:48:03Z"},{"article_number":"e51787","file_date_updated":"2020-07-14T12:48:03Z","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2020","volume":9,"date_created":"2020-05-04T08:50:47Z","date_updated":"2023-08-21T06:17:12Z","author":[{"full_name":"Kuhn, André","first_name":"André","last_name":"Kuhn"},{"full_name":"Ramans Harborough, Sigurd","first_name":"Sigurd","last_name":"Ramans Harborough"},{"full_name":"McLaughlin, Heather M","first_name":"Heather M","last_name":"McLaughlin"},{"last_name":"Natarajan","first_name":"Bhavani","full_name":"Natarajan, Bhavani"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Kepinski","first_name":"Stefan","full_name":"Kepinski, Stefan"},{"full_name":"Østergaard, Lars","first_name":"Lars","last_name":"Østergaard"}],"publication_identifier":{"issn":["2050-084X"]},"month":"04","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32267233"],"isi":["000527752200001"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.51787","type":"journal_article","abstract":[{"text":"Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner.","lang":"eng"}],"intvolume":" 9","status":"public","ddc":["580"],"title":"Direct ETTIN-auxin interaction controls chromatin states in gynoecium development","_id":"7793","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":2893082,"creator":"dernst","access_level":"open_access","file_name":"2020_eLife_Kuhn.pdf","checksum":"15d740de1a741fdcc6ec128c48eed017","date_created":"2020-05-04T09:06:43Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7794"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08","article_type":"original","citation":{"short":"A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020).","mla":"Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife, vol. 9, e51787, eLife Sciences Publications, 2020, doi:10.7554/elife.51787.","chicago":"Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.51787.","ama":"Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 2020;9. doi:10.7554/elife.51787","apa":"Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.51787","ieee":"A. Kuhn et al., “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” eLife, vol. 9. eLife Sciences Publications, 2020.","ista":"Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787."},"publication":"eLife","date_published":"2020-04-08T00:00:00Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1910.03372"],"isi":["000527342000001"]},"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1017/fms.2020.17","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20505094"]},"month":"03","year":"2020","department":[{"_id":"RoSe"}],"publisher":"Cambridge University Press","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7524"}]},"author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas"},{"full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","last_name":"Mayer","first_name":"Simon"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"volume":8,"date_updated":"2023-08-21T06:18:49Z","date_created":"2020-05-03T22:00:48Z","article_number":"e20","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","citation":{"ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 2020;8. doi:10.1017/fms.2020.17","ista":"Deuchert A, Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. 8, e20.","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” Forum of Mathematics, Sigma, vol. 8. Cambridge University Press, 2020.","apa":"Deuchert, A., Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2020.17","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma, vol. 8, e20, Cambridge University Press, 2020, doi:10.1017/fms.2020.17.","short":"A. Deuchert, S. Mayer, R. Seiringer, Forum of Mathematics, Sigma 8 (2020).","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” Forum of Mathematics, Sigma. Cambridge University Press, 2020. https://doi.org/10.1017/fms.2020.17."},"publication":"Forum of Mathematics, Sigma","article_type":"original","date_published":"2020-03-14T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","_id":"7790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 8","title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","status":"public","ddc":["510"],"oa_version":"Published Version","file":[{"checksum":"8a64da99d107686997876d7cad8cfe1e","date_created":"2020-05-04T12:02:41Z","date_updated":"2020-07-14T12:48:03Z","relation":"main_file","file_id":"7797","content_type":"application/pdf","file_size":692530,"creator":"dernst","access_level":"open_access","file_name":"2020_ForumMath_Deuchert.pdf"}],"type":"journal_article","abstract":[{"text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"2cba327c9e9416d75cb96be54b0fb441","date_created":"2020-10-06T07:47:53Z","date_updated":"2020-10-06T07:47:53Z","file_id":"8614","relation":"main_file","creator":"dernst","file_size":4743576,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureComm_Hurny.pdf"}],"title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","status":"public","ddc":["570"],"intvolume":" 11","_id":"7805","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-05-01T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 2020;11. doi:10.1038/s41467-020-15895-5","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15895-5","ieee":"A. Hurny et al., “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.","short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications, vol. 11, 2170, Springer Nature, 2020, doi:10.1038/s41467-020-15895-5.","chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15895-5."},"file_date_updated":"2020-10-06T07:47:53Z","ec_funded":1,"article_number":"2170","date_created":"2020-05-10T22:00:48Z","date_updated":"2023-08-21T06:21:56Z","volume":11,"author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","first_name":"Andrej"},{"last_name":"Cuesta","first_name":"Candela","orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","full_name":"Cuesta, Candela"},{"full_name":"Cavallari, Nicola","first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ötvös","first_name":"Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina"},{"first_name":"Jerome","last_name":"Duclercq","full_name":"Duclercq, Jerome"},{"last_name":"Dokládal","first_name":"Ladislav","full_name":"Dokládal, Ladislav"},{"first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","first_name":"Thomas","last_name":"Rauter","full_name":"Rauter, Thomas"},{"full_name":"Stenzel, Irene","last_name":"Stenzel","first_name":"Irene"},{"last_name":"Persiau","first_name":"Geert","full_name":"Persiau, Geert"},{"full_name":"Benade, Freia","first_name":"Freia","last_name":"Benade"},{"full_name":"Bhalearo, Rishikesh","last_name":"Bhalearo","first_name":"Rishikesh"},{"full_name":"Sýkorová, Eva","first_name":"Eva","last_name":"Sýkorová"},{"first_name":"András","last_name":"Gorzsás","full_name":"Gorzsás, András"},{"first_name":"Julien","last_name":"Sechet","full_name":"Sechet, Julien"},{"full_name":"Mouille, Gregory","first_name":"Gregory","last_name":"Mouille"},{"first_name":"Ingo","last_name":"Heilmann","full_name":"Heilmann, Ingo"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Ludwig-Müller, Jutta","last_name":"Ludwig-Müller","first_name":"Jutta"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer Nature","year":"2020","acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","pmid":1,"month":"05","publication_identifier":{"eissn":["20411723"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-15895-5","quality_controlled":"1","isi":1,"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"isi":["000531425900012"],"pmid":["32358503"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"year":"2020","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"MDPI","author":[{"last_name":"Armstrong","first_name":"Jeremy R.","full_name":"Armstrong, Jeremy R."},{"full_name":"Jensen, Aksel S.","last_name":"Jensen","first_name":"Aksel S."},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"},{"first_name":"Nikolaj T.","last_name":"Zinner","full_name":"Zinner, Nikolaj T."}],"date_created":"2020-05-24T22:01:00Z","date_updated":"2023-08-21T06:23:36Z","volume":8,"article_number":"484","file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000531824100024"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.3390/math8040484","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["22277390"]},"_id":"7882","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Clusters in separated tubes of tilted dipoles","ddc":["510"],"status":"public","intvolume":" 8","oa_version":"Published Version","file":[{"checksum":"a05a7df724522203d079673a0d4de4bc","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-25T14:42:22Z","file_id":"7887","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":990540,"access_level":"open_access","file_name":"2020_Mathematics_Armstrong.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes."}],"issue":"4","publication":"Mathematics","citation":{"chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8040484.","mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” Mathematics, vol. 8, no. 4, 484, MDPI, 2020, doi:10.3390/math8040484.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” Mathematics, vol. 8, no. 4. MDPI, 2020.","apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., & Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. Mathematics. MDPI. https://doi.org/10.3390/math8040484","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. Mathematics. 2020;8(4). doi:10.3390/math8040484"},"article_type":"original","date_published":"2020-04-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"article_number":"2099","file_date_updated":"2020-07-14T12:48:03Z","year":"2020","department":[{"_id":"MaDe"}],"publisher":"Springer Nature","publication_status":"published","author":[{"last_name":"Flynn","first_name":"Sean M.","full_name":"Flynn, Sean M."},{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat","last_name":"Artan","full_name":"Artan, Murat"},{"last_name":"Barratt","first_name":"Stephen","full_name":"Barratt, Stephen"},{"last_name":"Crisp","first_name":"Alastair","full_name":"Crisp, Alastair"},{"first_name":"Geoffrey M.","last_name":"Nelson","full_name":"Nelson, Geoffrey M."},{"first_name":"Sew Yeu","last_name":"Peak-Chew","full_name":"Peak-Chew, Sew Yeu"},{"full_name":"Begum, Farida","last_name":"Begum","first_name":"Farida"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario"}],"volume":11,"date_updated":"2023-08-21T06:21:14Z","date_created":"2020-05-10T22:00:47Z","publication_identifier":{"eissn":["20411723"]},"month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000531855500029"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-020-15872-y","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7804","intvolume":" 11","title":"MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity","status":"public","ddc":["570"],"file":[{"checksum":"dce367abf2c1a1d15f58fe6f7de82893","date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-11T10:36:33Z","relation":"main_file","file_id":"7817","content_type":"application/pdf","file_size":4609120,"creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Flynn.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29","citation":{"short":"S.M. Flynn, C. Chen, M. Artan, S. Barratt, A. Crisp, G.M. Nelson, S.Y. Peak-Chew, F. Begum, M. Skehel, M. de Bono, Nature Communications 11 (2020).","mla":"Flynn, Sean M., et al. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications, vol. 11, 2099, Springer Nature, 2020, doi:10.1038/s41467-020-15872-y.","chicago":"Flynn, Sean M., Changchun Chen, Murat Artan, Stephen Barratt, Alastair Crisp, Geoffrey M. Nelson, Sew Yeu Peak-Chew, Farida Begum, Mark Skehel, and Mario de Bono. “MALT-1 Mediates IL-17 Neural Signaling to Regulate C. Elegans Behavior, Immunity and Longevity.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-15872-y.","ama":"Flynn SM, Chen C, Artan M, et al. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 2020;11. doi:10.1038/s41467-020-15872-y","ieee":"S. M. Flynn et al., “MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Flynn, S. M., Chen, C., Artan, M., Barratt, S., Crisp, A., Nelson, G. M., … de Bono, M. (2020). MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-15872-y","ista":"Flynn SM, Chen C, Artan M, Barratt S, Crisp A, Nelson GM, Peak-Chew SY, Begum F, Skehel M, de Bono M. 2020. MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity. Nature Communications. 11, 2099."},"publication":"Nature Communications","article_type":"original","date_published":"2020-04-29T00:00:00Z"},{"abstract":[{"text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"8801","relation":"main_file","success":1,"checksum":"cb0b9c77842ae1214caade7b77e4d82d","date_created":"2020-11-24T13:25:13Z","date_updated":"2020-11-24T13:25:13Z","access_level":"open_access","file_name":"2020_JCellBiol_Kopf.pdf","creator":"dernst","file_size":7536712,"content_type":"application/pdf"}],"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","status":"public","ddc":["570"],"intvolume":" 219","_id":"7875","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-06-01T00:00:00Z","article_type":"original","publication":"The Journal of Cell Biology","citation":{"short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020).","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:10.1083/jcb.201907154.","chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.201907154.","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 2020;219(6). doi:10.1083/jcb.201907154","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201907154","ieee":"A. Kopf et al., “Microtubules control cellular shape and coherence in amoeboid migrating cells,” The Journal of Cell Biology, vol. 219, no. 6. Rockefeller University Press, 2020.","ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154."},"file_date_updated":"2020-11-24T13:25:13Z","ec_funded":1,"article_number":"e201907154","date_updated":"2023-08-21T06:28:17Z","date_created":"2020-05-24T22:00:56Z","volume":219,"author":[{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja","full_name":"Kopf, Aglaja"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz","full_name":"Renkawitz, Jörg"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Girkontaite, Irute","first_name":"Irute","last_name":"Girkontaite"},{"full_name":"Tedford, Kerry","first_name":"Kerry","last_name":"Tedford"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack"},{"full_name":"Thorn-Seshold, Oliver","last_name":"Thorn-Seshold","first_name":"Oliver"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425"},{"last_name":"Häcker","first_name":"Hans","full_name":"Häcker, Hans"},{"last_name":"Fischer","first_name":"Klaus Dieter","full_name":"Fischer, Klaus Dieter"},{"id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6165-5738","first_name":"Eva","last_name":"Kiermaier","full_name":"Kiermaier, Eva"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"publisher":"Rockefeller University Press","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","year":"2020","pmid":1,"month":"06","publication_identifier":{"eissn":["1540-8140"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1083/jcb.201907154","quality_controlled":"1","isi":1,"project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29911","_id":"26018E70-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanical adaptation of lamellipodial actin"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W 1250-B20","_id":"252C3B08-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000538141100020"],"pmid":["32379884"]}},{"month":"04","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.55190","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"},{"grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"article_number":"e55190","author":[{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra","last_name":"Schauer"},{"first_name":"Diana C","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"id":"12891","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-05-25T15:01:40Z","date_updated":"2023-08-21T06:25:49Z","volume":9,"year":"2020","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"},{"_id":"Bio"}],"day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-04-06T00:00:00Z","publication":"eLife","citation":{"ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., & Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.55190","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” eLife, vol. 9. eLife Sciences Publications, 2020.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 2020;9. doi:10.7554/elife.55190","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/elife.55190.","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” ELife, vol. 9, e55190, eLife Sciences Publications, 2020, doi:10.7554/elife.55190.","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020)."},"article_type":"original","abstract":[{"text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"f6aad884cf706846ae9357fcd728f8b5","date_created":"2020-05-25T15:15:43Z","date_updated":"2020-07-14T12:48:04Z","relation":"main_file","file_id":"7890","file_size":7744848,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_eLife_Schauer.pdf"}],"_id":"7888","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","intvolume":" 9"},{"month":"05","publication_identifier":{"eissn":["22111247"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2020.107647","isi":1,"quality_controlled":"1","tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000535655200005"]},"file_date_updated":"2020-07-14T12:48:04Z","article_number":"107647","date_created":"2020-05-24T22:00:57Z","date_updated":"2023-08-21T06:27:47Z","volume":31,"author":[{"full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","last_name":"Parenti","first_name":"Ilaria"},{"full_name":"Diab, Farah","last_name":"Diab","first_name":"Farah"},{"full_name":"Gil, Sara Ruiz","first_name":"Sara Ruiz","last_name":"Gil"},{"first_name":"Eskeatnaf","last_name":"Mulugeta","full_name":"Mulugeta, Eskeatnaf"},{"full_name":"Casa, Valentina","first_name":"Valentina","last_name":"Casa"},{"full_name":"Berutti, Riccardo","last_name":"Berutti","first_name":"Riccardo"},{"full_name":"Brouwer, Rutger W.W.","last_name":"Brouwer","first_name":"Rutger W.W."},{"full_name":"Dupé, Valerie","last_name":"Dupé","first_name":"Valerie"},{"full_name":"Eckhold, Juliane","first_name":"Juliane","last_name":"Eckhold"},{"full_name":"Graf, Elisabeth","first_name":"Elisabeth","last_name":"Graf"},{"full_name":"Puisac, Beatriz","first_name":"Beatriz","last_name":"Puisac"},{"full_name":"Ramos, Feliciano","first_name":"Feliciano","last_name":"Ramos"},{"last_name":"Schwarzmayr","first_name":"Thomas","full_name":"Schwarzmayr, Thomas"},{"last_name":"Gines","first_name":"Macarena Moronta","full_name":"Gines, Macarena Moronta"},{"full_name":"Van Staveren, Thomas","first_name":"Thomas","last_name":"Van Staveren"},{"full_name":"Van Ijcken, Wilfred F.J.","first_name":"Wilfred F.J.","last_name":"Van Ijcken"},{"last_name":"Strom","first_name":"Tim M.","full_name":"Strom, Tim M."},{"full_name":"Pié, Juan","first_name":"Juan","last_name":"Pié"},{"last_name":"Watrin","first_name":"Erwan","full_name":"Watrin, Erwan"},{"first_name":"Frank J.","last_name":"Kaiser","full_name":"Kaiser, Frank J."},{"full_name":"Wendt, Kerstin S.","last_name":"Wendt","first_name":"Kerstin S."}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaNo"}],"year":"2020","day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-05-19T00:00:00Z","article_type":"original","publication":"Cell Reports","citation":{"ista":"Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.","apa":"Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.107647","ieee":"I. Parenti et al., “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” Cell Reports, vol. 31, no. 7. Elsevier, 2020.","ama":"Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 2020;31(7). doi:10.1016/j.celrep.2020.107647","chicago":"Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.107647.","mla":"Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” Cell Reports, vol. 31, no. 7, 107647, Elsevier, 2020, doi:10.1016/j.celrep.2020.107647.","short":"I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020)."},"abstract":[{"lang":"eng","text":"The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions."}],"issue":"7","type":"journal_article","file":[{"file_id":"7892","relation":"main_file","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T11:05:01Z","checksum":"64d8f7467731ee5c166b10b939b8310b","file_name":"2020_CellReports_Parenti.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4695682}],"oa_version":"Published Version","ddc":["570"],"title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","status":"public","intvolume":" 31","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7877"},{"citation":{"mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife, vol. 9, e56839, eLife Sciences Publications, 2020, doi:10.7554/eLife.56839.","short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","chicago":"Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56839.","ama":"Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 2020;9. doi:10.7554/eLife.56839","ista":"Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.","apa":"Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56839","ieee":"J. Bao et al., “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” eLife, vol. 9. eLife Sciences Publications, 2020."},"publication":"eLife","article_type":"original","date_published":"2020-05-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"13","_id":"7878","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","ddc":["570"],"title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","oa_version":"Published Version","file":[{"file_name":"2020_eLife_Bao.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4832050,"creator":"dernst","relation":"main_file","file_id":"7891","date_created":"2020-05-26T09:34:54Z","date_updated":"2020-07-14T12:48:04Z","checksum":"8ea99bb6660cc407dbdb00c173b01683"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.56839","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050084X"]},"month":"05","pmid":1,"year":"2020","publisher":"eLife Sciences Publications","department":[{"_id":"RySh"}],"publication_status":"published","author":[{"first_name":"Jin","last_name":"Bao","full_name":"Bao, Jin"},{"full_name":"Graupner, Michael","first_name":"Michael","last_name":"Graupner"},{"full_name":"Astorga, Guadalupe","first_name":"Guadalupe","last_name":"Astorga"},{"full_name":"Collin, Thibault","last_name":"Collin","first_name":"Thibault"},{"first_name":"Abdelali","last_name":"Jalil","full_name":"Jalil, Abdelali"},{"first_name":"Dwi Wahyu","last_name":"Indriati","full_name":"Indriati, Dwi Wahyu"},{"full_name":"Bradley, Jonathan","first_name":"Jonathan","last_name":"Bradley"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"last_name":"Llano","first_name":"Isabel","full_name":"Llano, Isabel"}],"volume":9,"date_updated":"2023-08-21T06:26:50Z","date_created":"2020-05-24T22:00:58Z","article_number":"e56839","file_date_updated":"2020-07-14T12:48:04Z"},{"month":"04","publication_identifier":{"issn":["00219258"],"eissn":["1083351X"]},"oa":1,"external_id":{"isi":["000530288000006"],"pmid":["32132171"]},"main_file_link":[{"open_access":"1","url":"https://escholarship.umassmed.edu/oapubs/4187"}],"isi":1,"quality_controlled":"1","doi":"10.1074/jbc.RA120.012628","language":[{"iso":"eng"}],"year":"2020","pmid":1,"publication_status":"published","publisher":"ASBMB Publications","department":[{"_id":"SaSi"}],"author":[{"full_name":"Fagan, Rita R.","first_name":"Rita R.","last_name":"Fagan"},{"last_name":"Kearney","first_name":"Patrick J.","full_name":"Kearney, Patrick J."},{"last_name":"Sweeney","first_name":"Carolyn G.","full_name":"Sweeney, Carolyn G."},{"last_name":"Luethi","first_name":"Dino","full_name":"Luethi, Dino"},{"first_name":"Florianne E","last_name":"Schoot Uiterkamp","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E"},{"full_name":"Schicker, Klaus","last_name":"Schicker","first_name":"Klaus"},{"first_name":"Brian S.","last_name":"Alejandro","full_name":"Alejandro, Brian S."},{"full_name":"O'Connor, Lauren C.","first_name":"Lauren C.","last_name":"O'Connor"},{"full_name":"Sitte, Harald H.","first_name":"Harald H.","last_name":"Sitte"},{"full_name":"Melikian, Haley E.","first_name":"Haley E.","last_name":"Melikian"}],"date_updated":"2023-08-21T06:26:22Z","date_created":"2020-05-24T22:00:59Z","volume":295,"scopus_import":"1","day":"17","article_processing_charge":"No","publication":"Journal of Biological Chemistry","citation":{"ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 2020;295(16):5229-5244. doi:10.1074/jbc.RA120.012628","apa":"Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. ASBMB Publications. https://doi.org/10.1074/jbc.RA120.012628","ieee":"R. R. Fagan et al., “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” Journal of Biological Chemistry, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","ista":"Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.","short":"R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244.","mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:10.1074/jbc.RA120.012628.","chicago":"Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” Journal of Biological Chemistry. ASBMB Publications, 2020. https://doi.org/10.1074/jbc.RA120.012628."},"article_type":"original","page":"5229-5244","date_published":"2020-04-17T00:00:00Z","type":"journal_article","abstract":[{"text":"Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. ","lang":"eng"}],"issue":"16","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7880","title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","status":"public","intvolume":" 295","oa_version":"Submitted Version"},{"day":"19","article_processing_charge":"No","scopus_import":"1","date_published":"2020-05-19T00:00:00Z","article_type":"original","page":"721-723","publication":"Immunity","citation":{"apa":"Sixt, M. K., & Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. Immunity. Elsevier. https://doi.org/10.1016/j.immuni.2020.04.020","ieee":"M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” Immunity, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.","ista":"Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723.","ama":"Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. Immunity. 2020;52(5):721-723. doi:10.1016/j.immuni.2020.04.020","chicago":"Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity. Elsevier, 2020. https://doi.org/10.1016/j.immuni.2020.04.020.","short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","mla":"Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” Immunity, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:10.1016/j.immuni.2020.04.020."},"abstract":[{"lang":"eng","text":"In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. "}],"issue":"5","type":"journal_article","oa_version":"Published Version","title":"T cells: Bridge-and-channel commute to the white pulp","status":"public","intvolume":" 52","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7876","month":"05","publication_identifier":{"issn":["10747613"],"eissn":["10974180"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.immuni.2020.04.020","isi":1,"quality_controlled":"1","external_id":{"isi":["000535371100002"]},"main_file_link":[{"url":"https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf","open_access":"1"}],"oa":1,"date_updated":"2023-08-21T06:27:18Z","date_created":"2020-05-24T22:00:57Z","volume":52,"author":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Tim","last_name":"Lämmermann","full_name":"Lämmermann, Tim"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Elsevier","year":"2020"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_eLife_Damiano_Guercio.pdf","creator":"dernst","file_size":10535713,"content_type":"application/pdf","file_id":"7914","relation":"main_file","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-02T10:35:37Z"}],"intvolume":" 9","ddc":["570"],"title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","status":"public","_id":"7909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.","lang":"eng"}],"type":"journal_article","date_published":"2020-05-11T00:00:00Z","article_type":"original","citation":{"mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife, vol. 9, e55351, eLife Sciences Publications, 2020, doi:10.7554/eLife.55351.","short":"J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020).","chicago":"Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.55351.","ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 2020;9. doi:10.7554/eLife.55351","ista":"Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351.","apa":"Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.55351","ieee":"J. Damiano-Guercio et al., “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” eLife, vol. 9. eLife Sciences Publications, 2020."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","volume":9,"date_created":"2020-05-31T22:00:49Z","date_updated":"2023-08-21T06:32:25Z","author":[{"full_name":"Damiano-Guercio, Julia","first_name":"Julia","last_name":"Damiano-Guercio"},{"last_name":"Kurzawa","first_name":"Laëtitia","full_name":"Kurzawa, Laëtitia"},{"full_name":"Müller, Jan","last_name":"Müller","first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"full_name":"Schaks, Matthias","last_name":"Schaks","first_name":"Matthias"},{"last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"first_name":"Thomas","last_name":"Pokrant","full_name":"Pokrant, Thomas"},{"last_name":"Brühmann","first_name":"Stefan","full_name":"Brühmann, Stefan"},{"first_name":"Joern","last_name":"Linkner","full_name":"Linkner, Joern"},{"last_name":"Blanchoin","first_name":"Laurent","full_name":"Blanchoin, Laurent"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"}],"department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2020-07-14T12:48:05Z","article_number":"e55351","language":[{"iso":"eng"}],"doi":"10.7554/eLife.55351","project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000537208000001"]},"publication_identifier":{"eissn":["2050084X"]},"month":"05"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7908","title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","status":"public","ddc":["570"],"intvolume":" 40","file":[{"file_name":"2020_JourNeuroscience_Wang.pdf","access_level":"open_access","creator":"dernst","file_size":3817360,"content_type":"application/pdf","file_id":"7912","relation":"main_file","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-02T09:12:16Z","checksum":"6571607ea9036154b67cc78e848a7f7d"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses.","lang":"eng"}],"issue":"21","publication":"Journal of Neuroscience","citation":{"short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:10.1523/JNEUROSCI.2946-19.2020.","chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.2946-19.2020.","ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 2020;40(21):4103-4115. doi:10.1523/JNEUROSCI.2946-19.2020","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., & Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2946-19.2020","ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” Journal of Neuroscience, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020.","ista":"Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115."},"article_type":"original","page":"4103-4115","date_published":"2020-05-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","year":"2020","publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Society for Neuroscience","author":[{"first_name":"Han Ying","last_name":"Wang","full_name":"Wang, Han Ying"},{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku"},{"first_name":"Takayuki","last_name":"Yamashita","full_name":"Yamashita, Takayuki"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"date_created":"2020-05-31T22:00:48Z","date_updated":"2023-08-21T06:31:25Z","volume":40,"file_date_updated":"2020-07-14T12:48:05Z","external_id":{"isi":["000535694700004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1523/JNEUROSCI.2946-19.2020","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["15292401"]}},{"volume":10,"date_updated":"2023-08-21T07:00:17Z","date_created":"2020-06-07T22:00:51Z","author":[{"full_name":"Uroshlev, Leonid A.","last_name":"Uroshlev","first_name":"Leonid A."},{"full_name":"Abdullaev, Eldar T.","last_name":"Abdullaev","first_name":"Eldar T."},{"full_name":"Umarova, Iren R.","first_name":"Iren R.","last_name":"Umarova"},{"first_name":"Irina A.","last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A."},{"full_name":"Panchenko, Larisa A.","last_name":"Panchenko","first_name":"Larisa A."},{"last_name":"Polozov","first_name":"Robert V.","full_name":"Polozov, Robert V."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Nechipurenko, Yury D.","first_name":"Yury D.","last_name":"Nechipurenko"},{"last_name":"Grokhovsky","first_name":"Sergei L.","full_name":"Grokhovsky, Sergei L."}],"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2020","file_date_updated":"2020-07-14T12:48:05Z","article_number":"8635","language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-65406-1","quality_controlled":"1","isi":1,"external_id":{"isi":["000560774200007"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["20452322"]},"month":"05","file":[{"checksum":"099e51611a5b7ca04244d03b2faddf33","date_created":"2020-06-08T06:27:32Z","date_updated":"2020-07-14T12:48:05Z","relation":"main_file","file_id":"7947","file_size":1001724,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_ScientificReports_Uroshlev.pdf"}],"oa_version":"Published Version","intvolume":" 10","ddc":["570"],"title":"A method for identification of the methylation level of CpG islands from NGS data","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7931","abstract":[{"lang":"eng","text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data."}],"type":"journal_article","date_published":"2020-05-25T00:00:00Z","article_type":"original","citation":{"ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1","ieee":"L. A. Uroshlev et al., “A method for identification of the methylation level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer Nature, 2020.","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635, Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-65406-1."},"publication":"Scientific Reports","article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":"1"},{"citation":{"chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.184104.","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).","mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” Physical Review B, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:10.1103/PhysRevB.101.184104.","apa":"Maslov, M., Lemeshko, M., & Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.184104","ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” Physical Review B, vol. 101, no. 18. American Physical Society, 2020.","ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104.","ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 2020;101(18). doi:10.1103/PhysRevB.101.184104"},"publication":"Physical Review B","article_type":"original","date_published":"2020-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"7933","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 101","status":"public","title":"Synthetic spin-orbit coupling mediated by a bosonic environment","oa_version":"Preprint","type":"journal_article","issue":"18","abstract":[{"text":"We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.","lang":"eng"}],"external_id":{"isi":["000530754700003"],"arxiv":["1912.03092"]},"main_file_link":[{"url":"https://arxiv.org/abs/1912.03092","open_access":"1"}],"oa":1,"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevB.101.184104","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"month":"05","year":"2020","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"full_name":"Maslov, Mikhail","last_name":"Maslov","first_name":"Mikhail","orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"}],"volume":101,"date_updated":"2023-08-21T07:05:15Z","date_created":"2020-06-07T22:00:52Z","article_number":"184104 ","ec_funded":1},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"letter_note","page":"841-847","publication":"Nature Physics","citation":{"short":"M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo, J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian, N. Harrison, Nature Physics 16 (2020) 841–847.","mla":"Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics, vol. 16, Springer Nature, 2020, pp. 841–47, doi:10.1038/s41567-020-0910-0.","chicago":"Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Nature Physics. Springer Nature, 2020. https://doi.org/10.1038/s41567-020-0910-0.","ama":"Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 2020;16:841-847. doi:10.1038/s41567-020-0910-0","apa":"Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L., … Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-020-0910-0","ieee":"M. Hartstein et al., “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” Nature Physics, vol. 16. Springer Nature, pp. 841–847, 2020.","ista":"Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J, Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N. 2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 16, 841–847."},"date_published":"2020-08-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18."}],"status":"public","title":"Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors","intvolume":" 16","_id":"7942","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"08","publication_identifier":{"eissn":["17452481"],"issn":["17452473"]},"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000535464400005"],"arxiv":["2005.14123"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.14123"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41567-020-0910-0","publication_status":"published","department":[{"_id":"KiMo"}],"publisher":"Springer Nature","acknowledgement":"M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge support from the National Key Research and Development Program of China (grant no. 2016YFA0401704). A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by the National Science Foundation Cooperative Agreement no. DMR-1644779, the state of Florida and the US Department of Energy. Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science of 100 T’ programme.","year":"2020","date_updated":"2023-08-21T07:06:49Z","date_created":"2020-06-07T22:00:56Z","volume":16,"author":[{"full_name":"Hartstein, Máté","last_name":"Hartstein","first_name":"Máté"},{"last_name":"Hsu","first_name":"Yu Te","full_name":"Hsu, Yu Te"},{"full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147"},{"first_name":"Juan","last_name":"Porras","full_name":"Porras, Juan"},{"full_name":"Loew, Toshinao","first_name":"Toshinao","last_name":"Loew"},{"full_name":"Tacon, Matthieu Le","first_name":"Matthieu Le","last_name":"Tacon"},{"last_name":"Zuo","first_name":"Huakun","full_name":"Zuo, Huakun"},{"full_name":"Wang, Jinhua","first_name":"Jinhua","last_name":"Wang"},{"last_name":"Zhu","first_name":"Zengwei","full_name":"Zhu, Zengwei"},{"full_name":"Chan, Mun K.","last_name":"Chan","first_name":"Mun K."},{"last_name":"Mcdonald","first_name":"Ross D.","full_name":"Mcdonald, Ross D."},{"last_name":"Lonzarich","first_name":"Gilbert G.","full_name":"Lonzarich, Gilbert G."},{"full_name":"Keimer, Bernhard","last_name":"Keimer","first_name":"Bernhard"},{"full_name":"Sebastian, Suchitra E.","first_name":"Suchitra E.","last_name":"Sebastian"},{"full_name":"Harrison, Neil","first_name":"Neil","last_name":"Harrison"}],"related_material":{"record":[{"id":"9708","status":"public","relation":"research_data"}]}},{"date_published":"2020-07-25T00:00:00Z","citation":{"chicago":"Maghiaoui, A, E Bouguyon, Candela Cuesta, F Perrine-Walker, C Alcon, G Krouk, Eva Benková, P Nacry, A Gojon, and L Bach. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa242.","short":"A. Maghiaoui, E. Bouguyon, C. Cuesta, F. Perrine-Walker, C. Alcon, G. Krouk, E. Benková, P. Nacry, A. Gojon, L. Bach, Journal of Experimental Botany 71 (2020) 4480–4494.","mla":"Maghiaoui, A., et al. “The Arabidopsis NRT1.1 Transceptor Coordinately Controls Auxin Biosynthesis and Transport to Regulate Root Branching in Response to Nitrate.” Journal of Experimental Botany, vol. 71, no. 15, Oxford University Press, 2020, pp. 4480–94, doi:10.1093/jxb/eraa242.","apa":"Maghiaoui, A., Bouguyon, E., Cuesta, C., Perrine-Walker, F., Alcon, C., Krouk, G., … Bach, L. (2020). The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa242","ieee":"A. Maghiaoui et al., “The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate,” Journal of Experimental Botany, vol. 71, no. 15. Oxford University Press, pp. 4480–4494, 2020.","ista":"Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A, Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 71(15), 4480–4494.","ama":"Maghiaoui A, Bouguyon E, Cuesta C, et al. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany. 2020;71(15):4480-4494. doi:10.1093/jxb/eraa242"},"publication":"Journal of Experimental Botany","page":"4480-4494","article_type":"original","article_processing_charge":"No","day":"25","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7948","intvolume":" 71","status":"public","title":"The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate","issue":"15","abstract":[{"lang":"eng","text":"In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture."}],"type":"journal_article","doi":"10.1093/jxb/eraa242","language":[{"iso":"eng"}],"external_id":{"isi":["000553127600013"],"pmid":["32428238"]},"main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-02619371"}],"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"month":"07","author":[{"full_name":"Maghiaoui, A","first_name":"A","last_name":"Maghiaoui"},{"full_name":"Bouguyon, E","last_name":"Bouguyon","first_name":"E"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","first_name":"Candela","full_name":"Cuesta, Candela"},{"last_name":"Perrine-Walker","first_name":"F","full_name":"Perrine-Walker, F"},{"last_name":"Alcon","first_name":"C","full_name":"Alcon, C"},{"full_name":"Krouk, G","first_name":"G","last_name":"Krouk"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Nacry, P","first_name":"P","last_name":"Nacry"},{"full_name":"Gojon, A","last_name":"Gojon","first_name":"A"},{"full_name":"Bach, L","first_name":"L","last_name":"Bach"}],"volume":71,"date_created":"2020-06-08T10:10:28Z","date_updated":"2023-08-21T07:07:30Z","pmid":1,"year":"2020","department":[{"_id":"EvBe"}],"publisher":"Oxford University Press","publication_status":"published"},{"doi":"10.1007/s00031-020-09572-6","language":[{"iso":"eng"}],"external_id":{"isi":["000534874300003"],"arxiv":["1804.04375"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.04375","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["10834362"],"eissn":["1531586X"]},"month":"12","author":[{"full_name":"Yang, Yaping","first_name":"Yaping","last_name":"Yang","id":"360D8648-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhao","first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","full_name":"Zhao, Gufang"}],"volume":25,"date_created":"2020-06-07T22:00:55Z","date_updated":"2023-08-21T07:06:21Z","acknowledgement":"Gufang Zhao is affiliated to IST Austria, Hausel group until July of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593 of the European Research Council.","year":"2020","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"date_published":"2020-12-01T00:00:00Z","citation":{"ama":"Yang Y, Zhao G. The PBW theorem for affine Yangians. Transformation Groups. 2020;25:1371-1385. doi:10.1007/s00031-020-09572-6","ista":"Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385.","ieee":"Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” Transformation Groups, vol. 25. Springer Nature, pp. 1371–1385, 2020.","apa":"Yang, Y., & Zhao, G. (2020). The PBW theorem for affine Yangians. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-020-09572-6","mla":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:10.1007/s00031-020-09572-6.","short":"Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385.","chicago":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” Transformation Groups. Springer Nature, 2020. https://doi.org/10.1007/s00031-020-09572-6."},"publication":"Transformation Groups","page":"1371-1385","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"7940","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 25","title":"The PBW theorem for affine Yangians","status":"public","abstract":[{"lang":"eng","text":"We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18]."}],"type":"journal_article"},{"has_accepted_license":"1","article_processing_charge":"No","day":"29","month":"05","date_published":"2020-05-29T00:00:00Z","doi":"10.17863/cam.50169","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.17863/CAM.50169","open_access":"1"}],"citation":{"apa":"Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169","ieee":"M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020.","ista":"Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169.","ama":"Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169","chicago":"Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.","short":"M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020).","mla":"Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169."},"abstract":[{"lang":"eng","text":"This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided."}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7942"}]},"author":[{"full_name":"Hartstein, Mate","first_name":"Mate","last_name":"Hartstein"},{"full_name":"Hsu, Yu-Te","first_name":"Yu-Te","last_name":"Hsu"},{"full_name":"Modic, Kimberly A","last_name":"Modic","first_name":"Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"first_name":"Juan","last_name":"Porras","full_name":"Porras, Juan"},{"last_name":"Loew","first_name":"Toshinao","full_name":"Loew, Toshinao"},{"full_name":"Le Tacon, Matthieu","last_name":"Le Tacon","first_name":"Matthieu"},{"first_name":"Huakun","last_name":"Zuo","full_name":"Zuo, Huakun"},{"full_name":"Wang, Jinhua","first_name":"Jinhua","last_name":"Wang"},{"full_name":"Zhu, Zengwei","last_name":"Zhu","first_name":"Zengwei"},{"last_name":"Chan","first_name":"Mun","full_name":"Chan, Mun"},{"last_name":"McDonald","first_name":"Ross","full_name":"McDonald, Ross"},{"full_name":"Lonzarich, Gilbert","first_name":"Gilbert","last_name":"Lonzarich"},{"full_name":"Keimer, Bernhard","first_name":"Bernhard","last_name":"Keimer"},{"last_name":"Sebastian","first_name":"Suchitra","full_name":"Sebastian, Suchitra"},{"full_name":"Harrison, Neil","first_name":"Neil","last_name":"Harrison"}],"oa_version":"Published Version","date_created":"2021-07-23T10:00:35Z","date_updated":"2023-08-21T07:06:48Z","year":"2020","_id":"9708","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"KiMo"}],"publisher":"Apollo - University of Cambridge","status":"public","title":"Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'"},{"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000665014900010"],"arxiv":["1908.05106"]},"language":[{"iso":"eng"}],"doi":"10.1145/3373718.3394761","conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2020-07-08","location":"Saarbrücken, Germany","end_date":"2020-07-11"},"publication_identifier":{"isbn":["9781450371049"]},"month":"07","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","acknowledgement":"Pranav Ashok, Jan Křetínský and Maximilian Weininger were funded in part by TUM IGSSE Grant 10.06 (PARSEC) and the German Research Foundation (DFG) project KR 4890/2-1\r\n“Statistical Unbounded Verification”. Krishnendu Chatterjee was supported by the ERC CoG 863818 (ForM-SMArt) and Vienna Science and Technology Fund (WWTF) Project ICT15-\r\n003. Tobias Winkler was supported by the RTG 2236 UnRAVe.","date_created":"2020-06-14T22:00:48Z","date_updated":"2023-08-21T08:24:36Z","author":[{"full_name":"Ashok, Pranav","first_name":"Pranav","last_name":"Ashok"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}],"ec_funded":1,"file_date_updated":"2020-11-25T09:38:14Z","page":"102-115","citation":{"ama":"Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. Approximating values of generalized-reachability stochastic games. In: Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . Association for Computing Machinery; 2020:102-115. doi:10.1145/3373718.3394761","apa":"Ashok, P., Chatterjee, K., Kretinsky, J., Weininger, M., & Winkler, T. (2020). Approximating values of generalized-reachability stochastic games. In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 102–115). Saarbrücken, Germany: Association for Computing Machinery. https://doi.org/10.1145/3373718.3394761","ieee":"P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, and T. Winkler, “Approximating values of generalized-reachability stochastic games,” in Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Saarbrücken, Germany, 2020, pp. 102–115.","ista":"Ashok P, Chatterjee K, Kretinsky J, Weininger M, Winkler T. 2020. Approximating values of generalized-reachability stochastic games. Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science . LICS: Symposium on Logic in Computer Science, 102–115.","short":"P. Ashok, K. Chatterjee, J. Kretinsky, M. Weininger, T. Winkler, in:, Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–115.","mla":"Ashok, Pranav, et al. “Approximating Values of Generalized-Reachability Stochastic Games.” Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , Association for Computing Machinery, 2020, pp. 102–15, doi:10.1145/3373718.3394761.","chicago":"Ashok, Pranav, Krishnendu Chatterjee, Jan Kretinsky, Maximilian Weininger, and Tobias Winkler. “Approximating Values of Generalized-Reachability Stochastic Games.” In Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science , 102–15. Association for Computing Machinery, 2020. https://doi.org/10.1145/3373718.3394761."},"publication":"Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science ","date_published":"2020-07-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08","status":"public","ddc":["000"],"title":"Approximating values of generalized-reachability stochastic games","_id":"7955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_name":"2020_LICS_Ashok.pdf","access_level":"open_access","file_size":1001395,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8804","date_updated":"2020-11-25T09:38:14Z","date_created":"2020-11-25T09:38:14Z","checksum":"d0d0288fe991dd16cf5f02598b794240","success":1}],"type":"conference","abstract":[{"lang":"eng","text":"Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound."}]},{"isi":1,"quality_controlled":"1","project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32507511"],"isi":["000553090600008"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tins.2020.05.004","month":"08","publication_identifier":{"eissn":["1878108X"],"issn":["01662236"]},"publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"Elsevier","year":"2020","acknowledgement":"We wish to thank Jasmin Morandell for generously sharing Figure 2. This work was supported by the European Research Council Starting Grant (grant 715508 ) to G.N.","pmid":1,"date_updated":"2023-08-21T08:25:31Z","date_created":"2020-06-14T22:00:49Z","volume":43,"author":[{"full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","last_name":"Parenti","first_name":"Ilaria"},{"full_name":"Garcia Rabaneda, Luis E","last_name":"Garcia Rabaneda","first_name":"Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hanna","last_name":"Schön","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","full_name":"Schön, Hanna"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-11-25T09:43:40Z","ec_funded":1,"article_type":"original","page":"608-621","publication":"Trends in Neurosciences","citation":{"chicago":"Parenti, Ilaria, Luis E Garcia Rabaneda, Hanna Schön, and Gaia Novarino. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences. Elsevier, 2020. https://doi.org/10.1016/j.tins.2020.05.004.","short":"I. Parenti, L.E. Garcia Rabaneda, H. Schön, G. Novarino, Trends in Neurosciences 43 (2020) 608–621.","mla":"Parenti, Ilaria, et al. “Neurodevelopmental Disorders: From Genetics to Functional Pathways.” Trends in Neurosciences, vol. 43, no. 8, Elsevier, 2020, pp. 608–21, doi:10.1016/j.tins.2020.05.004.","apa":"Parenti, I., Garcia Rabaneda, L. E., Schön, H., & Novarino, G. (2020). Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2020.05.004","ieee":"I. Parenti, L. E. Garcia Rabaneda, H. Schön, and G. Novarino, “Neurodevelopmental disorders: From genetics to functional pathways,” Trends in Neurosciences, vol. 43, no. 8. Elsevier, pp. 608–621, 2020.","ista":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. 2020. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 43(8), 608–621.","ama":"Parenti I, Garcia Rabaneda LE, Schön H, Novarino G. Neurodevelopmental disorders: From genetics to functional pathways. Trends in Neurosciences. 2020;43(8):608-621. doi:10.1016/j.tins.2020.05.004"},"date_published":"2020-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Neurodevelopmental disorders: From genetics to functional pathways","intvolume":" 43","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7957","file":[{"file_id":"8805","relation":"main_file","date_updated":"2020-11-25T09:43:40Z","date_created":"2020-11-25T09:43:40Z","success":1,"checksum":"67db0251b1d415ae59005f876fcf9e34","file_name":"2020_TrendsNeuroscience_Parenti.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1439550}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of\r\nmutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches."}],"issue":"8"},{"date_published":"2020-09-01T00:00:00Z","article_type":"original","page":"304-323","publication":"Discrete and Computational Geometry","citation":{"ama":"Kalai G, Patakova Z. Intersection patterns of planar sets. Discrete and Computational Geometry. 2020;64:304-323. doi:10.1007/s00454-020-00205-z","ista":"Kalai G, Patakova Z. 2020. Intersection patterns of planar sets. Discrete and Computational Geometry. 64, 304–323.","ieee":"G. Kalai and Z. Patakova, “Intersection patterns of planar sets,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 304–323, 2020.","apa":"Kalai, G., & Patakova, Z. (2020). Intersection patterns of planar sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00205-z","mla":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 304–23, doi:10.1007/s00454-020-00205-z.","short":"G. Kalai, Z. Patakova, Discrete and Computational Geometry 64 (2020) 304–323.","chicago":"Kalai, Gil, and Zuzana Patakova. “Intersection Patterns of Planar Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00205-z."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Intersection patterns of planar sets","status":"public","intvolume":" 64","_id":"7960","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00205-z","isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1907.00885"],"isi":["000537329400001"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.00885"}],"month":"09","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"date_created":"2020-06-14T22:00:50Z","date_updated":"2023-08-21T08:26:34Z","volume":64,"author":[{"first_name":"Gil","last_name":"Kalai","full_name":"Kalai, Gil"},{"first_name":"Zuzana","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana"}],"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","acknowledgement":"We are very grateful to Pavel Paták for many helpful discussions and remarks. We also thank the referees for helpful comments, which greatly improved the presentation.\r\nThe project was supported by ERC Advanced Grant 320924. GK was also partially supported by NSF grant DMS1300120. The research stay of ZP at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466 Improvement of internationalization in the field of research and development at Charles University, through the support of quality projects MSCA-IF.","year":"2020"},{"author":[{"last_name":"Pach","first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János"},{"full_name":"Reed, Bruce","first_name":"Bruce","last_name":"Reed"},{"full_name":"Yuditsky, Yelena","last_name":"Yuditsky","first_name":"Yelena"}],"volume":63,"date_created":"2020-06-14T22:00:51Z","date_updated":"2023-08-21T08:49:18Z","year":"2020","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"month":"06","doi":"10.1007/s00454-020-00213-z","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1803.06710"],"isi":["000538229000001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.06710","open_access":"1"}],"project":[{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"issue":"4","abstract":[{"lang":"eng","text":"A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets."}],"type":"journal_article","oa_version":"Preprint","_id":"7962","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 63","title":"Almost all string graphs are intersection graphs of plane convex sets","status":"public","article_processing_charge":"No","day":"05","scopus_import":"1","date_published":"2020-06-05T00:00:00Z","citation":{"chicago":"Pach, János, Bruce Reed, and Yelena Yuditsky. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00213-z.","short":"J. Pach, B. Reed, Y. Yuditsky, Discrete and Computational Geometry 63 (2020) 888–917.","mla":"Pach, János, et al. “Almost All String Graphs Are Intersection Graphs of Plane Convex Sets.” Discrete and Computational Geometry, vol. 63, no. 4, Springer Nature, 2020, pp. 888–917, doi:10.1007/s00454-020-00213-z.","apa":"Pach, J., Reed, B., & Yuditsky, Y. (2020). Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00213-z","ieee":"J. Pach, B. Reed, and Y. Yuditsky, “Almost all string graphs are intersection graphs of plane convex sets,” Discrete and Computational Geometry, vol. 63, no. 4. Springer Nature, pp. 888–917, 2020.","ista":"Pach J, Reed B, Yuditsky Y. 2020. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 63(4), 888–917.","ama":"Pach J, Reed B, Yuditsky Y. Almost all string graphs are intersection graphs of plane convex sets. Discrete and Computational Geometry. 2020;63(4):888-917. doi:10.1007/s00454-020-00213-z"},"publication":"Discrete and Computational Geometry","page":"888-917","article_type":"original"},{"abstract":[{"text":"Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. ","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_NatureComm_Bayesian.pdf","creator":"dernst","content_type":"application/pdf","file_size":1475657,"file_id":"8000","relation":"main_file","checksum":"4c96babd4cfb0d153334f6c598c0bacb","date_created":"2020-06-22T11:24:32Z","date_updated":"2020-07-14T12:48:07Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7999","intvolume":" 11","ddc":["570"],"status":"public","title":"Bayesian reassessment of the epigenetic architecture of complex traits","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","date_published":"2020-06-08T00:00:00Z","citation":{"short":"D. Trejo Banos, D. McCartney, M. Patxot, L. Anchieri, T. Battram, C. Christiansen, R. Costeira, R. Walker, S. Morris, A. Campbell, Q. Zhang, D. Porteous, A. McRae, N. Wray, P. Visscher, C. Haley, K. Evans, I. Deary, A. McIntosh, G. Hemani, J. Bell, R. Marioni, M.R. Robinson, Nature Communications 11 (2020).","mla":"Trejo Banos, D., et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications, vol. 11, 2865, Springer Nature, 2020, doi:10.1038/s41467-020-16520-1.","chicago":"Trejo Banos, D, DL McCartney, M Patxot, L Anchieri, T Battram, C Christiansen, R Costeira, et al. “Bayesian Reassessment of the Epigenetic Architecture of Complex Traits.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-16520-1.","ama":"Trejo Banos D, McCartney D, Patxot M, et al. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 2020;11. doi:10.1038/s41467-020-16520-1","ieee":"D. Trejo Banos et al., “Bayesian reassessment of the epigenetic architecture of complex traits,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Trejo Banos, D., McCartney, D., Patxot, M., Anchieri, L., Battram, T., Christiansen, C., … Robinson, M. R. (2020). Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-16520-1","ista":"Trejo Banos D, McCartney D, Patxot M, Anchieri L, Battram T, Christiansen C, Costeira R, Walker R, Morris S, Campbell A, Zhang Q, Porteous D, McRae A, Wray N, Visscher P, Haley C, Evans K, Deary I, McIntosh A, Hemani G, Bell J, Marioni R, Robinson MR. 2020. Bayesian reassessment of the epigenetic architecture of complex traits. Nature Communications. 11, 2865."},"publication":"Nature Communications","article_type":"original","file_date_updated":"2020-07-14T12:48:07Z","article_number":"2865","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19099-9"}]},"author":[{"last_name":"Trejo Banos","first_name":"D","full_name":"Trejo Banos, D"},{"last_name":"McCartney","first_name":"DL","full_name":"McCartney, DL"},{"last_name":"Patxot","first_name":"M","full_name":"Patxot, M"},{"full_name":"Anchieri, L","first_name":"L","last_name":"Anchieri"},{"full_name":"Battram, T","first_name":"T","last_name":"Battram"},{"full_name":"Christiansen, C","first_name":"C","last_name":"Christiansen"},{"full_name":"Costeira, R","last_name":"Costeira","first_name":"R"},{"full_name":"Walker, RM","first_name":"RM","last_name":"Walker"},{"last_name":"Morris","first_name":"SW","full_name":"Morris, SW"},{"full_name":"Campbell, A","first_name":"A","last_name":"Campbell"},{"full_name":"Zhang, Q","last_name":"Zhang","first_name":"Q"},{"last_name":"Porteous","first_name":"DJ","full_name":"Porteous, DJ"},{"first_name":"AF","last_name":"McRae","full_name":"McRae, AF"},{"full_name":"Wray, NR","last_name":"Wray","first_name":"NR"},{"last_name":"Visscher","first_name":"PM","full_name":"Visscher, PM"},{"last_name":"Haley","first_name":"CS","full_name":"Haley, CS"},{"full_name":"Evans, KL","last_name":"Evans","first_name":"KL"},{"first_name":"IJ","last_name":"Deary","full_name":"Deary, IJ"},{"full_name":"McIntosh, AM","last_name":"McIntosh","first_name":"AM"},{"first_name":"G","last_name":"Hemani","full_name":"Hemani, G"},{"full_name":"Bell, JT","last_name":"Bell","first_name":"JT"},{"full_name":"Marioni, RE","first_name":"RE","last_name":"Marioni"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"}],"volume":11,"date_created":"2020-06-22T11:18:25Z","date_updated":"2023-08-22T07:13:09Z","pmid":1,"year":"2020","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"month":"06","doi":"10.1038/s41467-020-16520-1","language":[{"iso":"eng"}],"external_id":{"pmid":["32513961"],"isi":["000541702400004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1"},{"type":"journal_article","abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"issue":"7","status":"public","ddc":["570"],"title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","intvolume":" 74","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7995","oa_version":"Published Version","file":[{"file_id":"8808","relation":"main_file","success":1,"checksum":"56235bf1e2a9e25f96196bb13b6b754d","date_updated":"2020-11-25T10:49:48Z","date_created":"2020-11-25T10:49:48Z","access_level":"open_access","file_name":"2020_Evolution_Perini.pdf","creator":"dernst","file_size":1080810,"content_type":"application/pdf"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"1482-1497","publication":"Evolution","citation":{"chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027.","mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027.","short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497.","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027","ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027"},"date_published":"2020-07-01T00:00:00Z","file_date_updated":"2020-11-25T10:49:48Z","ec_funded":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2020","acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","date_created":"2020-06-22T09:14:21Z","date_updated":"2023-08-22T07:13:38Z","volume":74,"author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"8809"}]},"month":"07","publication_identifier":{"issn":["00143820"],"eissn":["15585646"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000539780800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/evo.14027"},{"author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Rafajlovic, Marina","first_name":"Marina","last_name":"Rafajlovic"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"related_material":{"record":[{"id":"7995","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-22T07:13:37Z","date_created":"2020-11-25T11:07:25Z","oa_version":"Published Version","_id":"8809","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","date_published":"2020-07-01T00:00:00Z","doi":"10.5061/dryad.qrfj6q5cn","tmp":{"short":"CC0 (1.0)","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)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"citation":{"ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn."},"oa":1,"day":"01","month":"07","has_accepted_license":"1","article_processing_charge":"No"},{"issue":"3","abstract":[{"lang":"eng","text":"Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_Neuron_Vandael.pdf","creator":"dernst","file_size":4390833,"content_type":"application/pdf","file_id":"8811","relation":"main_file","success":1,"checksum":"4030b2be0c9625d54694a1e9fb00305e","date_updated":"2020-11-25T11:23:02Z","date_created":"2020-11-25T11:23:02Z"}],"_id":"8001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 107","ddc":["570"],"status":"public","title":"Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation","article_processing_charge":"No","has_accepted_license":"1","day":"05","scopus_import":"1","date_published":"2020-08-05T00:00:00Z","citation":{"ieee":"D. H. Vandael, C. Borges Merjane, X. Zhang, and P. M. Jonas, “Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation,” Neuron, vol. 107, no. 3. Elsevier, pp. 509–521, 2020.","apa":"Vandael, D. H., Borges Merjane, C., Zhang, X., & Jonas, P. M. (2020). Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.05.013","ista":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. 2020. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 107(3), 509–521.","ama":"Vandael DH, Borges Merjane C, Zhang X, Jonas PM. Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation. Neuron. 2020;107(3):509-521. doi:10.1016/j.neuron.2020.05.013","chicago":"Vandael, David H, Carolina Borges Merjane, Xiaomin Zhang, and Peter M Jonas. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.05.013.","short":"D.H. Vandael, C. Borges Merjane, X. Zhang, P.M. Jonas, Neuron 107 (2020) 509–521.","mla":"Vandael, David H., et al. “Short-Term Plasticity at Hippocampal Mossy Fiber Synapses Is Induced by Natural Activity Patterns and Associated with Vesicle Pool Engram Formation.” Neuron, vol. 107, no. 3, Elsevier, 2020, pp. 509–21, doi:10.1016/j.neuron.2020.05.013."},"publication":"Neuron","page":"509-521","article_type":"original","ec_funded":1,"file_date_updated":"2020-11-25T11:23:02Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/possible-physical-trace-of-short-term-memory-found/"}]},"author":[{"orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H","full_name":"Vandael, David H"},{"first_name":"Carolina","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina"},{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"volume":107,"date_created":"2020-06-22T13:29:05Z","date_updated":"2023-08-22T07:45:25Z","pmid":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union Horizon 2020 Research and Innovation Program (grant agreement 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung ( Z 312-B27 , Wittgenstein award to P.J. and V 739-B27 to C.B.-M.). We thank Drs. Jozsef Csicsvari, Jose Guzman, Erwin Neher, and Ryuichi Shigemoto for commenting on earlier versions of the manuscript. We are grateful to Walter Kaufmann, Daniel Gütl, and Vanessa Zheden for EM training; Alois Schlögl for programming; Florian Marr for excellent technical assistance and cell reconstruction; Christina Altmutter for technical help; Eleftheria Kralli-Beller for manuscript editing; Taija Makinen for providing the Prox1-CreERT2 mouse line; and the Scientific Service Units of IST Austria for support.","year":"2020","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","publication_identifier":{"issn":["0896-6273"],"eissn":["10974199"]},"month":"08","doi":"10.1016/j.neuron.2020.05.013","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"external_id":{"pmid":["32492366"],"isi":["000556135600004"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739"}],"quality_controlled":"1","isi":1},{"month":"05","publication_identifier":{"eissn":["20589565"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000539300800001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"doi":"10.1088/2058-9565/ab8dce","language":[{"iso":"eng"}],"article_number":"034011","file_date_updated":"2020-07-14T12:48:08Z","ec_funded":1,"year":"2020","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","author":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Kalaee, M.","first_name":"M.","last_name":"Kalaee"},{"full_name":"Norte, R.","first_name":"R.","last_name":"Norte"},{"full_name":"Pitanti, A.","last_name":"Pitanti","first_name":"A."},{"last_name":"Painter","first_name":"O.","full_name":"Painter, O."}],"date_updated":"2023-08-22T07:49:01Z","date_created":"2020-06-29T07:59:35Z","volume":5,"scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Quantum Science and Technology","citation":{"chicago":"Fink, Johannes M, M. Kalaee, R. Norte, A. Pitanti, and O. Painter. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab8dce.","mla":"Fink, Johannes M., et al. “Efficient Microwave Frequency Conversion Mediated by a Photonics Compatible Silicon Nitride Nanobeam Oscillator.” Quantum Science and Technology, vol. 5, no. 3, 034011, IOP Publishing, 2020, doi:10.1088/2058-9565/ab8dce.","short":"J.M. Fink, M. Kalaee, R. Norte, A. Pitanti, O. Painter, Quantum Science and Technology 5 (2020).","ista":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. 2020. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 5(3), 034011.","ieee":"J. M. Fink, M. Kalaee, R. Norte, A. Pitanti, and O. Painter, “Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator,” Quantum Science and Technology, vol. 5, no. 3. IOP Publishing, 2020.","apa":"Fink, J. M., Kalaee, M., Norte, R., Pitanti, A., & Painter, O. (2020). Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab8dce","ama":"Fink JM, Kalaee M, Norte R, Pitanti A, Painter O. Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator. Quantum Science and Technology. 2020;5(3). doi:10.1088/2058-9565/ab8dce"},"article_type":"original","date_published":"2020-05-25T00:00:00Z","type":"journal_article","abstract":[{"text":"Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.","lang":"eng"}],"issue":"3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8038","ddc":["530"],"title":"Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator","status":"public","intvolume":" 5","file":[{"checksum":"8f25f05053f511f892ae8fa93f341e61","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-30T10:29:10Z","relation":"main_file","file_id":"8072","content_type":"application/pdf","file_size":2600967,"creator":"cziletti","access_level":"open_access","file_name":"2020_QuantumSciTechnol_Fink.pdf"}],"oa_version":"Published Version"},{"type":"journal_article","abstract":[{"lang":"eng","text":"When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves."}],"_id":"8036","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"title":"Magnetically powered metachronal waves induce locomotion in self-assemblies","status":"public","intvolume":" 3","oa_version":"Published Version","file":[{"file_name":"2020_CommunicationsPhysics_Collard.pdf","access_level":"open_access","file_size":1907821,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"8045","date_created":"2020-06-29T13:21:24Z","date_updated":"2020-07-14T12:48:08Z","checksum":"ed984f7a393f19140b5279a54a3336ad"}],"scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","publication":"Communications Physics","citation":{"ista":"Collard Y, Grosjean GM, Vandewalle N. 2020. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 3, 112.","ieee":"Y. Collard, G. M. Grosjean, and N. Vandewalle, “Magnetically powered metachronal waves induce locomotion in self-assemblies,” Communications Physics, vol. 3. Springer Nature, 2020.","apa":"Collard, Y., Grosjean, G. M., & Vandewalle, N. (2020). Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-0380-9","ama":"Collard Y, Grosjean GM, Vandewalle N. Magnetically powered metachronal waves induce locomotion in self-assemblies. Communications Physics. 2020;3. doi:10.1038/s42005-020-0380-9","chicago":"Collard, Ylona, Galien M Grosjean, and Nicolas Vandewalle. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-0380-9.","mla":"Collard, Ylona, et al. “Magnetically Powered Metachronal Waves Induce Locomotion in Self-Assemblies.” Communications Physics, vol. 3, 112, Springer Nature, 2020, doi:10.1038/s42005-020-0380-9.","short":"Y. Collard, G.M. Grosjean, N. Vandewalle, Communications Physics 3 (2020)."},"article_type":"original","date_published":"2020-06-19T00:00:00Z","article_number":"112","file_date_updated":"2020-07-14T12:48:08Z","ec_funded":1,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ScWa"}],"author":[{"full_name":"Collard, Ylona","first_name":"Ylona","last_name":"Collard"},{"last_name":"Grosjean","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M"},{"full_name":"Vandewalle, Nicolas","first_name":"Nicolas","last_name":"Vandewalle"}],"date_created":"2020-06-29T07:59:35Z","date_updated":"2023-08-22T07:47:30Z","volume":3,"month":"06","publication_identifier":{"eissn":["23993650"]},"external_id":{"isi":["000543328000002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1038/s42005-020-0380-9","language":[{"iso":"eng"}]},{"oa_version":"Published Version","file":[{"checksum":"3f487bf6d9286787096306eaa18702e8","date_created":"2020-06-30T08:37:37Z","date_updated":"2020-07-14T12:48:08Z","file_id":"8070","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":767873,"access_level":"open_access","file_name":"2020_JournalOfFluidMech_Paranjape.pdf"}],"intvolume":" 897","status":"public","title":"Oblique stripe solutions of channel flow","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8043","abstract":[{"lang":"eng","text":"With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain."}],"type":"journal_article","date_published":"2020-08-25T00:00:00Z","article_type":"original","citation":{"short":"C.S. Paranjape, Y. Duguet, B. Hof, Journal of Fluid Mechanics 897 (2020).","mla":"Paranjape, Chaitanya S., et al. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics, vol. 897, A7, Cambridge University Press, 2020, doi:10.1017/jfm.2020.322.","chicago":"Paranjape, Chaitanya S, Yohann Duguet, and Björn Hof. “Oblique Stripe Solutions of Channel Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2020. https://doi.org/10.1017/jfm.2020.322.","ama":"Paranjape CS, Duguet Y, Hof B. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 2020;897. doi:10.1017/jfm.2020.322","ieee":"C. S. Paranjape, Y. Duguet, and B. Hof, “Oblique stripe solutions of channel flow,” Journal of Fluid Mechanics, vol. 897. Cambridge University Press, 2020.","apa":"Paranjape, C. S., Duguet, Y., & Hof, B. (2020). Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2020.322","ista":"Paranjape CS, Duguet Y, Hof B. 2020. Oblique stripe solutions of channel flow. Journal of Fluid Mechanics. 897, A7."},"publication":"Journal of Fluid Mechanics","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","scopus_import":"1","volume":897,"date_updated":"2023-08-22T07:48:02Z","date_created":"2020-06-29T07:59:35Z","author":[{"full_name":"Paranjape, Chaitanya S","last_name":"Paranjape","first_name":"Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Duguet, Yohann","last_name":"Duguet","first_name":"Yohann"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"The authors thank S. Zammert and B. Budanur for useful discussions. J. F. Gibson is gratefully acknowledged for the development and the maintenance of the code Channelflow. Y.D. would like to thank P. Schlatter and D. S. Henningson for an early collaboration on a similar topic in the case of plane Couette flow during the years 2008–2013.","year":"2020","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:48:08Z","article_number":"A7","language":[{"iso":"eng"}],"doi":"10.1017/jfm.2020.322","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000539132300001"]},"oa":1,"publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"month":"08"},{"article_processing_charge":"No","day":"20","month":"05","doi":"10.1021/jacs.9b13450.s002","date_published":"2020-05-20T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"main_file_link":[{"open_access":"1"}],"citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.","mla":"Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.","short":"C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","ista":"Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020.","apa":"Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002","ama":"Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002"},"abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"research_data_reference","related_material":{"record":[{"id":"8040","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Gupta, Chitrak","first_name":"Chitrak","last_name":"Gupta"},{"last_name":"Khaniya","first_name":"Umesh","full_name":"Khaniya, Umesh"},{"full_name":"Chan, Chun","last_name":"Chan","first_name":"Chun"},{"full_name":"Dehez, Francois","first_name":"Francois","last_name":"Dehez"},{"full_name":"Shekhar, Mrinal","first_name":"Mrinal","last_name":"Shekhar"},{"full_name":"Gunner, M. R.","last_name":"Gunner","first_name":"M. R."},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"full_name":"Singharoy, Abhishek","first_name":"Abhishek","last_name":"Singharoy"}],"oa_version":"Published Version","date_updated":"2023-08-22T07:49:37Z","date_created":"2021-04-14T12:05:20Z","year":"2020","_id":"9326","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LeSa"}],"publisher":"American Chemical Society","title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","status":"public"},{"date_published":"2020-07-01T00:00:00Z","article_type":"original","page":"2331-2403","publication":"Journal of the European Mathematical Society","citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/966","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. European Mathematical Society, pp. 2331–2403, 2020.","mla":"Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, European Mathematical Society, 2020, pp. 2331–403, doi:10.4171/JEMS/966.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. European Mathematical Society, 2020. https://doi.org/10.4171/JEMS/966."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"The excitation spectrum of Bose gases interacting through singular potentials","status":"public","intvolume":" 22","_id":"8042","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.","lang":"eng"}],"issue":"7","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.4171/JEMS/966","isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1704.04819"],"isi":["000548174700006"]},"main_file_link":[{"url":"https://arxiv.org/abs/1704.04819","open_access":"1"}],"month":"07","publication_identifier":{"issn":["14359855"]},"date_created":"2020-06-29T07:59:35Z","date_updated":"2023-08-22T07:47:04Z","volume":22,"author":[{"last_name":"Boccato","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"first_name":"Serena","last_name":"Cenatiempo","full_name":"Cenatiempo, Serena"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"}],"publication_status":"published","publisher":"European Mathematical Society","department":[{"_id":"RoSe"}],"year":"2020"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41416-020-0943-2","quality_controlled":"1","isi":1,"external_id":{"pmid":["32601464"],"isi":["000544152500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1532-1827"],"issn":["0007-0920"]},"month":"09","volume":123,"date_updated":"2023-08-22T07:51:12Z","date_created":"2020-07-05T22:00:46Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}],"record":[{"relation":"later_version","status":"deleted","id":"10170"}]},"author":[{"last_name":"Hippe","first_name":"Andreas","full_name":"Hippe, Andreas"},{"full_name":"Braun, Stephan Alexander","last_name":"Braun","first_name":"Stephan Alexander"},{"full_name":"Oláh, Péter","first_name":"Péter","last_name":"Oláh"},{"full_name":"Gerber, Peter Arne","last_name":"Gerber","first_name":"Peter Arne"},{"full_name":"Schorr, Anne","first_name":"Anne","last_name":"Schorr"},{"first_name":"Stephan","last_name":"Seeliger","full_name":"Seeliger, Stephan"},{"first_name":"Stephanie","last_name":"Holtz","full_name":"Holtz, Stephanie"},{"full_name":"Jannasch, Katharina","first_name":"Katharina","last_name":"Jannasch"},{"last_name":"Pivarcsi","first_name":"Andor","full_name":"Pivarcsi, Andor"},{"full_name":"Buhren, Bettina","last_name":"Buhren","first_name":"Bettina"},{"full_name":"Schrumpf, Holger","last_name":"Schrumpf","first_name":"Holger"},{"full_name":"Kislat, Andreas","first_name":"Andreas","last_name":"Kislat"},{"full_name":"Bünemann, Erich","last_name":"Bünemann","first_name":"Erich"},{"full_name":"Steinhoff, Martin","first_name":"Martin","last_name":"Steinhoff"},{"first_name":"Jens","last_name":"Fischer","full_name":"Fischer, Jens"},{"first_name":"Sérgio A.","last_name":"Lira","full_name":"Lira, Sérgio A."},{"last_name":"Boukamp","first_name":"Petra","full_name":"Boukamp, Petra"},{"full_name":"Hevezi, Peter","last_name":"Hevezi","first_name":"Peter"},{"full_name":"Stoecklein, Nikolas Hendrik","first_name":"Nikolas Hendrik","last_name":"Stoecklein"},{"full_name":"Hoffmann, Thomas","first_name":"Thomas","last_name":"Hoffmann"},{"first_name":"Frauke","last_name":"Alves","full_name":"Alves, Frauke"},{"first_name":"Jonathan","last_name":"Sleeman","full_name":"Sleeman, Jonathan"},{"full_name":"Bauer, Thomas","first_name":"Thomas","last_name":"Bauer"},{"full_name":"Klufa, Jörg","last_name":"Klufa","first_name":"Jörg"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Sibilia","full_name":"Sibilia, Maria"},{"full_name":"Zlotnik, Albert","last_name":"Zlotnik","first_name":"Albert"},{"last_name":"Müller-Homey","first_name":"Anja","full_name":"Müller-Homey, Anja"},{"full_name":"Homey, Bernhard","first_name":"Bernhard","last_name":"Homey"}],"department":[{"_id":"SiHi"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","year":"2020","file_date_updated":"2021-12-02T12:35:12Z","date_published":"2020-09-15T00:00:00Z","page":"942-954","article_type":"original","citation":{"ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","ieee":"A. Hippe et al., “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” British Journal of Cancer, vol. 123. Springer Nature, pp. 942–954, 2020.","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. Springer Nature. https://doi.org/10.1038/s41416-020-0943-2","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 2020;123:942-954. doi:10.1038/s41416-020-0943-2","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer. Springer Nature, 2020. https://doi.org/10.1038/s41416-020-0943-2.","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” British Journal of Cancer, vol. 123, Springer Nature, 2020, pp. 942–54, doi:10.1038/s41416-020-0943-2.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954."},"publication":"British Journal of Cancer","article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_BrJournalCancer_Hippe.pdf","file_size":3620691,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10398","checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","success":1,"date_updated":"2021-12-02T12:35:12Z","date_created":"2021-12-02T12:35:12Z"}],"intvolume":" 123","ddc":["610"],"title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8093","abstract":[{"lang":"eng","text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"text":"In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8091","ddc":["530"],"status":"public","title":"Emergence of Haldane pseudo-potentials in systems with short-range interactions","intvolume":" 181","oa_version":"Published Version","file":[{"file_size":404778,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_JourStatPhysics_Seiringer.pdf","checksum":"5cbeef52caf18d0d952f17fed7b5545a","success":1,"date_created":"2020-11-25T15:05:04Z","date_updated":"2020-11-25T15:05:04Z","relation":"main_file","file_id":"8812"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Journal of Statistical Physics","citation":{"short":"R. Seiringer, J. Yngvason, Journal of Statistical Physics 181 (2020) 448–464.","mla":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics, vol. 181, Springer, 2020, pp. 448–64, doi:10.1007/s10955-020-02586-0.","chicago":"Seiringer, Robert, and Jakob Yngvason. “Emergence of Haldane Pseudo-Potentials in Systems with Short-Range Interactions.” Journal of Statistical Physics. Springer, 2020. https://doi.org/10.1007/s10955-020-02586-0.","ama":"Seiringer R, Yngvason J. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 2020;181:448-464. doi:10.1007/s10955-020-02586-0","apa":"Seiringer, R., & Yngvason, J. (2020). Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-020-02586-0","ieee":"R. Seiringer and J. Yngvason, “Emergence of Haldane pseudo-potentials in systems with short-range interactions,” Journal of Statistical Physics, vol. 181. Springer, pp. 448–464, 2020.","ista":"Seiringer R, Yngvason J. 2020. Emergence of Haldane pseudo-potentials in systems with short-range interactions. Journal of Statistical Physics. 181, 448–464."},"article_type":"original","page":"448-464","date_published":"2020-10-01T00:00:00Z","file_date_updated":"2020-11-25T15:05:04Z","ec_funded":1,"year":"2020","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\nThe work of R.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 694227). J.Y. gratefully acknowledges hospitality at the LPMMC Grenoble and valuable discussions with Alessandro Olgiati and Nicolas Rougerie. ","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","author":[{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"date_updated":"2023-08-22T07:51:47Z","date_created":"2020-07-05T22:00:46Z","volume":181,"month":"10","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"external_id":{"isi":["000543030000002"],"arxiv":["2001.07144"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"doi":"10.1007/s10955-020-02586-0","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods."}],"_id":"8077","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 157","title":"Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence","status":"public","ddc":["510"],"file":[{"access_level":"open_access","file_name":"2020_AppliedNumericalMath_Shehu.pdf","file_size":2874203,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8078","checksum":"87d81324a62c82baa925c009dfcb0200","date_updated":"2020-07-14T12:48:09Z","date_created":"2020-07-02T09:08:59Z"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"apa":"Shehu, Y., & Iyiola, O. S. (2020). Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. Elsevier. https://doi.org/10.1016/j.apnum.2020.06.009","ieee":"Y. Shehu and O. S. Iyiola, “Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence,” Applied Numerical Mathematics, vol. 157. Elsevier, pp. 315–337, 2020.","ista":"Shehu Y, Iyiola OS. 2020. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 157, 315–337.","ama":"Shehu Y, Iyiola OS. Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence. Applied Numerical Mathematics. 2020;157:315-337. doi:10.1016/j.apnum.2020.06.009","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics. Elsevier, 2020. https://doi.org/10.1016/j.apnum.2020.06.009.","short":"Y. Shehu, O.S. Iyiola, Applied Numerical Mathematics 157 (2020) 315–337.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Projection Methods with Alternating Inertial Steps for Variational Inequalities: Weak and Linear Convergence.” Applied Numerical Mathematics, vol. 157, Elsevier, 2020, pp. 315–37, doi:10.1016/j.apnum.2020.06.009."},"publication":"Applied Numerical Mathematics","page":"315-337","article_type":"original","date_published":"2020-11-01T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:48:09Z","year":"2020","acknowledgement":"The authors are grateful to the two anonymous referees for their insightful comments and suggestions which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union Seventh Framework Programme (FP7 - 2007-2013) (Grant agreement No. 616160).","publisher":"Elsevier","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","first_name":"Yekini","full_name":"Shehu, Yekini"},{"full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola","first_name":"Olaniyi S."}],"volume":157,"date_created":"2020-07-02T09:02:33Z","date_updated":"2023-08-22T07:50:43Z","publication_identifier":{"issn":["0168-9274"]},"month":"11","external_id":{"isi":["000564648400018"]},"oa":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.apnum.2020.06.009","language":[{"iso":"eng"}]},{"oa_version":"Published Version","file":[{"success":1,"date_created":"2020-07-22T06:27:38Z","date_updated":"2020-07-22T06:27:38Z","relation":"main_file","file_id":"8145","file_size":1136983,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_GenomeMedicine_Hillary.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8133","ddc":["570"],"status":"public","title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","intvolume":" 12","abstract":[{"lang":"eng","text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease."}],"issue":"1","type":"journal_article","date_published":"2020-07-08T00:00:00Z","publication":"Genome Medicine","citation":{"chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine. Springer Nature, 2020. https://doi.org/10.1186/s13073-020-00754-1.","mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Genome Medicine, vol. 12, no. 1, 60, Springer Nature, 2020, doi:10.1186/s13073-020-00754-1.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-020-00754-1","ieee":"R. F. Hillary et al., “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” Genome Medicine, vol. 12, no. 1. Springer Nature, 2020.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 2020;12(1). doi:10.1186/s13073-020-00754-1"},"article_type":"original","day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."},{"last_name":"Trejo-Banos","first_name":"Daniel","full_name":"Trejo-Banos, Daniel"},{"full_name":"Kousathanas, Athanasios","first_name":"Athanasios","last_name":"Kousathanas"},{"last_name":"Mccartney","first_name":"Daniel L.","full_name":"Mccartney, Daniel L."},{"first_name":"Sarah E.","last_name":"Harris","full_name":"Harris, Sarah E."},{"last_name":"Stevenson","first_name":"Anna J.","full_name":"Stevenson, Anna J."},{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"last_name":"Ojavee","first_name":"Sven Erik","full_name":"Ojavee, Sven Erik"},{"full_name":"Zhang, Qian","first_name":"Qian","last_name":"Zhang"},{"full_name":"Liewald, David C.","last_name":"Liewald","first_name":"David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"full_name":"Tucker-Drob, Elliot M.","last_name":"Tucker-Drob","first_name":"Elliot M."},{"full_name":"Wray, Naomi R.","first_name":"Naomi R.","last_name":"Wray"},{"last_name":"Mcrae","first_name":"Allan F.","full_name":"Mcrae, Allan F."},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"},{"first_name":"Ian J.","last_name":"Deary","full_name":"Deary, Ian J."},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"}],"related_material":{"record":[{"id":"9706","status":"public","relation":"research_data"}]},"date_created":"2020-07-19T22:00:58Z","date_updated":"2023-08-22T07:55:37Z","volume":12,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","file_date_updated":"2020-07-22T06:27:38Z","article_number":"60","doi":"10.1186/s13073-020-00754-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32641083"],"isi":["000551778400001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"07","publication_identifier":{"eissn":["1756994X"]}},{"intvolume":" 9","status":"public","title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","ddc":["570"],"_id":"8127","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2020_eLife_Gonçalves.pdf","access_level":"open_access","creator":"cziletti","file_size":17355867,"content_type":"application/pdf","file_id":"8709","relation":"main_file","date_updated":"2020-10-27T11:37:32Z","date_created":"2020-10-27T11:37:32Z","success":1,"checksum":"c4300ddcd93ed03fc9c6cdf1f77890be"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics."}],"article_type":"original","citation":{"ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020)."},"publication":"eLife","date_published":"2020-09-17T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"17","department":[{"_id":"TiVo"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","year":"2020","volume":9,"date_created":"2020-07-16T12:26:04Z","date_updated":"2023-08-22T07:54:52Z","author":[{"full_name":"Gonçalves, Pedro J.","last_name":"Gonçalves","first_name":"Pedro J.","orcid":"0000-0002-6987-4836"},{"last_name":"Lueckmann","first_name":"Jan-Matthis","orcid":"0000-0003-4320-4663","full_name":"Lueckmann, Jan-Matthis"},{"full_name":"Deistler, Michael","last_name":"Deistler","first_name":"Michael","orcid":"0000-0002-3573-0404"},{"full_name":"Nonnenmacher, Marcel","orcid":"0000-0001-6044-6627","first_name":"Marcel","last_name":"Nonnenmacher"},{"first_name":"Kaan","last_name":"Öcal","orcid":"0000-0002-8528-6858","full_name":"Öcal, Kaan"},{"first_name":"Giacomo","last_name":"Bassetto","full_name":"Bassetto, Giacomo"},{"full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","first_name":"Chaitanya","orcid":"0000-0003-4252-1608","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E"},{"orcid":"0000-0001-6619-7502","first_name":"William F.","last_name":"Podlaski","full_name":"Podlaski, William F."},{"full_name":"Haddad, Sara A.","first_name":"Sara A.","last_name":"Haddad","orcid":"0000-0003-0807-0823"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","full_name":"Vogels, Tim P"},{"first_name":"David S.","last_name":"Greenberg","full_name":"Greenberg, David S."},{"first_name":"Jakob H.","last_name":"Macke","orcid":"0000-0001-5154-8912","full_name":"Macke, Jakob H."}],"article_number":"e56261","ec_funded":1,"file_date_updated":"2020-10-27T11:37:32Z","project":[{"name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["32940606"],"isi":["000584989400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.56261","publication_identifier":{"eissn":["2050-084X"]},"month":"09"},{"oa_version":"Published Version","file":[{"success":1,"checksum":"7977e4dd6b89357d1a5cc88babac56da","date_created":"2020-12-28T08:31:47Z","date_updated":"2020-12-28T08:31:47Z","file_id":"8977","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2750920,"access_level":"open_access","file_name":"2020_JourNeuroscience_Agnes.pdf"}],"intvolume":" 40","status":"public","ddc":["570"],"title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","_id":"8126","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"50","abstract":[{"text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.","lang":"eng"}],"type":"journal_article","date_published":"2020-12-09T00:00:00Z","page":"9634-9649","article_type":"original","citation":{"short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:10.1523/JNEUROSCI.0276-20.2020.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” The Journal of Neuroscience. Society for Neuroscience, 2020. https://doi.org/10.1523/JNEUROSCI.0276-20.2020.","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 2020;40(50):9634-9649. doi:10.1523/JNEUROSCI.0276-20.2020","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” The Journal of Neuroscience, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","apa":"Agnes, E. J., Luppi, A. I., & Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0276-20.2020","ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649."},"publication":"The Journal of Neuroscience","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","volume":40,"date_updated":"2023-08-22T07:54:26Z","date_created":"2020-07-16T12:25:04Z","author":[{"full_name":"Agnes, Everton J.","last_name":"Agnes","first_name":"Everton J.","orcid":"0000-0001-7184-7311"},{"full_name":"Luppi, Andrea I.","last_name":"Luppi","first_name":"Andrea I."},{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels"}],"publisher":"Society for Neuroscience","department":[{"_id":"TiVo"}],"publication_status":"published","pmid":1,"year":"2020","file_date_updated":"2020-12-28T08:31:47Z","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0276-20.2020","isi":1,"quality_controlled":"1","external_id":{"pmid":["33168622"],"isi":["000606706400009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1529-2401"]},"month":"12"},{"other_data_license":"CC0 + CC BY (4.0)","month":"07","day":"09","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.12629697.v1"}],"oa":1,"citation":{"mla":"Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020).","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1","ista":"Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.","ieee":"R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1"},"doi":"10.6084/m9.figshare.12629697.v1","date_published":"2020-07-09T00:00:00Z","type":"research_data_reference","abstract":[{"text":"Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).","lang":"eng"}],"status":"public","title":"Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","_id":"9706","year":"2020","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-07-23T08:59:15Z","date_updated":"2023-08-22T07:55:36Z","oa_version":"Published Version","author":[{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos","first_name":"Daniel"},{"full_name":"Kousathanas, Athanasios","first_name":"Athanasios","last_name":"Kousathanas"},{"full_name":"McCartney, Daniel L.","last_name":"McCartney","first_name":"Daniel L."},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"last_name":"Stevenson","first_name":"Anna J.","full_name":"Stevenson, Anna J."},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"full_name":"Ojavee, Sven Erik","first_name":"Sven Erik","last_name":"Ojavee"},{"first_name":"Qian","last_name":"Zhang","full_name":"Zhang, Qian"},{"full_name":"Liewald, David C.","last_name":"Liewald","first_name":"David C."},{"full_name":"Ritchie, Craig W.","last_name":"Ritchie","first_name":"Craig W."},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"last_name":"Tucker-Drob","first_name":"Elliot M.","full_name":"Tucker-Drob, Elliot M."},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."},{"full_name":"McRae, Allan F. ","first_name":"Allan F. ","last_name":"McRae"},{"first_name":"Peter M.","last_name":"Visscher","full_name":"Visscher, Peter M."},{"full_name":"Deary, Ian J.","first_name":"Ian J.","last_name":"Deary"},{"full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard"},{"full_name":"Marioni, Riccardo E. ","first_name":"Riccardo E. ","last_name":"Marioni"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8133"}]}},{"year":"2020","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"first_name":"Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"volume":61,"date_created":"2020-07-19T22:00:59Z","date_updated":"2023-08-22T08:12:40Z","article_number":"061901","ec_funded":1,"external_id":{"arxiv":["2002.08281"],"isi":["000544595100001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"quality_controlled":"1","isi":1,"doi":"10.1063/5.0005950","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00222488"]},"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8134","intvolume":" 61","status":"public","title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.","lang":"eng"}],"citation":{"chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005950.","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” Journal of Mathematical Physics, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:10.1063/5.0005950.","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” Journal of Mathematical Physics, vol. 61, no. 6. AIP Publishing, 2020.","apa":"Mayer, S., & Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0005950","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 2020;61(6). doi:10.1063/5.0005950"},"publication":"Journal of Mathematical Physics","article_type":"original","date_published":"2020-06-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22"},{"month":"09","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2020.06.031","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000579698700006"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-12-02T09:26:46Z","ec_funded":1,"author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","first_name":"Susanne","last_name":"Laukoter","full_name":"Laukoter, Susanne"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Beattie, Robert J","first_name":"Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753"},{"last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H"},{"first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Penz, Thomas","last_name":"Penz","first_name":"Thomas"},{"full_name":"Bock, Christoph","orcid":"0000-0001-6091-3088","first_name":"Christoph","last_name":"Bock"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/"}]},"date_updated":"2023-08-22T08:20:11Z","date_created":"2020-07-23T16:03:12Z","volume":107,"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","year":"2020","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","day":"23","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-09-23T00:00:00Z","publication":"Neuron","citation":{"ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 2020;107(6):1160-1179.e9. doi:10.1016/j.neuron.2020.06.031","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","ieee":"S. Laukoter et al., “Cell-type specificity of genomic imprinting in cerebral cortex,” Neuron, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.06.031","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:10.1016/j.neuron.2020.06.031.","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.06.031."},"article_type":"original","page":"1160-1179.e9","abstract":[{"lang":"eng","text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity."}],"issue":"6","type":"journal_article","file":[{"content_type":"application/pdf","file_size":8911830,"creator":"dernst","file_name":"2020_Neuron_Laukoter.pdf","access_level":"open_access","date_updated":"2020-12-02T09:26:46Z","date_created":"2020-12-02T09:26:46Z","checksum":"7becdc16a6317304304631087ae7dd7f","success":1,"relation":"main_file","file_id":"8828"}],"oa_version":"Published Version","_id":"8162","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Cell-type specificity of genomic imprinting in cerebral cortex","intvolume":" 107"},{"article_type":"original","page":"3508","publication":"Nature Communications","citation":{"short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:10.1038/s41467-020-17252-y.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17252-y.","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 2020;11(1):3508. doi:10.1038/s41467-020-17252-y","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17252-y","ieee":"J. Zhang et al., “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” Nature Communications, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508."},"date_published":"2020-07-14T00:00:00Z","scopus_import":"1","day":"14","has_accepted_license":"1","article_processing_charge":"No","ddc":["580"],"status":"public","title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8138","file":[{"access_level":"open_access","file_name":"2020_NatureComm_Zhang.pdf","file_size":1759490,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8148","success":1,"date_updated":"2020-07-22T08:32:55Z","date_created":"2020-07-22T08:32:55Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration."}],"issue":"1","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32665554"],"isi":["000550062200004"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17252-y","month":"07","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","year":"2020","pmid":1,"date_updated":"2023-08-22T08:13:44Z","date_created":"2020-07-21T08:58:07Z","volume":11,"author":[{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"full_name":"Mazur, E","first_name":"E","last_name":"Mazur"},{"last_name":"Balla","first_name":"J","full_name":"Balla, J"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kalousek","first_name":"P","full_name":"Kalousek, P"},{"first_name":"Z","last_name":"Medveďová","full_name":"Medveďová, Z"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"full_name":"Wang, Y","last_name":"Wang","first_name":"Y"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"},{"full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reinöhl, V","first_name":"V","last_name":"Reinöhl"},{"last_name":"Procházka","first_name":"S","full_name":"Procházka, S"},{"full_name":"Halouzka, R","last_name":"Halouzka","first_name":"R"},{"first_name":"P","last_name":"Tarkowski","full_name":"Tarkowski, P"},{"full_name":"Luschnig, C","first_name":"C","last_name":"Luschnig"},{"last_name":"Brewer","first_name":"PB","full_name":"Brewer, PB"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"}]},"file_date_updated":"2020-07-22T08:32:55Z","ec_funded":1},{"article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2020-07-12T00:00:00Z","article_type":"original","citation":{"ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528."},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","issue":"1806","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 375","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8168","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0528","project":[{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0528","open_access":"1"}],"oa":1,"ec_funded":1,"article_number":"20190528","volume":375,"date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:21:31Z","author":[{"full_name":"Kulmuni, Jonna","first_name":"Jonna","last_name":"Kulmuni"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Kay","last_name":"Lucek","full_name":"Lucek, Kay"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"year":"2020"},{"article_number":"20190545","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","year":"2020","volume":375,"date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:22:13Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Eyres, Isobel","first_name":"Isobel","last_name":"Eyres"},{"full_name":"Broquet, Thomas","last_name":"Broquet","first_name":"Thomas"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"publication_identifier":{"eissn":["1471-2970"]},"month":"07","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0545"}],"oa":1,"external_id":{"pmid":["32654639"],"isi":["000552662100014"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0545","type":"journal_article","issue":"1806","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"intvolume":" 375","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8167","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"12","article_type":"original","citation":{"ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545."},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","date_published":"2020-07-12T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.125.013001","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["2006.02694"],"isi":["000544526900006"]},"main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}],"month":"07","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"date_updated":"2023-08-22T08:22:43Z","date_created":"2020-07-26T22:01:02Z","volume":125,"author":[{"first_name":"Adam S.","last_name":"Chatterley","full_name":"Chatterley, Adam S."},{"first_name":"Lars","last_name":"Christiansen","full_name":"Christiansen, Lars"},{"full_name":"Schouder, Constant A.","first_name":"Constant A.","last_name":"Schouder"},{"full_name":"Jørgensen, Anders V.","first_name":"Anders V.","last_name":"Jørgensen"},{"full_name":"Shepperson, Benjamin","last_name":"Shepperson","first_name":"Benjamin"},{"full_name":"Cherepanov, Igor","last_name":"Cherepanov","first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo"},{"full_name":"Zillich, Robert E.","last_name":"Zillich","first_name":"Robert E."},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","year":"2020","ec_funded":1,"article_number":"013001","date_published":"2020-07-03T00:00:00Z","article_type":"original","publication":"Physical Review Letters","citation":{"ieee":"A. S. Chatterley et al., “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” Physical Review Letters, vol. 125, no. 1. American Physical Society, 2020.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.013001","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 2020;125(1). doi:10.1103/PhysRevLett.125.013001","chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.013001.","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” Physical Review Letters, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.013001."},"day":"03","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","status":"public","intvolume":" 125","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8170","abstract":[{"lang":"eng","text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes."}],"issue":"1","type":"journal_article"},{"author":[{"full_name":"Baranowski, Marek","first_name":"Marek","last_name":"Baranowski"},{"full_name":"He, Shaobo","last_name":"He","first_name":"Shaobo"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Nguyen, Thanh Son","last_name":"Nguyen","first_name":"Thanh Son"},{"first_name":"Zvonimir","last_name":"Rakamarić","full_name":"Rakamarić, Zvonimir"}],"volume":12166,"date_created":"2020-08-02T22:00:59Z","date_updated":"2023-08-22T08:27:25Z","year":"2020","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["03029743"],"isbn":["9783030510732"],"eissn":["16113349"]},"month":"06","doi":"10.1007/978-3-030-51074-9_2","conference":{"name":"IJCAR: International Joint Conference on Automated Reasoning","start_date":"2020-07-01","location":"Paris, France","end_date":"2020-07-04"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"external_id":{"isi":["000884318000002"]},"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Published Version","_id":"8194","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12166","status":"public","title":"An SMT theory of fixed-point arithmetic","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2020-06-24T00:00:00Z","citation":{"ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: Automated Reasoning. Vol 12166. Springer Nature; 2020:13-31. doi:10.1007/978-3-030-51074-9_2","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in Automated Reasoning, Paris, France, 2020, vol. 12166, pp. 13–31.","apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., & Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In Automated Reasoning (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-030-51074-9_2","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” Automated Reasoning, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:10.1007/978-3-030-51074-9_2.","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In Automated Reasoning, 12166:13–31. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-51074-9_2."},"publication":"Automated Reasoning","page":"13-31"},{"oa_version":"Published Version","file":[{"file_name":"2020_PNAS_Corominas.pdf","access_level":"open_access","file_size":1111604,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8223","date_created":"2020-08-10T06:50:28Z","date_updated":"2020-08-10T06:50:28Z","success":1}],"_id":"8220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Stem cell lineage survival as a noisy competition for niche access","ddc":["570"],"status":"public","intvolume":" 117","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"issue":"29","type":"journal_article","date_published":"2020-07-21T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117."},"article_type":"original","page":"16969-16975","day":"21","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."},{"full_name":"Kishi, Kasumi","last_name":"Kishi","first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ellenbroek, Saskia I.J.","last_name":"Ellenbroek","first_name":"Saskia I.J."},{"full_name":"Simons, Benjamin D.","last_name":"Simons","first_name":"Benjamin D."},{"last_name":"Van Rheenen","first_name":"Jacco","full_name":"Van Rheenen, Jacco"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"date_updated":"2023-08-22T08:29:30Z","date_created":"2020-08-09T22:00:52Z","volume":117,"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"National Academy of Sciences","file_date_updated":"2020-08-10T06:50:28Z","ec_funded":1,"doi":"10.1073/pnas.1921205117","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"quality_controlled":"1","isi":1,"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"month":"07","publication_identifier":{"eissn":["10916490"]}},{"article_type":"original","citation":{"ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 2020;9. doi:10.21468/scipostphys.9.1.015","apa":"Gulden, T., Berg, E., Rudner, M. S., & Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.9.1.015","ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” SciPost Physics, vol. 9. SciPost Foundation, 2020.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015.","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics, vol. 9, 015, SciPost Foundation, 2020, doi:10.21468/scipostphys.9.1.015.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” SciPost Physics. SciPost Foundation, 2020. https://doi.org/10.21468/scipostphys.9.1.015."},"publication":"SciPost Physics","date_published":"2020-07-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"29","intvolume":" 9","status":"public","ddc":["530"],"title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8199","oa_version":"Published Version","file":[{"file_id":"8202","relation":"main_file","date_updated":"2020-08-06T08:56:06Z","date_created":"2020-08-06T08:56:06Z","success":1,"file_name":"2020_SciPostPhys_Gulden.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":531137}],"type":"journal_article","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000557362300008"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.9.1.015","publication_identifier":{"issn":["2542-4653"]},"month":"07","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","year":"2020","volume":9,"date_created":"2020-08-04T13:04:15Z","date_updated":"2023-08-22T08:28:24Z","author":[{"orcid":"0000-0001-6814-7541","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden","first_name":"Tobias","full_name":"Gulden, Tobias"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"first_name":"Mark Spencer","last_name":"Rudner","full_name":"Rudner, Mark Spencer"},{"full_name":"Lindner, Netanel","first_name":"Netanel","last_name":"Lindner"}],"article_number":"015","ec_funded":1,"file_date_updated":"2020-08-06T08:56:06Z"},{"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000579698700009"],"pmid":["32763145"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2020.07.006","publication_identifier":{"issn":["0896-6273"]},"month":"09","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","year":"2020","volume":107,"date_created":"2020-08-14T09:36:05Z","date_updated":"2023-08-22T08:30:55Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","relation":"press_release","description":"News on IST Website"}]},"author":[{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"ec_funded":1,"file_date_updated":"2020-12-04T09:29:21Z","page":"1212-1225","article_type":"original","citation":{"apa":"Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” Neuron, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225. doi:10.1016/j.neuron.2020.07.006","chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006."},"publication":"Neuron","date_published":"2020-09-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23","intvolume":" 107","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","ddc":["570"],"status":"public","_id":"8261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"8920","relation":"main_file","date_created":"2020-12-04T09:29:21Z","date_updated":"2020-12-04T09:29:21Z","success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc","file_name":"2020_Neuron_Zhang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3011120}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion."}]},{"month":"07","publication_identifier":{"eissn":["19410476"],"issn":["1053587X"]},"language":[{"iso":"eng"}],"doi":"10.1109/TSP.2020.3010355","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"oa":1,"external_id":{"isi":["000562044500001"],"arxiv":["1802.04907"]},"date_created":"2020-08-16T22:00:56Z","date_updated":"2023-08-22T08:40:08Z","volume":68,"author":[{"full_name":"Gurel, Nezihe Merve","first_name":"Nezihe Merve","last_name":"Gurel"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"full_name":"Stojanov, Alen","first_name":"Alen","last_name":"Stojanov"},{"first_name":"Tyler","last_name":"Smith","full_name":"Smith, Tyler"},{"full_name":"Lemmin, Thomas","last_name":"Lemmin","first_name":"Thomas"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Puschel","first_name":"Markus","full_name":"Puschel, Markus"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"publication_status":"published","publisher":"IEEE","department":[{"_id":"DaAl"}],"year":"2020","acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-20T00:00:00Z","article_type":"original","page":"4268-4282","publication":"IEEE Transactions on Signal Processing","citation":{"chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing. IEEE, 2020. https://doi.org/10.1109/TSP.2020.3010355.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” IEEE Transactions on Signal Processing, vol. 68, IEEE, 2020, pp. 4268–82, doi:10.1109/TSP.2020.3010355.","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","ieee":"N. M. Gurel et al., “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” IEEE Transactions on Signal Processing, vol. 68. IEEE, pp. 4268–4282, 2020.","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2020.3010355","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 2020;68:4268-4282. doi:10.1109/TSP.2020.3010355"},"abstract":[{"lang":"eng","text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality."}],"type":"journal_article","oa_version":"Preprint","status":"public","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","intvolume":" 68","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8268"},{"file_date_updated":"2020-08-17T15:54:20Z","ec_funded":1,"article_number":"082602","date_created":"2020-07-07T11:33:54Z","date_updated":"2023-08-22T08:41:32Z","volume":4,"author":[{"last_name":"Grosjean","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","full_name":"Grosjean, Galien M"},{"full_name":"Wald, Sebastian","last_name":"Wald","first_name":"Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425"},{"last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","full_name":"Sobarzo Ponce, Juan Carlos A"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"}],"related_material":{"record":[{"id":"12697","relation":"popular_science","status":"public"}]},"publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","year":"2020","acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","month":"08","publication_identifier":{"issn":["2475-9953"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevMaterials.4.082602","isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2006.07120"],"isi":["000561897000001"]},"abstract":[{"lang":"eng","text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature."}],"issue":"8","type":"journal_article","file":[{"file_name":"Grosjean2020.pdf","access_level":"open_access","file_size":853753,"content_type":"application/pdf","creator":"ggrosjea","relation":"main_file","file_id":"8277","date_created":"2020-08-17T15:54:20Z","date_updated":"2020-08-17T15:54:20Z","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","success":1}],"oa_version":"Published Version","status":"public","title":"Quantitatively consistent scale-spanning model for same-material tribocharging","ddc":["530"],"intvolume":" 4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8101","day":"17","has_accepted_license":"1","article_processing_charge":"Yes","keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"scopus_import":"1","date_published":"2020-08-17T00:00:00Z","article_type":"original","publication":"Physical Review Materials","citation":{"short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:10.1103/PhysRevMaterials.4.082602.","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” Physical Review Materials. American Physical Society, 2020. https://doi.org/10.1103/PhysRevMaterials.4.082602.","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 2020;4(8). doi:10.1103/PhysRevMaterials.4.082602","ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” Physical Review Materials, vol. 4, no. 8. American Physical Society, 2020.","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., & Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.4.082602","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602."}},{"date_published":"2020-09-01T00:00:00Z","page":"1649-1675","article_type":"original","citation":{"chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8"},"publication":"Communications in Mathematical Physics","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 378","title":"Sandpile solitons via smoothing of superharmonic functions","status":"public","_id":"8325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","abstract":[{"text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. ","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00220-020-03828-8","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"external_id":{"isi":["000560620600001"],"arxiv":["1711.04285"]},"oa":1,"publication_identifier":{"issn":["00103616"],"eissn":["14320916"]},"month":"09","volume":378,"date_created":"2020-08-30T22:01:13Z","date_updated":"2023-08-22T09:00:03Z","author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"TaHa"}],"publisher":"Springer Nature","publication_status":"published","year":"2020","acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","ec_funded":1},{"scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020)."},"article_type":"original","date_published":"2020-08-18T00:00:00Z","type":"journal_article","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8318","title":"Key role of quinone in the mechanism of respiratory complex I","ddc":["570"],"status":"public","intvolume":" 11","file":[{"relation":"main_file","file_id":"8326","checksum":"52b96f41d7d0db9728064c08da00d030","success":1,"date_updated":"2020-08-31T13:40:00Z","date_created":"2020-08-31T13:40:00Z","access_level":"open_access","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","file_size":7527373,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","month":"08","publication_identifier":{"eissn":["20411723"]},"external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-020-17957-0","language":[{"iso":"eng"}],"article_number":"4135","file_date_updated":"2020-08-31T13:40:00Z","year":"2020","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","author":[{"full_name":"Gutierrez-Fernandez, Javier","first_name":"Javier","last_name":"Gutierrez-Fernandez","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","full_name":"Kaszuba, Karol"},{"last_name":"Minhas","first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S."},{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh"},{"full_name":"Tambalo, Margherita","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita"},{"full_name":"Gallagher, David T.","last_name":"Gallagher","first_name":"David T."},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release","description":"News on IST Homepage"}]},"date_updated":"2023-08-22T09:03:00Z","date_created":"2020-08-30T22:01:10Z","volume":11},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020."},"publication":"Discrete and Computational Geometry","page":"571-574","article_type":"letter_note","type":"journal_article","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8323","intvolume":" 64","title":"A farewell to Ricky Pollack","status":"public","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"10","doi":"10.1007/s00454-020-00237-5","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"oa":1,"external_id":{"isi":["000561483500001"]},"isi":1,"author":[{"full_name":"Pach, János","first_name":"János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"volume":64,"date_created":"2020-08-30T22:01:12Z","date_updated":"2023-08-22T09:05:04Z","year":"2020","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published"},{"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis."},{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1038/s41467-020-17949-0","publication_identifier":{"eissn":["20411723"]},"month":"08","department":[{"_id":"EvBe"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","year":"2020","volume":11,"date_updated":"2023-08-22T09:09:06Z","date_created":"2020-09-06T22:01:12Z","author":[{"first_name":"Karolina","last_name":"Kubiasova","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","orcid":"0000-0001-5630-9419","full_name":"Kubiasova, Karolina"},{"full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C"},{"full_name":"Šamajová, Olga","last_name":"Šamajová","first_name":"Olga"},{"first_name":"Jaroslav","last_name":"Nisler","full_name":"Nisler, Jaroslav"},{"full_name":"Mik, Václav","first_name":"Václav","last_name":"Mik"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Marhavý, Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavý","first_name":"Peter"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"last_name":"Zalabák","first_name":"David","full_name":"Zalabák, David"},{"first_name":"Karel","last_name":"Berka","full_name":"Berka, Karel"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"first_name":"Petr","last_name":"Galuszka","full_name":"Galuszka, Petr"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"full_name":"Spíchal, Lukáš","first_name":"Lukáš","last_name":"Spíchal"}],"article_number":"4285","ec_funded":1,"file_date_updated":"2020-09-10T08:05:19Z","article_type":"original","citation":{"ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0."},"publication":"Nature Communications","date_published":"2020-08-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","intvolume":" 11","status":"public","ddc":["580"],"title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8336","file":[{"file_name":"2020_NatureComm_Kubiasova.pdf","access_level":"open_access","file_size":3455704,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8357","date_created":"2020-09-10T08:05:19Z","date_updated":"2020-09-10T08:05:19Z","checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","success":1}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER."}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses."}],"status":"public","title":"Cell-surface receptors enable perception of extracellular cytokinins","ddc":["580"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8337","oa_version":"Published Version","file":[{"checksum":"5b96f39b598de7510cfefefb819b9a6d","success":1,"date_created":"2020-12-10T12:23:56Z","date_updated":"2020-12-10T12:23:56Z","relation":"main_file","file_id":"8936","file_size":3526415,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_NatureComm_Antoniadi.pdf"}],"scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Nature Communications","citation":{"ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9.","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9."},"date_published":"2020-08-27T00:00:00Z","article_number":"4284","file_date_updated":"2020-12-10T12:23:56Z","ec_funded":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","year":"2020","acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","date_updated":"2023-08-22T09:10:32Z","date_created":"2020-09-06T22:01:13Z","volume":11,"author":[{"full_name":"Antoniadi, Ioanna","first_name":"Ioanna","last_name":"Antoniadi"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová","full_name":"Gelová, Zuzana"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"last_name":"Plíhal","first_name":"Ondřej","full_name":"Plíhal, Ondřej"},{"last_name":"Simerský","first_name":"Radim","full_name":"Simerský, Radim"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"last_name":"Vain","first_name":"Thomas","full_name":"Vain, Thomas"},{"last_name":"Mateo-Bonmatí","first_name":"Eduardo","full_name":"Mateo-Bonmatí, Eduardo"},{"last_name":"Karady","first_name":"Michal","full_name":"Karady, Michal"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"full_name":"Plačková, Lenka","last_name":"Plačková","first_name":"Lenka"},{"last_name":"Opassathian","first_name":"Korawit","full_name":"Opassathian, Korawit"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Doležal, Karel","last_name":"Doležal","first_name":"Karel"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"last_name":"Turnbull","first_name":"Colin","full_name":"Turnbull, Colin"}],"month":"08","publication_identifier":{"eissn":["20411723"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000567931000001"]},"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-17700-9"},{"month":"07","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:ISTA:8067","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:48:08Z","author":[{"last_name":"Varzi","first_name":"Alberto","full_name":"Varzi, Alberto"},{"full_name":"Thanner, Katharina","last_name":"Thanner","first_name":"Katharina"},{"last_name":"Scipioni","first_name":"Roberto","full_name":"Scipioni, Roberto"},{"last_name":"Di Lecce","first_name":"Daniele","full_name":"Di Lecce, Daniele"},{"first_name":"Jusef","last_name":"Hassoun","full_name":"Hassoun, Jusef"},{"full_name":"Dörfler, Susanne","last_name":"Dörfler","first_name":"Susanne"},{"full_name":"Altheus, Holger","last_name":"Altheus","first_name":"Holger"},{"first_name":"Stefan","last_name":"Kaskel","full_name":"Kaskel, Stefan"},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"related_material":{"record":[{"id":"8361","relation":"later_version","status":"public"}]},"date_created":"2020-06-30T07:37:39Z","date_updated":"2023-08-22T09:20:36Z","year":"2020","publication_status":"submitted","department":[{"_id":"StFr"}],"publisher":"IST Austria","day":"01","has_accepted_license":"1","article_processing_charge":"No","keyword":["Battery","Lithium metal","Lithium-sulphur","Lithium-air","All-solid-state"],"date_published":"2020-07-01T00:00:00Z","citation":{"ieee":"A. Varzi et al., Current status and future perspectives of Lithium metal batteries. IST Austria.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (n.d.). Current status and future perspectives of Lithium metal batteries. IST Austria. https://doi.org/10.15479/AT:ISTA:8067","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. Current status and future perspectives of Lithium metal batteries, IST Austria, 63p.","ama":"Varzi A, Thanner K, Scipioni R, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria doi:10.15479/AT:ISTA:8067","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, n.d. https://doi.org/10.15479/AT:ISTA:8067.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Current Status and Future Perspectives of Lithium Metal Batteries, IST Austria, n.d.","mla":"Varzi, Alberto, et al. Current Status and Future Perspectives of Lithium Metal Batteries. IST Austria, doi:10.15479/AT:ISTA:8067."},"page":"63","abstract":[{"text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the\r\nmid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.","lang":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file":[{"creator":"dernst","file_size":2612498,"content_type":"application/pdf","file_name":"20200612_JPS_review_Li_metal_submitted.pdf","access_level":"open_access","date_created":"2020-07-02T07:36:04Z","date_updated":"2020-07-14T12:48:08Z","checksum":"d183ca1465a1cbb4f8db27875cd156f7","file_id":"8076","relation":"main_file"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"8067","title":"Current status and future perspectives of Lithium metal batteries","status":"public","ddc":["540"]},{"day":"31","article_processing_charge":"No","publication":"Journal of Power Sources","citation":{"mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources, vol. 480, no. 12, 228803, Elsevier, 2020, doi:10.1016/j.jpowsour.2020.228803.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020).","chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” Journal of Power Sources. Elsevier, 2020. https://doi.org/10.1016/j.jpowsour.2020.228803.","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 2020;480(12). doi:10.1016/j.jpowsour.2020.228803","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803.","ieee":"A. Varzi et al., “Current status and future perspectives of lithium metal batteries,” Journal of Power Sources, vol. 480, no. 12. Elsevier, 2020.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2020.228803"},"article_type":"original","date_published":"2020-12-31T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"issue":"12","_id":"8361","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Current status and future perspectives of lithium metal batteries","status":"public","intvolume":" 480","oa_version":"Published Version","month":"12","publication_identifier":{"issn":["0378-7753"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.jpowsour.2020.228803","open_access":"1"}],"external_id":{"isi":["000593857300001"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.jpowsour.2020.228803","language":[{"iso":"eng"}],"article_number":"228803","acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of Ferrara (Department of Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at Dresden and would like to acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","year":"2020","publication_status":"published","department":[{"_id":"StFr"}],"publisher":"Elsevier","author":[{"full_name":"Varzi, Alberto","orcid":"0000-0001-5069-0589","first_name":"Alberto","last_name":"Varzi"},{"full_name":"Thanner, Katharina","orcid":"0000-0001-5394-2323","last_name":"Thanner","first_name":"Katharina"},{"last_name":"Scipioni","first_name":"Roberto","orcid":"0000-0003-1926-421X","full_name":"Scipioni, Roberto"},{"first_name":"Daniele","last_name":"Di Lecce","full_name":"Di Lecce, Daniele"},{"full_name":"Hassoun, Jusef","last_name":"Hassoun","first_name":"Jusef"},{"last_name":"Dörfler","first_name":"Susanne","full_name":"Dörfler, Susanne"},{"last_name":"Altheus","first_name":"Holger","full_name":"Altheus, Holger"},{"full_name":"Kaskel, Stefan","first_name":"Stefan","last_name":"Kaskel"},{"orcid":"0000-0003-0654-0940","first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"}],"related_material":{"record":[{"id":"8067","status":"public","relation":"earlier_version"}]},"date_updated":"2023-08-22T09:20:37Z","date_created":"2020-09-10T10:48:40Z","volume":480},{"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"day":"08","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Nature Communications","citation":{"ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 2020;11. doi:10.1038/s41467-020-18269-z","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18269-z","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications, vol. 11, 4460, Springer Nature, 2020, doi:10.1038/s41467-020-18269-z.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020).","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18269-z."},"date_published":"2020-09-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.","lang":"eng"}],"ddc":["530"],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","status":"public","intvolume":" 11","_id":"8529","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"8530","checksum":"88f92544889eb18bb38e25629a422a86","success":1,"date_updated":"2020-09-18T13:02:37Z","date_created":"2020-09-18T13:02:37Z","access_level":"open_access","file_name":"2020_NatureComm_Arnold.pdf","file_size":1002818,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","month":"09","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577280200001"]},"acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-18269-z","article_number":"4460","file_date_updated":"2020-09-18T13:02:37Z","ec_funded":1,"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","year":"2020","date_updated":"2023-08-22T09:27:12Z","date_created":"2020-09-18T10:56:20Z","volume":11,"author":[{"full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease"},{"orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/"}],"record":[{"id":"13056","status":"public","relation":"research_data"}]}},{"article_number":"65","ec_funded":1,"file_date_updated":"2020-09-21T07:51:44Z","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2020","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","volume":39,"date_updated":"2023-08-22T09:28:27Z","date_created":"2020-09-20T22:01:37Z","author":[{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"full_name":"Soderstrom, Andreas","first_name":"Andreas","last_name":"Soderstrom"},{"full_name":"Johansson, John","first_name":"John","last_name":"Johansson"},{"full_name":"Sprenger, Christoph","first_name":"Christoph","last_name":"Sprenger"},{"full_name":"Museth, Ken","last_name":"Museth","first_name":"Ken"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"month":"07","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000583700300038"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3386569.3392466","type":"journal_article","issue":"4","abstract":[{"text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.","lang":"eng"}],"intvolume":" 39","status":"public","ddc":["000"],"title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8535","oa_version":"Published Version","file":[{"checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","success":1,"date_created":"2020-09-21T07:51:44Z","date_updated":"2020-09-21T07:51:44Z","relation":"main_file","file_id":"8541","file_size":20223953,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_ACM_Skrivan.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"08","article_type":"original","citation":{"short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392466.","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392466.","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392466","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., & Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392466","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65."},"publication":"ACM Transactions on Graphics","date_published":"2020-07-08T00:00:00Z"},{"volume":53,"date_created":"2020-09-20T22:01:38Z","date_updated":"2023-08-22T09:27:57Z","author":[{"first_name":"C.","last_name":"Su","full_name":"Su, C."},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","last_name":"Zhao","full_name":"Zhao, Gufang"},{"last_name":"Zhong","first_name":"C.","full_name":"Zhong, C."}],"department":[{"_id":"TaHa"}],"publisher":"Société Mathématique de France","publication_status":"published","year":"2020","publication_identifier":{"issn":["0012-9593"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.24033/asens.2431","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"oa":1,"issue":"3","abstract":[{"text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.","lang":"eng"},{"lang":"fre","text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. "}],"type":"journal_article","oa_version":"Preprint","intvolume":" 53","status":"public","title":"On the K-theory stable bases of the springer resolution","_id":"8539","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-06-01T00:00:00Z","page":"663-671","article_type":"original","citation":{"ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","apa":"Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France. https://doi.org/10.24033/asens.2431","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Société Mathématique de France, 2020. https://doi.org/10.24033/asens.2431.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:10.24033/asens.2431.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671."},"publication":"Annales Scientifiques de l'Ecole Normale Superieure"},{"month":"07","day":"27","article_processing_charge":"No","date_published":"2020-07-27T00:00:00Z","doi":"10.5281/ZENODO.3961561","citation":{"short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020).","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3961562"}],"abstract":[{"text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"type":"research_data_reference","author":[{"full_name":"Arnold, Georg M","first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"last_name":"Wulf","first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"last_name":"Hease","first_name":"William J","orcid":"0000-0001-9868-2166","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"id":"8529","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-22T09:27:11Z","date_created":"2023-05-23T13:37:41Z","oa_version":"Published Version","_id":"13056","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","status":"public","publisher":"Zenodo","department":[{"_id":"JoFi"}]},{"file":[{"content_type":"application/pdf","file_size":4612258,"creator":"dernst","file_name":"2020_Membranes_Andrei.pdf","access_level":"open_access","date_created":"2020-09-28T11:36:50Z","date_updated":"2020-09-28T11:36:50Z","checksum":"ceb43d7554e712dea6f36f9287271737","success":1,"relation":"main_file","file_id":"8583"}],"oa_version":"Published Version","intvolume":" 10","ddc":["570"],"status":"public","title":"Cu homeostasis in bacteria: The ins and outs","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8579","issue":"9","abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"type":"journal_article","date_published":"2020-09-01T00:00:00Z","article_type":"original","citation":{"apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. Membranes. MDPI. https://doi.org/10.3390/membranes10090242","ieee":"A. Andrei et al., “Cu homeostasis in bacteria: The ins and outs,” Membranes, vol. 10, no. 9. MDPI, 2020.","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. Membranes. 2020;10(9). doi:10.3390/membranes10090242","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes. MDPI, 2020. https://doi.org/10.3390/membranes10090242.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” Membranes, vol. 10, no. 9, 242, MDPI, 2020, doi:10.3390/membranes10090242."},"publication":"Membranes","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","volume":10,"date_updated":"2023-08-22T09:34:06Z","date_created":"2020-09-28T08:59:26Z","author":[{"first_name":"Andreea","last_name":"Andrei","full_name":"Andrei, Andreea"},{"full_name":"Öztürk, Yavuz","last_name":"Öztürk","first_name":"Yavuz"},{"last_name":"Khalfaoui-Hassani","first_name":"Bahia","full_name":"Khalfaoui-Hassani, Bahia"},{"first_name":"Juna","last_name":"Rauch","full_name":"Rauch, Juna"},{"full_name":"Marckmann, Dorian","first_name":"Dorian","last_name":"Marckmann"},{"full_name":"Trasnea, Petru Iulian","id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Petru Iulian","last_name":"Trasnea"},{"first_name":"Fevzi","last_name":"Daldal","full_name":"Daldal, Fevzi"},{"last_name":"Koch","first_name":"Hans-Georg","full_name":"Koch, Hans-Georg"}],"department":[{"_id":"LeSa"}],"publisher":"MDPI","publication_status":"published","year":"2020","file_date_updated":"2020-09-28T11:36:50Z","article_number":"242","language":[{"iso":"eng"}],"doi":"10.3390/membranes10090242","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000581446000001"]},"publication_identifier":{"eissn":["20770375"]},"month":"09"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma."}],"issue":"21","_id":"8592","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting","intvolume":" 7","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_AdvScience_Tian.pdf","creator":"dernst","file_size":7835833,"content_type":"application/pdf","file_id":"8938","relation":"main_file","success":1,"checksum":"92818c23ecc70e35acfa671f3cfb9909","date_created":"2020-12-10T14:07:24Z","date_updated":"2020-12-10T14:07:24Z"}],"keyword":["General Engineering","General Physics and Astronomy","General Materials Science","Medicine (miscellaneous)","General Chemical Engineering","Biochemistry","Genetics and Molecular Biology (miscellaneous)"],"day":"04","has_accepted_license":"1","article_processing_charge":"No","publication":"Advanced Science","citation":{"ista":"Tian A, Kang B, Li B, Qiu B, Jiang W, Shao F, Gao Q, Liu R, Cai C, Jing R, Wang W, Chen P, Liang Q, Bao L, Man J, Wang Y, Shi Y, Li J, Yang M, Wang L, Zhang J, Hippenmeyer S, Zhu J, Bian X, Wang Y, Liu C. 2020. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 7(21), 2001724.","apa":"Tian, A., Kang, B., Li, B., Qiu, B., Jiang, W., Shao, F., … Liu, C. (2020). Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. Wiley. https://doi.org/10.1002/advs.202001724","ieee":"A. Tian et al., “Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting,” Advanced Science, vol. 7, no. 21. Wiley, 2020.","ama":"Tian A, Kang B, Li B, et al. Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting. Advanced Science. 2020;7(21). doi:10.1002/advs.202001724","chicago":"Tian, Anhao, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Fangjie Shao, Qingqing Gao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.202001724.","mla":"Tian, Anhao, et al. “Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R Targeting.” Advanced Science, vol. 7, no. 21, 2001724, Wiley, 2020, doi:10.1002/advs.202001724.","short":"A. Tian, B. Kang, B. Li, B. Qiu, W. Jiang, F. Shao, Q. Gao, R. Liu, C. Cai, R. Jing, W. Wang, P. Chen, Q. Liang, L. Bao, J. Man, Y. Wang, Y. Shi, J. Li, M. Yang, L. Wang, J. Zhang, S. Hippenmeyer, J. Zhu, X. Bian, Y. Wang, C. Liu, Advanced Science 7 (2020)."},"article_type":"original","date_published":"2020-11-04T00:00:00Z","article_number":"2001724","file_date_updated":"2020-12-10T14:07:24Z","ec_funded":1,"acknowledgement":"The authors thank Drs. J. Eisen, QR. Lu, S. Duan, Z‐H. Li, W. Mo, and Q. Wu for their critical comments on the manuscript. They also thank Dr. H. Zong for providing the CKO_NG2‐CreER model. This work is supported by the National Key Research and Development Program of China, Stem Cell and Translational Research (2016YFA0101201 to C.L., 2016YFA0100303 to Y.J.W.), the National Natural Science Foundation of China (81673035 and 81972915 to C.L., 81472722 to Y.J.W.), the Science Foundation for Distinguished Young Scientists of Zhejiang Province (LR17H160001 to C.L.), Fundamental Research Funds for the Central Universities (2016QNA7023 and 2017QNA7028 to C.L.) and the Thousand Talent Program for Young Outstanding Scientists, China (to C.L.), IST Austria institutional funds (to S.H.), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (725780 LinPro to S.H.). C.L. is a scholar of K. C. Wong Education Foundation.","year":"2020","publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Wiley","author":[{"full_name":"Tian, Anhao","last_name":"Tian","first_name":"Anhao"},{"full_name":"Kang, Bo","last_name":"Kang","first_name":"Bo"},{"full_name":"Li, Baizhou","first_name":"Baizhou","last_name":"Li"},{"first_name":"Biying","last_name":"Qiu","full_name":"Qiu, Biying"},{"last_name":"Jiang","first_name":"Wenhong","full_name":"Jiang, Wenhong"},{"first_name":"Fangjie","last_name":"Shao","full_name":"Shao, Fangjie"},{"full_name":"Gao, Qingqing","first_name":"Qingqing","last_name":"Gao"},{"full_name":"Liu, Rui","last_name":"Liu","first_name":"Rui"},{"full_name":"Cai, Chengwei","first_name":"Chengwei","last_name":"Cai"},{"full_name":"Jing, Rui","last_name":"Jing","first_name":"Rui"},{"full_name":"Wang, Wei","first_name":"Wei","last_name":"Wang"},{"last_name":"Chen","first_name":"Pengxiang","full_name":"Chen, Pengxiang"},{"full_name":"Liang, Qinghui","last_name":"Liang","first_name":"Qinghui"},{"full_name":"Bao, Lili","first_name":"Lili","last_name":"Bao"},{"full_name":"Man, Jianghong","last_name":"Man","first_name":"Jianghong"},{"full_name":"Wang, Yan","first_name":"Yan","last_name":"Wang"},{"full_name":"Shi, Yu","last_name":"Shi","first_name":"Yu"},{"full_name":"Li, Jin","first_name":"Jin","last_name":"Li"},{"full_name":"Yang, Minmin","first_name":"Minmin","last_name":"Yang"},{"last_name":"Wang","first_name":"Lisha","full_name":"Wang, Lisha"},{"last_name":"Zhang","first_name":"Jianmin","full_name":"Zhang, Jianmin"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Zhu, Junming","last_name":"Zhu","first_name":"Junming"},{"last_name":"Bian","first_name":"Xiuwu","full_name":"Bian, Xiuwu"},{"full_name":"Wang, Ying‐Jie","first_name":"Ying‐Jie","last_name":"Wang"},{"last_name":"Liu","first_name":"Chong","full_name":"Liu, Chong"}],"date_updated":"2023-08-22T09:53:01Z","date_created":"2020-10-01T09:44:13Z","volume":7,"month":"11","publication_identifier":{"issn":["2198-3844"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000573860700001"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1002/advs.202001724","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["2041-1723"]},"month":"09","external_id":{"isi":["000573756600004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-020-18610-6","language":[{"iso":"eng"}],"article_number":"4838","file_date_updated":"2020-09-28T13:16:15Z","year":"2020","department":[{"_id":"StFr"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"last_name":"Fitzek","first_name":"Harald","full_name":"Fitzek, Harald"},{"full_name":"Kothleitner, Gerald","first_name":"Gerald","last_name":"Kothleitner"},{"first_name":"Volker","last_name":"Presser","full_name":"Presser, Volker"},{"full_name":"Gollas, Bernhard","first_name":"Bernhard","last_name":"Gollas"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Abbas, Qamar","first_name":"Qamar","last_name":"Abbas"}],"volume":11,"date_created":"2020-09-25T07:23:13Z","date_updated":"2023-08-22T09:37:24Z","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","ieee":"C. Prehal et al., “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., & Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18610-6","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 2020;11. doi:10.1038/s41467-020-18610-6","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18610-6.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” Nature Communications, vol. 11, 4838, Springer Nature, 2020, doi:10.1038/s41467-020-18610-6.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020)."},"publication":"Nature Communications","article_type":"original","date_published":"2020-09-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8568","intvolume":" 11","status":"public","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","ddc":["530"],"file":[{"creator":"dernst","file_size":1822469,"content_type":"application/pdf","file_name":"2020_NatureComm_Prehal.pdf","access_level":"open_access","date_updated":"2020-09-28T13:16:15Z","date_created":"2020-09-28T13:16:15Z","success":1,"checksum":"eada7bc8dd16a49390137cff882ef328","file_id":"8585","relation":"main_file"}],"oa_version":"Published Version"},{"date_published":"2020-10-01T00:00:00Z","article_type":"original","citation":{"mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020."},"publication":"Scientific Reports","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2020_ScientificReport_Deichler.pdf","access_level":"open_access","file_size":3906744,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8651","date_created":"2020-10-12T12:39:10Z","date_updated":"2020-10-12T12:39:10Z","checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","success":1}],"intvolume":" 10","ddc":["570"],"status":"public","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8643","abstract":[{"text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41598-020-72848-0","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000577142600032"]},"oa":1,"publication_identifier":{"eissn":["20452322"]},"month":"10","volume":10,"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:58:21Z","author":[{"full_name":"Deichler, Alfonso","last_name":"Deichler","first_name":"Alfonso"},{"full_name":"Carrasco, Denisse","first_name":"Denisse","last_name":"Carrasco"},{"last_name":"Lopez-Jury","first_name":"Luciana","full_name":"Lopez-Jury, Luciana"},{"full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","last_name":"Vega Zuniga","first_name":"Tomas A"},{"full_name":"Marquez, Natalia","first_name":"Natalia","last_name":"Marquez"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"},{"full_name":"Marin, Gonzalo","last_name":"Marin","first_name":"Gonzalo"}],"publisher":"Springer Nature","department":[{"_id":"MaJö"}],"publication_status":"published","year":"2020","acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","file_date_updated":"2020-10-12T12:39:10Z","article_number":"16220"},{"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Oxford Academic","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","year":"2020","pmid":1,"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-08-22T09:57:29Z","volume":36,"author":[{"full_name":"Esteban, Laura A","first_name":"Laura A","last_name":"Esteban"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"last_name":"Leleytner","first_name":"Gregory","full_name":"Leleytner, Gregory"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"first_name":"Dmitry N ","last_name":"Ivankov","full_name":"Ivankov, Dmitry N "}],"file_date_updated":"2020-10-12T12:02:09Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btz841","month":"03","publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"status":"public","ddc":["000","570"],"title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","intvolume":" 36","_id":"8645","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"21d6f71839deb3b83e4a356193f72767","success":1,"date_updated":"2020-10-12T12:02:09Z","date_created":"2020-10-12T12:02:09Z","relation":"main_file","file_id":"8649","file_size":308341,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_Bioinformatics_Esteban.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data."}],"issue":"6","article_type":"original","page":"1960-1962","publication":"Bioinformatics","citation":{"ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841."},"date_published":"2020-03-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8597","intvolume":" 17","status":"public","ddc":["510","570"],"title":"Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide","oa_version":"Published Version","file":[{"checksum":"fec9bdd355ed349f09990faab20838a7","success":1,"date_updated":"2020-10-05T13:53:59Z","date_created":"2020-10-05T13:53:59Z","relation":"main_file","file_id":"8609","content_type":"application/pdf","file_size":1667111,"creator":"dernst","access_level":"open_access","file_name":"2020_PhysBio_Merrin.pdf"}],"type":"journal_article","issue":"6","abstract":[{"text":"Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.","lang":"eng"}],"citation":{"ama":"Merrin J. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 2020;17(6). doi:10.1088/1478-3975/abb2db","ieee":"J. Merrin, “Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide,” Physical Biology, vol. 17, no. 6. IOP Publishing, 2020.","apa":"Merrin, J. (2020). Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/abb2db","ista":"Merrin J. 2020. Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide. Physical Biology. 17(6), 065005.","short":"J. Merrin, Physical Biology 17 (2020).","mla":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology, vol. 17, no. 6, 065005, IOP Publishing, 2020, doi:10.1088/1478-3975/abb2db.","chicago":"Merrin, Jack. “Differences in Power Law Growth over Time and Indicators of COVID-19 Pandemic Progression Worldwide.” Physical Biology. IOP Publishing, 2020. https://doi.org/10.1088/1478-3975/abb2db."},"publication":"Physical Biology","article_type":"original","date_published":"2020-09-23T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"23","acknowledgement":"I would especially like to thank Michael Sixt for encouraging me to think about these problems while working at home due to restrictions in place. I want to thank Nick Barton, Katka Bodova, Matthew Robinson, Simon Rella, Federico Sau, Ivan Prieto, and Pradeep Kumar for useful discussions.","year":"2020","department":[{"_id":"NanoFab"}],"publisher":"IOP Publishing","publication_status":"published","author":[{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"}],"volume":17,"date_created":"2020-10-04T22:01:35Z","date_updated":"2023-08-22T09:53:29Z","article_number":"065005","file_date_updated":"2020-10-05T13:53:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000575539700001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1088/1478-3975/abb2db","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14783975"]},"month":"09"},{"pmid":1,"year":"2020","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","publisher":"Elsevier","department":[{"_id":"HaJa"}],"publication_status":"published","author":[{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"first_name":"Lucie","last_name":"Bard","full_name":"Bard, Lucie"},{"full_name":"Panatier, Aude","first_name":"Aude","last_name":"Panatier"},{"full_name":"Reynolds, James P.","first_name":"James P.","last_name":"Reynolds"},{"first_name":"Olga","last_name":"Kopach","full_name":"Kopach, Olga"},{"full_name":"Medvedev, Nikolay I.","last_name":"Medvedev","first_name":"Nikolay I."},{"full_name":"Minge, Daniel","last_name":"Minge","first_name":"Daniel"},{"full_name":"Herde, Michel K.","first_name":"Michel K.","last_name":"Herde"},{"full_name":"Anders, Stefanie","first_name":"Stefanie","last_name":"Anders"},{"full_name":"Kraev, Igor","last_name":"Kraev","first_name":"Igor"},{"first_name":"Janosch P.","last_name":"Heller","full_name":"Heller, Janosch P."},{"first_name":"Sylvain","last_name":"Rama","full_name":"Rama, Sylvain"},{"full_name":"Zheng, Kaiyu","last_name":"Zheng","first_name":"Kaiyu"},{"full_name":"Jensen, Thomas P.","last_name":"Jensen","first_name":"Thomas P."},{"full_name":"Sanchez-Romero, Inmaculada","last_name":"Sanchez-Romero","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Colin J.","last_name":"Jackson","full_name":"Jackson, Colin J."},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"},{"full_name":"Ottersen, Ole Petter","first_name":"Ole Petter","last_name":"Ottersen"},{"first_name":"Erlend Arnulf","last_name":"Nagelhus","full_name":"Nagelhus, Erlend Arnulf"},{"full_name":"Oliet, Stephane H.R.","last_name":"Oliet","first_name":"Stephane H.R."},{"full_name":"Stewart, Michael G.","last_name":"Stewart","first_name":"Michael G."},{"full_name":"Nägerl, U. VAlentin","last_name":"Nägerl","first_name":"U. VAlentin"},{"last_name":"Rusakov","first_name":"Dmitri A. ","full_name":"Rusakov, Dmitri A. "}],"volume":108,"date_created":"2020-10-18T22:01:38Z","date_updated":"2023-08-22T09:59:29Z","file_date_updated":"2020-12-10T14:42:09Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000603428000010"],"pmid":["32976770"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1016/j.neuron.2020.08.030","language":[{"iso":"eng"}],"publication_identifier":{"issn":["08966273"],"eissn":["10974199"]},"month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8674","intvolume":" 108","status":"public","title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","ddc":["570"],"file":[{"success":1,"checksum":"054562bb50165ef9a1f46631c1c5e36b","date_updated":"2020-12-10T14:42:09Z","date_created":"2020-12-10T14:42:09Z","file_id":"8939","relation":"main_file","creator":"dernst","file_size":7518960,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Neuron_Henneberger.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections."}],"citation":{"chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030.","mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11.","ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030"},"publication":"Neuron","page":"P919-936.E11","article_type":"original","date_published":"2020-12-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09"},{"publication_identifier":{"issn":["2399-3650"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1038/s42005-020-00445-8","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000581681000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"ec_funded":1,"file_date_updated":"2020-10-14T15:16:28Z","article_number":"178","volume":3,"date_updated":"2023-08-22T09:58:46Z","date_created":"2020-10-13T09:48:59Z","author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"publisher":"Springer Nature","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2020","acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","has_accepted_license":"1","article_processing_charge":"Yes","day":"09","scopus_import":"1","date_published":"2020-10-09T00:00:00Z","article_type":"original","citation":{"short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8.","ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178."},"publication":"Communications Physics","abstract":[{"text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_CommPhysics_Ghazaryan.pdf","content_type":"application/pdf","file_size":1462934,"creator":"dernst","relation":"main_file","file_id":"8662","checksum":"60cd35b99f0780acffc7b6060e49ec8b","success":1,"date_created":"2020-10-14T15:16:28Z","date_updated":"2020-10-14T15:16:28Z"}],"intvolume":" 3","status":"public","ddc":["530"],"title":"Filtering spins by scattering from a lattice of point magnets","_id":"8652","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_type":"original","publication":"Nature Communications","citation":{"ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3."},"date_published":"2020-10-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"title":"Tracing the cellular basis of islet specification in mouse pancreas","status":"public","intvolume":" 11","_id":"8669","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"date_created":"2020-10-19T11:27:46Z","date_updated":"2020-10-19T11:27:46Z","success":1,"checksum":"0ecc0eab72d2d50694852579611a6624","file_id":"8677","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5540540,"file_name":"2020_NatureComm_Sznurkowska.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development."}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-18837-3","month":"10","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","year":"2020","pmid":1,"date_created":"2020-10-18T22:01:35Z","date_updated":"2023-08-22T10:18:17Z","volume":11,"author":[{"full_name":"Sznurkowska, Magdalena K.","first_name":"Magdalena K.","last_name":"Sznurkowska"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Azzarelli","first_name":"Roberta","full_name":"Azzarelli, Roberta"},{"first_name":"Lemonia","last_name":"Chatzeli","full_name":"Chatzeli, Lemonia"},{"first_name":"Tatsuro","last_name":"Ikeda","full_name":"Ikeda, Tatsuro"},{"last_name":"Yoshida","first_name":"Shosei","full_name":"Yoshida, Shosei"},{"last_name":"Philpott","first_name":"Anna","full_name":"Philpott, Anna"},{"full_name":"Simons, Benjamin D","last_name":"Simons","first_name":"Benjamin D"}],"article_number":"5037","file_date_updated":"2020-10-19T11:27:46Z"},{"quality_controlled":"1","isi":1,"external_id":{"pmid":["32979313"],"isi":["000582501100012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2020.09.001","month":"10","publication_identifier":{"eissn":["18781551"],"issn":["15345807"]},"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Elsevier","year":"2020","acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","pmid":1,"date_created":"2020-10-18T22:01:37Z","date_updated":"2023-08-22T10:16:58Z","volume":55,"author":[{"last_name":"Chaigne","first_name":"Agathe","full_name":"Chaigne, Agathe"},{"last_name":"Labouesse","first_name":"Céline","full_name":"Labouesse, Céline"},{"full_name":"White, Ian J.","first_name":"Ian J.","last_name":"White"},{"first_name":"Meghan","last_name":"Agnew","full_name":"Agnew, Meghan"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Chalut, Kevin J.","last_name":"Chalut","first_name":"Kevin J."},{"first_name":"Ewa K.","last_name":"Paluch","full_name":"Paluch, Ewa K."}],"file_date_updated":"2021-02-04T10:20:02Z","article_type":"original","page":"195-208","publication":"Developmental Cell","citation":{"short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208."},"date_published":"2020-10-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"Abscission couples cell division to embryonic stem cell fate","intvolume":" 55","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8672","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_DevelopmCell_Chaigne.pdf","creator":"dernst","content_type":"application/pdf","file_size":6929686,"file_id":"9086","relation":"main_file","success":1,"checksum":"88e1a031a61689165d19a19c2f16d795","date_updated":"2021-02-04T10:20:02Z","date_created":"2021-02-04T10:20:02Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions."}],"issue":"2"},{"month":"11","publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"language":[{"iso":"eng"}],"doi":"10.1088/1361-6544/ab9728","quality_controlled":"1","isi":1,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1906.12245"],"isi":["000576492700001"]},"license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2020-10-27T12:09:57Z","date_updated":"2023-08-22T10:38:38Z","date_created":"2020-10-25T23:01:16Z","volume":33,"author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael"}],"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"IOP Publishing","year":"2020","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2020-11-01T00:00:00Z","article_type":"original","page":"5733-5772","publication":"Nonlinearity","citation":{"short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020.","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772."},"abstract":[{"lang":"eng","text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest."}],"issue":"11","type":"journal_article","file":[{"date_created":"2020-10-27T12:09:57Z","date_updated":"2020-10-27T12:09:57Z","checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","success":1,"relation":"main_file","file_id":"8710","content_type":"application/pdf","file_size":1223899,"creator":"cziletti","file_name":"2020_Nonlinearity_Fischer.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["510"],"title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","status":"public","intvolume":" 33","_id":"8697","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_type":"original","page":"113-116","publication":"Science","citation":{"ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637."},"date_published":"2020-10-02T00:00:00Z","keyword":["Multidisciplinary"],"scopus_import":"1","day":"02","article_processing_charge":"No","status":"public","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","intvolume":" 370","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8680","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.","lang":"eng"}],"issue":"6512","isi":1,"quality_controlled":"1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/803635v1","open_access":"1"}],"oa":1,"external_id":{"isi":["000579169000053"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aba6637","month":"10","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","year":"2020","date_created":"2020-10-19T14:09:38Z","date_updated":"2023-08-22T10:36:35Z","volume":370,"author":[{"first_name":"Tony Y.-C.","last_name":"Tsai","full_name":"Tsai, Tony Y.-C."},{"last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756","first_name":"Peng","last_name":"Xia"},{"first_name":"Tugba","last_name":"Colak-Champollion","full_name":"Colak-Champollion, Tugba"},{"full_name":"Knaut, Holger","last_name":"Knaut","first_name":"Holger"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Megason, Sean G.","first_name":"Sean G.","last_name":"Megason"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/sticking-together/"}]},"ec_funded":1},{"publication_identifier":{"issn":["00222488"]},"month":"10","doi":"10.1063/5.0022787","language":[{"iso":"eng"}],"external_id":{"arxiv":["2007.06644"],"isi":["000578529200001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06644"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"ec_funded":1,"article_number":"102201","author":[{"full_name":"Zhang, Haonan","last_name":"Zhang","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"volume":61,"date_created":"2020-10-18T22:01:36Z","date_updated":"2023-08-22T10:32:29Z","acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","year":"2020","department":[{"_id":"JaMa"}],"publisher":"AIP Publishing","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-10-01T00:00:00Z","citation":{"apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787."},"publication":"Journal of Mathematical Physics","article_type":"original","issue":"10","abstract":[{"text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"8670","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 61","status":"public","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies"},{"date_published":"2020-10-06T00:00:00Z","citation":{"apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"25066-25073","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","file":[{"date_updated":"2020-10-27T14:57:50Z","date_created":"2020-10-27T14:57:50Z","checksum":"c6a24fdecf3f28faf447078e7a274a88","success":1,"relation":"main_file","file_id":"8713","content_type":"application/pdf","file_size":1755359,"creator":"cziletti","file_name":"2020_PNAS_Maoz.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8698","intvolume":" 117","ddc":["570"],"status":"public","title":"Learning probabilistic neural representations with randomly connected circuits","issue":"40","abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"type":"journal_article","doi":"10.1073/pnas.1912804117","language":[{"iso":"eng"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000579045200012"],"pmid":["32948691"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"10","author":[{"last_name":"Maoz","first_name":"Ori","full_name":"Maoz, Ori"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"full_name":"Esteki, Mohamad Saleh","first_name":"Mohamad Saleh","last_name":"Esteki"},{"last_name":"Kiani","first_name":"Roozbeh","full_name":"Kiani, Roozbeh"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"}],"volume":117,"date_updated":"2023-08-22T12:11:23Z","date_created":"2020-10-25T23:01:16Z","pmid":1,"acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","year":"2020","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","publication_status":"published","file_date_updated":"2020-10-27T14:57:50Z"},{"publication_identifier":{"isbn":["9781728173955"],"issn":["10504729"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1109/ICRA40945.2020.9196608","conference":{"end_date":"2020-08-31","start_date":"2020-05-31","location":"Paris, France","name":"ICRA: International Conference on Robotics and Automation"},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000712319503110"]},"file_date_updated":"2020-11-06T10:58:49Z","date_updated":"2023-08-22T10:40:15Z","date_created":"2020-10-25T23:01:19Z","author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","year":"2020","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2020-05-01T00:00:00Z","page":"5446-5452","citation":{"apa":"Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452.","ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.","ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452.","mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608."},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","abstract":[{"text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.","lang":"eng"}],"alternative_title":["ICRA"],"type":"conference","file":[{"relation":"main_file","file_id":"8733","date_created":"2020-11-06T10:58:49Z","date_updated":"2020-11-06T10:58:49Z","checksum":"fccf7b986ac78046918a298cc6849a50","success":1,"file_name":"2020_ICRA_Lechner.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1070010,"creator":"dernst"}],"oa_version":"Submitted Version","status":"public","ddc":["000"],"title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8704"},{"language":[{"iso":"eng"}],"date_published":"2020-11-12T00:00:00Z","doi":"10.48550/arXiv.2011.06630","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"citation":{"apa":"Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630","ieee":"J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. .","ista":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630.","ama":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630","chicago":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630.","short":"J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.).","mla":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630."},"oa":1,"external_id":{"arxiv":["2011.06630"]},"publication":"arXiv","article_processing_charge":"No","day":"12","month":"11","oa_version":"Preprint","date_updated":"2023-08-22T11:03:00Z","date_created":"2023-08-21T10:10:41Z","author":[{"full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith","first_name":"Jamie A. P. Law-Smith"},{"full_name":"Everson, Rosa Wallace","first_name":"Rosa Wallace","last_name":"Everson"},{"last_name":"Enrico Ramirez-Ruiz","first_name":"Enrico Ramirez-Ruiz","full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz"},{"full_name":"Mink, Selma E. de","first_name":"Selma E. de","last_name":"Mink"},{"first_name":"Lieke A. C. van","last_name":"Son","full_name":"Son, Lieke A. C. van"},{"full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Zellmann, Stefan","last_name":"Zellmann","first_name":"Stefan"},{"full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez","first_name":"Alejandro Vigna-Gómez","last_name":"Alejandro Vigna-Gómez"},{"full_name":"Renzo, Mathieu","last_name":"Renzo","first_name":"Mathieu"},{"last_name":"Wu","first_name":"Samantha","full_name":"Wu, Samantha"},{"first_name":"Sophie L.","last_name":"Schrøder","full_name":"Schrøder, Sophie L."},{"last_name":"Foley","first_name":"Ryan J.","full_name":"Foley, Ryan J."},{"first_name":"Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith","full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith"}],"status":"public","title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","publication_status":"submitted","_id":"14096","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","abstract":[{"lang":"eng","text":"A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources."}],"type":"preprint","article_number":"2011.06630"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"06","page":"24764-24770","article_type":"original","citation":{"ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020.","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770.","mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_published":"2020-10-06T00:00:00Z","type":"journal_article","issue":"40","abstract":[{"text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling.","lang":"eng"}],"intvolume":" 117","ddc":["530"],"status":"public","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","_id":"8699","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"8715","date_updated":"2020-10-28T11:53:12Z","date_created":"2020-10-28T11:53:12Z","checksum":"1638fa36b442e2868576c6dd7d6dc505","success":1,"file_name":"2020_PNAS_Paris.pdf","access_level":"open_access","file_size":1176522,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"month":"10","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000579059100029"],"pmid":["32958669"],"arxiv":["2009.12262"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2012043117","ec_funded":1,"file_date_updated":"2020-10-28T11:53:12Z","department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","year":"2020","volume":117,"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T12:11:52Z","author":[{"full_name":"Paris, Eugenio","first_name":"Eugenio","last_name":"Paris"},{"full_name":"Tseng, Yi","first_name":"Yi","last_name":"Tseng"},{"full_name":"Paerschke, Ekaterina","orcid":"0000-0003-0853-8182","id":"8275014E-6063-11E9-9B7F-6338E6697425","last_name":"Paerschke","first_name":"Ekaterina"},{"full_name":"Zhang, Wenliang","last_name":"Zhang","first_name":"Wenliang"},{"full_name":"Upton, Mary H","last_name":"Upton","first_name":"Mary H"},{"first_name":"Anna","last_name":"Efimenko","full_name":"Efimenko, Anna"},{"full_name":"Rolfs, Katharina","first_name":"Katharina","last_name":"Rolfs"},{"full_name":"McNally, Daniel E","first_name":"Daniel E","last_name":"McNally"},{"full_name":"Maurel, Laura","first_name":"Laura","last_name":"Maurel"},{"first_name":"Muntaser","last_name":"Naamneh","full_name":"Naamneh, Muntaser"},{"full_name":"Caputo, Marco","last_name":"Caputo","first_name":"Marco"},{"full_name":"Strocov, Vladimir N","last_name":"Strocov","first_name":"Vladimir N"},{"last_name":"Wang","first_name":"Zhiming","full_name":"Wang, Zhiming"},{"first_name":"Diego","last_name":"Casa","full_name":"Casa, Diego"},{"first_name":"Christof W","last_name":"Schneider","full_name":"Schneider, Christof W"},{"last_name":"Pomjakushina","first_name":"Ekaterina","full_name":"Pomjakushina, Ekaterina"},{"last_name":"Wohlfeld","first_name":"Krzysztof","full_name":"Wohlfeld, Krzysztof"},{"first_name":"Milan","last_name":"Radovic","full_name":"Radovic, Milan"},{"last_name":"Schmitt","first_name":"Thorsten","full_name":"Schmitt, Thorsten"}]},{"publication_identifier":{"eissn":["10959203"]},"month":"10","external_id":{"isi":["000583031800004"],"pmid":["32972993"]},"oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","isi":1,"doi":"10.1126/science.abc4209","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_number":"eabc4209","ec_funded":1,"file_date_updated":"2020-11-26T18:47:58Z","pmid":1,"year":"2020","acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","department":[{"_id":"LeSa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"first_name":"Domen","last_name":"Kampjut","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"volume":370,"date_updated":"2023-08-22T12:35:38Z","date_created":"2020-11-08T23:01:23Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","citation":{"chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","apa":"Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209","ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209"},"publication":"Science","article_type":"original","date_published":"2020-10-30T00:00:00Z","type":"journal_article","issue":"6516","abstract":[{"lang":"eng","text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions."}],"_id":"8737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 370","title":"The coupling mechanism of mammalian respiratory complex I","ddc":["572"],"status":"public","file":[{"success":1,"checksum":"658ba90979ca9528a2efdfac8547047a","date_created":"2020-11-26T18:47:58Z","date_updated":"2020-11-26T18:47:58Z","file_id":"8820","relation":"main_file","creator":"lsazanov","file_size":7618987,"content_type":"application/pdf","access_level":"open_access","file_name":"Full_manuscript_with_SI_opt_red.pdf"}],"oa_version":"Submitted Version"},{"day":"01","article_processing_charge":"No","date_published":"2020-02-01T00:00:00Z","publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61.","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.","short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61.","chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528."},"page":"45-61","abstract":[{"text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"8722","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Taming unbalanced training workloads in deep learning with partial collective operations","month":"02","conference":{"end_date":"2020-02-26","start_date":"2020-02-22","location":"San Diego, CA, United States","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3332466.3374528","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.04207"}],"oa":1,"external_id":{"arxiv":["1908.04207"],"isi":["000564476500004"]},"quality_controlled":"1","isi":1,"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"ec_funded":1,"author":[{"full_name":"Li, Shigang","last_name":"Li","first_name":"Shigang"},{"first_name":"Tal Ben-Nun","last_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun"},{"first_name":"Salvatore Di","last_name":"Girolamo","full_name":"Girolamo, Salvatore Di"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Torsten","last_name":"Hoefler","full_name":"Hoefler, Torsten"}],"date_updated":"2023-08-22T12:13:48Z","date_created":"2020-11-05T15:25:30Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}]},{"doi":"10.1038/s41467-020-19372-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000592028600001"]},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"month":"11","author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"full_name":"Mao, Jiafei","last_name":"Mao","first_name":"Jiafei"},{"first_name":"Julian","last_name":"Reitz","full_name":"Reitz, Julian"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"first_name":"Denis","last_name":"Kudlinzki","full_name":"Kudlinzki, Denis"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"full_name":"Meier-Credo, Jakob","last_name":"Meier-Credo","first_name":"Jakob"},{"first_name":"Krishna","last_name":"Saxena","full_name":"Saxena, Krishna"},{"last_name":"Buhr","first_name":"Florian","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","first_name":"Julian D.","last_name":"Langer"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"first_name":"Achilleas S.","last_name":"Frangakis","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"first_name":"Harald","last_name":"Schwalbe","full_name":"Schwalbe, Harald"}],"volume":11,"date_created":"2020-11-09T07:49:36Z","date_updated":"2023-08-22T12:36:07Z","year":"2020","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"publication_status":"published","file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","date_published":"2020-11-04T00:00:00Z","citation":{"ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x.","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x."},"publication":"Nature Communications","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file":[{"file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1670898,"creator":"dernst","relation":"main_file","file_id":"8745","date_created":"2020-11-09T07:56:24Z","date_updated":"2020-11-09T07:56:24Z","checksum":"b2688f0347e69e6629bba582077278c5","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8744","intvolume":" 11","ddc":["570"],"status":"public","title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"type":"journal_article"},{"date_published":"2020-11-05T00:00:00Z","article_type":"original","citation":{"short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402."},"publication":"PLOS Computational Biology","article_processing_charge":"No","has_accepted_license":"1","day":"05","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"scopus_import":"1","file":[{"date_updated":"2020-11-18T07:26:10Z","date_created":"2020-11-18T07:26:10Z","success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","file_id":"8768","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2498594,"file_name":"2020_PlosCompBio_Kaveh.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 16","ddc":["000"],"title":"The Moran process on 2-chromatic graphs","status":"public","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","abstract":[{"text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1008402","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000591317200004"]},"oa":1,"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"month":"11","volume":16,"date_updated":"2023-08-22T12:49:18Z","date_created":"2020-11-18T07:20:23Z","author":[{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"full_name":"McAvoy, Alex","first_name":"Alex","last_name":"McAvoy"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","publication_status":"published","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2020","file_date_updated":"2020-11-18T07:26:10Z","article_number":"e1008402"},{"conference":{"name":"MEMOCODE: Conference on Formal Methods and Models for System Design","end_date":"2020-12-04","start_date":"2020-12-02","location":"Virtual Conference"},"doi":"10.1109/MEMOCODE51338.2020.9314994","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2006.12325","open_access":"1"}],"oa":1,"external_id":{"isi":["000661920400013"],"arxiv":["2006.12325"]},"quality_controlled":"1","isi":1,"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"12","publication_identifier":{"isbn":["9781728191485"]},"author":[{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Freire, Daniel","first_name":"Daniel","last_name":"Freire"},{"last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"}],"date_created":"2020-11-10T07:04:57Z","date_updated":"2023-08-22T12:48:18Z","year":"2020","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"ec_funded":1,"article_number":"9314994","date_published":"2020-12-04T00:00:00Z","publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","citation":{"ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994","ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020.","apa":"Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994.","chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994."},"day":"04","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8750","status":"public","title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","abstract":[{"lang":"eng","text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost."}],"type":"conference"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2004.02831"],"isi":["000587107200002"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF"}],"doi":"10.1007/s10955-020-02663-4","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"year":"2020","acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","author":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"},{"last_name":"Mielke","first_name":"Alexander","full_name":"Mielke, Alexander"}],"date_created":"2020-11-15T23:01:18Z","date_updated":"2023-08-22T13:24:27Z","volume":181,"file_date_updated":"2021-02-04T10:29:11Z","ec_funded":1,"publication":"Journal of Statistical Physics","citation":{"ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” Journal of Statistical Physics, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","apa":"Maas, J., & Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02663-4","ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303.","ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 2020;181(6):2257-2303. doi:10.1007/s10955-020-02663-4","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02663-4.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:10.1007/s10955-020-02663-4."},"article_type":"original","page":"2257-2303","date_published":"2020-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8758","ddc":["510"],"title":"Modeling of chemical reaction systems with detailed balance using gradient structures","status":"public","intvolume":" 181","oa_version":"Published Version","file":[{"checksum":"bc2b63a90197b97cbc73eccada4639f5","success":1,"date_created":"2021-02-04T10:29:11Z","date_updated":"2021-02-04T10:29:11Z","relation":"main_file","file_id":"9087","content_type":"application/pdf","file_size":753596,"creator":"dernst","access_level":"open_access","file_name":"2020_JourStatPhysics_Maas.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels."}],"issue":"6"},{"day":"27","month":"09","article_processing_charge":"No","date_published":"2020-09-27T00:00:00Z","doi":"10.5281/ZENODO.4052882","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"citation":{"apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882."},"abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"type":"research_data_reference","author":[{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni"},{"last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8755"}]},"date_updated":"2023-08-22T13:23:57Z","date_created":"2023-05-23T16:42:30Z","oa_version":"Published Version","_id":"13070","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Surpassing the resistance quantum with a geometric superinductor","status":"public","ddc":["530"],"publisher":"Zenodo","department":[{"_id":"JoFi"}]},{"month":"11","publication_identifier":{"eissn":["20411723"]},"quality_controlled":"1","isi":1,"project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33188196"],"isi":["000594648000014"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19515-0","article_number":"5778","file_date_updated":"2020-11-23T13:29:49Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","year":"2020","pmid":1,"date_created":"2020-11-22T23:01:23Z","date_updated":"2023-08-22T13:26:26Z","volume":11,"author":[{"first_name":"Leo","last_name":"Nicolai","full_name":"Nicolai, Leo"},{"last_name":"Schiefelbein","first_name":"Karin","full_name":"Schiefelbein, Karin"},{"full_name":"Lipsky, Silvia","last_name":"Lipsky","first_name":"Silvia"},{"full_name":"Leunig, Alexander","last_name":"Leunig","first_name":"Alexander"},{"full_name":"Hoffknecht, Marie","first_name":"Marie","last_name":"Hoffknecht"},{"full_name":"Pekayvaz, Kami","first_name":"Kami","last_name":"Pekayvaz"},{"full_name":"Raude, Ben","first_name":"Ben","last_name":"Raude"},{"last_name":"Marx","first_name":"Charlotte","full_name":"Marx, Charlotte"},{"last_name":"Ehrlich","first_name":"Andreas","full_name":"Ehrlich, Andreas"},{"full_name":"Pircher, Joachim","first_name":"Joachim","last_name":"Pircher"},{"first_name":"Zhe","last_name":"Zhang","full_name":"Zhang, Zhe"},{"full_name":"Saleh, Inas","first_name":"Inas","last_name":"Saleh"},{"last_name":"Marel","first_name":"Anna-Kristina","full_name":"Marel, Anna-Kristina"},{"last_name":"Löf","first_name":"Achim","full_name":"Löf, Achim"},{"full_name":"Petzold, Tobias","last_name":"Petzold","first_name":"Tobias"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"full_name":"Stark, Konstantin","first_name":"Konstantin","last_name":"Stark"},{"first_name":"Robert","last_name":"Pick","full_name":"Pick, Robert"},{"full_name":"Rosenberger, Gerhild","last_name":"Rosenberger","first_name":"Gerhild"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"full_name":"Uhl, Bernd","last_name":"Uhl","first_name":"Bernd"},{"full_name":"Xia, Sheng","last_name":"Xia","first_name":"Sheng"},{"full_name":"Reichel, Christoph Andreas","last_name":"Reichel","first_name":"Christoph Andreas"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"first_name":"Markus","last_name":"Bender","full_name":"Bender, Markus"},{"full_name":"Li, Rong","last_name":"Li","first_name":"Rong"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"},{"orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Nature Communications","citation":{"short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778."},"date_published":"2020-11-13T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"ddc":["570"],"status":"public","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8787","oa_version":"Published Version","file":[{"file_id":"8798","relation":"main_file","success":1,"checksum":"485b7b6cf30198ba0ce126491a28f125","date_created":"2020-11-23T13:29:49Z","date_updated":"2020-11-23T13:29:49Z","access_level":"open_access","file_name":"2020_NatureComm_Nicolai.pdf","creator":"dernst","file_size":7035340,"content_type":"application/pdf"}]},{"language":[{"iso":"eng"}],"doi":"10.3390/math8111945","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000593962100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["22277390"]},"month":"11","volume":8,"date_updated":"2023-08-22T13:25:45Z","date_created":"2020-11-22T23:01:24Z","author":[{"full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Kleshnina"},{"first_name":"Sabrina","last_name":"Streipert","full_name":"Streipert, Sabrina"},{"first_name":"Jerzy","last_name":"Filar","full_name":"Filar, Jerzy"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"publisher":"MDPI","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","year":"2020","ec_funded":1,"file_date_updated":"2020-11-23T13:06:30Z","article_number":"1945","date_published":"2020-11-04T00:00:00Z","article_type":"original","citation":{"ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.","apa":"Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. Mathematics. 2020;8(11). doi:10.3390/math8111945","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8111945.","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics, vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020)."},"publication":"Mathematics","has_accepted_license":"1","article_processing_charge":"No","day":"04","scopus_import":"1","file":[{"file_name":"2020_Mathematics_Kleshnina.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":565191,"file_id":"8797","relation":"main_file","date_updated":"2020-11-23T13:06:30Z","date_created":"2020-11-23T13:06:30Z","success":1,"checksum":"61cfcc3b35760656ce7a9385a4ace5d2"}],"oa_version":"Published Version","intvolume":" 8","status":"public","ddc":["000"],"title":"Prioritised learning in snowdrift-type games","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8789","issue":"11","abstract":[{"text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.","lang":"eng"}],"type":"journal_article"},{"abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"type":"conference","file":[{"file_size":696384,"content_type":"application/pdf","creator":"cschilli","access_level":"open_access","file_name":"2020EMSOFT.pdf","checksum":"d19e97d0f8a3a441dc078ec812297d75","success":1,"date_updated":"2020-08-24T12:53:15Z","date_created":"2020-08-24T12:53:15Z","relation":"main_file","file_id":"8288"}],"oa_version":"Preprint","status":"public","title":"Reachability analysis of linear hybrid systems via block decomposition","ddc":["000"],"_id":"8287","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","has_accepted_license":"1","keyword":["reachability","hybrid systems","decomposition"],"date_published":"2020-01-01T00:00:00Z","publication":"Proceedings of the International Conference on Embedded Software","citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020."},"file_date_updated":"2020-08-24T12:53:15Z","ec_funded":1,"date_updated":"2023-08-22T13:27:32Z","date_created":"2020-08-24T12:56:20Z","author":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","last_name":"Bogomolov"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"last_name":"Potomkin","first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"}],"related_material":{"record":[{"id":"8790","status":"public","relation":"later_version"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"year":"2020","language":[{"iso":"eng"}],"conference":{"end_date":"2020-09-25","start_date":"2020-09-20","location":"Virtual ","name":"EMSOFT: International Conference on Embedded Software"},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1905.02458"]},"oa":1},{"type":"journal_article","issue":"11","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"_id":"8790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 39","status":"public","title":"Reachability analysis of linear hybrid systems via block decomposition","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012859","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029."},"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","page":"4018-4029","article_type":"original","date_published":"2020-11-01T00:00:00Z","ec_funded":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","year":"2020","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"8287","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"}],"volume":39,"date_updated":"2023-08-22T13:27:33Z","date_created":"2020-11-22T23:01:25Z","publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"month":"11","external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.02458"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1109/TCAD.2020.3012859","language":[{"iso":"eng"}]}]