[{"quality_controlled":"1","date_created":"2023-02-15T14:46:14Z","citation":{"mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2023. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>.","apa":"Ladle, D. R., &#38; Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00172.2022\">https://doi.org/10.1152/jn.00172.2022</a>","short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” <i>Journal of Neurophysiology</i>, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. <i>Journal of Neurophysiology</i>. 2023;129(3):501-512. doi:<a href=\"https://doi.org/10.1152/jn.00172.2022\">10.1152/jn.00172.2022</a>"},"page":"501-512","title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","pmid":1,"acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","publication":"Journal of Neurophysiology","day":"01","volume":129,"date_published":"2023-03-01T00:00:00Z","intvolume":"       129","doi":"10.1152/jn.00172.2022","article_processing_charge":"No","publisher":"American Physiological Society","external_id":{"pmid":["36695533"],"isi":["000957721600001"]},"publication_status":"published","issue":"3","_id":"12562","type":"journal_article","oa_version":"None","year":"2023","month":"03","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"isi":1,"article_type":"original","department":[{"_id":"SiHi"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T12:13:34Z","keyword":["Physiology","General Neuroscience"],"abstract":[{"lang":"eng","text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons."}],"status":"public","author":[{"full_name":"Ladle, David R.","last_name":"Ladle","first_name":"David R."},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}]},{"oa":1,"quality_controlled":"1","arxiv":1,"date_created":"2023-02-16T07:03:52Z","citation":{"apa":"Krokhin, A., Opršal, J., Wrochna, M., &#38; Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>. Society for Industrial &#38; Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20m1378223\">https://doi.org/10.1137/20m1378223</a>.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” <i>SIAM Journal on Computing</i>, vol. 52, no. 1, Society for Industrial &#38; Applied Mathematics, 2023, pp. 38–79, doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. <i>SIAM Journal on Computing</i>. 2023;52(1):38-79. doi:<a href=\"https://doi.org/10.1137/20m1378223\">10.1137/20m1378223</a>","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” <i>SIAM Journal on Computing</i>, vol. 52, no. 1. Society for Industrial &#38; Applied Mathematics, pp. 38–79, 2023.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79."},"page":"38-79","title":"Topology and adjunction in promise constraint satisfaction","publication":"SIAM Journal on Computing","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","day":"01","volume":52,"date_published":"2023-01-01T00:00:00Z","intvolume":"        52","doi":"10.1137/20m1378223","article_processing_charge":"No","ec_funded":1,"publisher":"Society for Industrial & Applied Mathematics","publication_status":"published","external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"_id":"12563","issue":"1","oa_version":"Preprint","type":"journal_article","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"year":"2023","month":"01","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"isi":1,"article_type":"original","department":[{"_id":"UlWa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-01T13:11:30Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2003.11351","open_access":"1"}],"keyword":["General Mathematics","General Computer Science"],"abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"status":"public","author":[{"last_name":"Krokhin","full_name":"Krokhin, Andrei","first_name":"Andrei"},{"id":"ec596741-c539-11ec-b829-c79322a91242","first_name":"Jakub","last_name":"Opršal","full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456"},{"first_name":"Marcin","last_name":"Wrochna","full_name":"Wrochna, Marcin"},{"first_name":"Stanislav","full_name":"Živný, Stanislav","last_name":"Živný"}]},{"isi":1,"publication_identifier":{"issn":["0304-3975"]},"year":"2023","month":"02","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems"}],"department":[{"_id":"DaAl"}],"article_type":"original","publisher":"Elsevier","oa_version":"Published Version","type":"journal_article","ddc":["000"],"file":[{"file_name":"2023_TheoreticalCompScience_Alistarh.pdf","relation":"main_file","creator":"dernst","file_id":"12570","date_updated":"2023-02-20T07:30:20Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-02-20T07:30:20Z","checksum":"b27c5290f2f1500c403494364ee39c9f","success":1,"file_size":602333}],"_id":"12566","issue":"2","publication_status":"published","external_id":{"isi":["000934262700001"]},"license":"https://creativecommons.org/licenses/by/4.0/","author":[{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Faith","full_name":"Ellen, Faith","last_name":"Ellen"},{"orcid":"0000-0002-6432-6646","last_name":"Rybicki","full_name":"Rybicki, Joel","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_updated":"2023-08-01T13:17:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among  processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs."}],"scopus_import":"1","title":"Wait-free approximate agreement on graphs","article_number":"113733","oa":1,"date_created":"2023-02-19T23:00:55Z","citation":{"ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” <i>Theoretical Computer Science</i>, vol. 948, no. 2. Elsevier, 2023.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. 2023;948(2). doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>, vol. 948, no. 2, 113733, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">10.1016/j.tcs.2023.113733</a>.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>.","apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2023). Wait-free approximate agreement on graphs. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.113733\">https://doi.org/10.1016/j.tcs.2023.113733</a>"},"quality_controlled":"1","doi":"10.1016/j.tcs.2023.113733","file_date_updated":"2023-02-20T07:30:20Z","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":948,"day":"28","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","publication":"Theoretical Computer Science","intvolume":"       948","has_accepted_license":"1","date_published":"2023-02-28T00:00:00Z"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","doi":"10.3390/ijms24032128","file_date_updated":"2023-02-20T07:09:27Z","has_accepted_license":"1","intvolume":"        24","date_published":"2023-01-21T00:00:00Z","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","publication":"International Journal of Molecular Sciences","day":"21","volume":24,"title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","date_created":"2023-02-19T23:00:56Z","citation":{"mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3, 2128, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., &#38; Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms24032128\">https://doi.org/10.3390/ijms24032128</a>","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 3. MDPI, 2023.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. <i>International Journal of Molecular Sciences</i>. 2023;24(3). doi:<a href=\"https://doi.org/10.3390/ijms24032128\">10.3390/ijms24032128</a>"},"quality_controlled":"1","oa":1,"article_number":"2128","status":"public","author":[{"first_name":"Achmed","last_name":"Mrestani","full_name":"Mrestani, Achmed"},{"last_name":"Lichter","full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina"},{"first_name":"Anna Leena","last_name":"Sirén","full_name":"Sirén, Anna Leena"},{"first_name":"Manfred","last_name":"Heckmann","full_name":"Heckmann, Manfred"},{"first_name":"Mila M.","full_name":"Paul, Mila M.","last_name":"Paul"},{"full_name":"Pauli, Martin","last_name":"Pauli","first_name":"Martin"}],"abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"scopus_import":"1","date_updated":"2023-08-01T13:16:36Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"article_type":"original","publication_identifier":{"eissn":["1422-0067"]},"isi":1,"year":"2023","month":"01","oa_version":"Published Version","ddc":["570"],"file":[{"creator":"dernst","file_id":"12569","relation":"main_file","file_name":"2023_IJMS_Mrestani.pdf","file_size":2823025,"checksum":"69a35dcd3e0249f902ab881b06ee2e58","success":1,"date_created":"2023-02-20T07:09:27Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-02-20T07:09:27Z"}],"type":"journal_article","external_id":{"isi":["000930324700001"]},"publication_status":"published","issue":"3","_id":"12567","publisher":"MDPI"},{"article_type":"original","department":[{"_id":"XiFe"}],"year":"2023","month":"01","publication_identifier":{"issn":["1474-760X"]},"_id":"12668","external_id":{"pmid":["36639687"]},"publication_status":"published","type":"journal_article","oa_version":"Published Version","publisher":"Springer Nature","author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"first_name":"Yiman","last_name":"Yang","full_name":"Yang, Yiman"},{"full_name":"Chen, Jinchao","last_name":"Chen","first_name":"Jinchao"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"full_name":"Zhang, Hao","last_name":"Zhang","first_name":"Hao"},{"last_name":"Wang","full_name":"Wang, Hao","first_name":"Hao"},{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"full_name":"Bie, Xiaomin","last_name":"Bie","first_name":"Xiaomin"},{"first_name":"Jiafu","last_name":"Jiang","full_name":"Jiang, Jiafu"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi"},{"last_name":"Fu","full_name":"Fu, Xiangdong","first_name":"Xiangdong"},{"first_name":"Xiansheng","last_name":"Zhang","full_name":"Zhang, Xiansheng"},{"full_name":"Du, Zhuo","last_name":"Du","first_name":"Zhuo"},{"first_name":"Jun","full_name":"Xiao, Jun","last_name":"Xiao"}],"status":"public","extern":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"main_file_link":[{"url":"https://doi.org/10.1186/s13059-022-02844-2","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-08T10:52:49Z","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","quality_controlled":"1","date_created":"2023-02-23T09:13:49Z","citation":{"ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. 2023;24. doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>","ieee":"L. Zhao <i>et al.</i>, “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” <i>Genome Biology</i>, vol. 24. Springer Nature, 2023.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>, vol. 24, 7, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13059-022-02844-2\">10.1186/s13059-022-02844-2</a>.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” <i>Genome Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13059-022-02844-2\">https://doi.org/10.1186/s13059-022-02844-2</a>."},"article_number":"7","oa":1,"article_processing_charge":"No","doi":"10.1186/s13059-022-02844-2","date_published":"2023-01-13T00:00:00Z","intvolume":"        24","pmid":1,"volume":24,"day":"13","publication":"Genome Biology"},{"title":"Beyond transcription: compelling open questions in plant RNA biology","quality_controlled":"1","date_created":"2023-02-23T09:14:59Z","citation":{"mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>.","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. 2023;35(6). doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>","ieee":"P. A. Manavella <i>et al.</i>, “Beyond transcription: compelling open questions in plant RNA biology,” <i>The Plant Cell</i>, vol. 35, no. 6. Oxford University Press, 2023.","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346."},"oa":1,"article_number":"koac346","article_processing_charge":"No","doi":"10.1093/plcell/koac346","date_published":"2023-06-01T00:00:00Z","intvolume":"        35","pmid":1,"day":"01","publication":"The Plant Cell","volume":35,"article_type":"original","department":[{"_id":"XiFe"}],"month":"06","year":"2023","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"publication_status":"published","external_id":{"pmid":["36477566"]},"issue":"6","_id":"12669","type":"journal_article","oa_version":"Published Version","publisher":"Oxford University Press","status":"public","author":[{"first_name":"Pablo A","last_name":"Manavella","full_name":"Manavella, Pablo A"},{"last_name":"Godoy Herz","full_name":"Godoy Herz, Micaela A","first_name":"Micaela A"},{"last_name":"Kornblihtt","full_name":"Kornblihtt, Alberto R","first_name":"Alberto R"},{"last_name":"Sorenson","full_name":"Sorenson, Reed","first_name":"Reed"},{"full_name":"Sieburth, Leslie E","last_name":"Sieburth","first_name":"Leslie E"},{"first_name":"Kentaro","full_name":"Nakaminami, Kentaro","last_name":"Nakaminami"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"first_name":"Yiliang","last_name":"Ding","full_name":"Ding, Yiliang"},{"full_name":"Sun, Qianwen","last_name":"Sun","first_name":"Qianwen"},{"first_name":"Hunseung","last_name":"Kang","full_name":"Kang, Hunseung"},{"full_name":"Ariel, Federico D","last_name":"Ariel","first_name":"Federico D"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"last_name":"Giudicatti","full_name":"Giudicatti, Axel J","first_name":"Axel J"},{"full_name":"Cai, Qiang","last_name":"Cai","first_name":"Qiang"},{"full_name":"Jin, Hailing","last_name":"Jin","first_name":"Hailing"},{"orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Qi","full_name":"Qi, Yijun","first_name":"Yijun"},{"full_name":"Pikaard, Craig S","last_name":"Pikaard","first_name":"Craig S"}],"scopus_import":"1","extern":"1","keyword":["Cell Biology","Plant Science"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"abstract":[{"text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-04T09:48:43Z"},{"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-02T12:23:45Z","scopus_import":"1","abstract":[{"text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.","lang":"eng"}],"status":"public","author":[{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"last_name":"Briffa","full_name":"Briffa, Amy","first_name":"Amy"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"last_name":"Choi","full_name":"Choi, Jaemyung","first_name":"Jaemyung"},{"last_name":"Hollwey","full_name":"Hollwey, Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","first_name":"Elizabeth"},{"full_name":"Colicchio, Jack","last_name":"Colicchio","first_name":"Jack"},{"full_name":"Anderson, Ian","last_name":"Anderson","first_name":"Ian"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"publisher":"Elsevier","external_id":{"isi":["000944921600001"]},"publication_status":"published","_id":"12672","issue":"3","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-05-11T10:41:42Z","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","file_size":8401261,"success":1,"date_created":"2023-05-11T10:41:42Z","file_name":"2023_CellReports_Lyons.pdf","file_id":"12941","creator":"kschuh","relation":"main_file"}],"type":"journal_article","ddc":["580"],"oa_version":"Published Version","project":[{"grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068"}],"year":"2023","month":"03","publication_identifier":{"eissn":["2211-1247"]},"isi":1,"article_type":"original","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","publication":"Cell Reports","day":"28","volume":42,"date_published":"2023-03-28T00:00:00Z","has_accepted_license":"1","intvolume":"        42","file_date_updated":"2023-05-11T10:41:42Z","doi":"10.1016/j.celrep.2023.112132","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","ec_funded":1,"oa":1,"article_number":"112132","quality_controlled":"1","citation":{"ieee":"D. B. Lyons <i>et al.</i>, “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” <i>Cell Reports</i>, vol. 42, no. 3. Elsevier, 2023.","ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">https://doi.org/10.1016/j.celrep.2023.112132</a>","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” <i>Cell Reports</i>, vol. 42, no. 3, 112132, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.112132\">10.1016/j.celrep.2023.112132</a>."},"date_created":"2023-02-23T09:17:44Z","title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons"},{"isi":1,"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"year":"2023","month":"05","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"article_type":"original","publisher":"Wiley","oa_version":"Published Version","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-16T12:33:31Z","checksum":"7dd083ed8850faa55c34e411ed390de9","file_size":1422445,"success":1,"date_created":"2023-08-16T12:33:31Z","file_name":"2023_AngewChemInt_Becker.pdf","creator":"dernst","file_id":"14072","relation":"main_file"}],"ddc":["540"],"type":"journal_article","_id":"12675","issue":"19","external_id":{"pmid":["36738230"],"isi":["000956919900001"]},"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"},{"last_name":"Berbon","full_name":"Berbon, Mélanie","first_name":"Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"full_name":"Morvan, Estelle","last_name":"Morvan","first_name":"Estelle"},{"first_name":"Benjamin","full_name":"Bardiaux, Benjamin","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"},{"last_name":"Loquet","full_name":"Loquet, Antoine","first_name":"Antoine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"status":"public","date_updated":"2024-02-21T12:14:06Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"keyword":["General Chemistry","Catalysis"],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/","relation":"press_release","description":"News on ISTA website"}],"record":[{"relation":"other","status":"public","id":"14861"},{"status":"public","relation":"research_data","id":"12497"}]},"title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","article_number":"e202219314","oa":1,"citation":{"mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>.","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. 2023;62(19). doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","ieee":"L. M. Becker <i>et al.</i>, “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19. Wiley, 2023.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023)."},"date_created":"2023-02-24T10:45:01Z","quality_controlled":"1","doi":"10.1002/anie.202219314","file_date_updated":"2023-08-16T12:33:31Z","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"volume":62,"acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","day":"01","publication":"Angewandte Chemie International Edition","pmid":1,"intvolume":"        62","has_accepted_license":"1","date_published":"2023-05-01T00:00:00Z"},{"date_updated":"2025-07-14T09:09:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub","last_name":"Svoboda"}],"status":"public","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Published Version","type":"conference","_id":"12676","publication_status":"published","publication_identifier":{"isbn":["9781611977554"]},"year":"2023","month":"02","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","date_published":"2023-02-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch173","ec_funded":1,"article_processing_charge":"No","oa":1,"date_created":"2023-02-24T12:20:47Z","citation":{"chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 4590–4605. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., &#38; Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, pp. 4590–4605.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>"},"conference":{"location":"Florence, Italy","end_date":"2023-01-25","name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22"},"quality_controlled":"1","page":"4590-4605","title":"Faster algorithm for turn-based stochastic games with bounded treewidth"},{"author":[{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression."}],"keyword":["General Neuroscience"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-08-16T12:30:25Z","article_type":"review","department":[{"_id":"SiHi"}],"month":"04","year":"2023","project":[{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"isi":1,"publication_identifier":{"issn":["0959-4388"]},"_id":"12679","issue":"4","publication_status":"published","external_id":{"pmid":["36842274"],"isi":["000953497700001"]},"file":[{"file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","relation":"main_file","creator":"dernst","file_id":"14071","date_updated":"2023-08-16T12:29:06Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-08-16T12:29:06Z","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","file_size":1787894,"success":1}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article","publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-08-16T12:29:06Z","doi":"10.1016/j.conb.2023.102695","date_published":"2023-04-01T00:00:00Z","intvolume":"        79","has_accepted_license":"1","pmid":1,"volume":79,"day":"01","publication":"Current Opinion in Neurobiology","acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","quality_controlled":"1","citation":{"ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. 2023;79(4). doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4. Elsevier, 2023.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.conb.2023.102695\">https://doi.org/10.1016/j.conb.2023.102695</a>.","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” <i>Current Opinion in Neurobiology</i>, vol. 79, no. 4, 102695, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.conb.2023.102695\">10.1016/j.conb.2023.102695</a>."},"date_created":"2023-02-26T12:24:21Z","article_number":"102695","oa":1},{"article_number":"113363","oa":1,"citation":{"ieee":"G. Ivanov and S. Köse, “Erdős-Ko-Rado and Hilton-Milner theorems for two-forms,” <i>Discrete Mathematics</i>, vol. 346, no. 6. Elsevier, 2023.","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","ama":"Ivanov G, Köse S. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. 2023;346(6). doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>","chicago":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>.","apa":"Ivanov, G., &#38; Köse, S. (2023). Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>","mla":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>, vol. 346, no. 6, 113363, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>."},"date_created":"2023-02-26T23:01:00Z","quality_controlled":"1","arxiv":1,"title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","volume":346,"day":"01","publication":"Discrete Mathematics","intvolume":"       346","date_published":"2023-06-01T00:00:00Z","doi":"10.1016/j.disc.2023.113363","article_processing_charge":"No","publisher":"Elsevier","type":"journal_article","oa_version":"Preprint","issue":"6","_id":"12680","external_id":{"arxiv":["2201.10892"]},"publication_status":"published","publication_identifier":{"issn":["0012-365X"]},"month":"06","year":"2023","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"article_type":"letter_note","date_updated":"2023-10-04T11:54:57Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of  was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.","lang":"eng"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2201.10892","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"13331"}]},"scopus_import":"1","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"last_name":"Köse","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda"}],"status":"public"},{"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-02-27T09:23:02Z","doi":"10.1146/annurev-fluid-032822-025933","date_published":"2023-01-19T00:00:00Z","intvolume":"        55","has_accepted_license":"1","volume":55,"day":"19","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","publication":"Annual Review of Fluid Mechanics","title":"Elasto-inertial turbulence","page":"675-705","quality_controlled":"1","date_created":"2023-02-26T23:01:01Z","citation":{"ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. 2023;55(1):675-705. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>.","apa":"Dubief, Y., Terrapon, V. E., &#38; Hof, B. (2023). Elasto-inertial turbulence. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">https://doi.org/10.1146/annurev-fluid-032822-025933</a>","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-032822-025933\">10.1146/annurev-fluid-032822-025933</a>."},"oa":1,"author":[{"first_name":"Yves","last_name":"Dubief","full_name":"Dubief, Yves"},{"last_name":"Terrapon","full_name":"Terrapon, Vincent E.","first_name":"Vincent E."},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-01T13:19:47Z","article_type":"original","department":[{"_id":"BjHo"}],"year":"2023","month":"01","isi":1,"publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"issue":"1","_id":"12681","publication_status":"published","external_id":{"isi":["000915418100026"]},"type":"journal_article","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-02-27T09:23:02Z","success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","file_size":4036706,"date_created":"2023-02-27T09:23:02Z","file_name":"2023_AnnReviewFluidMech_Dubief.pdf","creator":"dernst","file_id":"12690","relation":"main_file"}],"ddc":["530"],"oa_version":"Published Version","publisher":"Annual Reviews"},{"publisher":"Annual Reviews","_id":"12682","external_id":{"isi":["000915418100023"]},"publication_status":"published","oa_version":"Published Version","type":"journal_article","file":[{"checksum":"f99ef30f76cabc9e5e1946b380c16db4","file_size":4769537,"success":1,"date_created":"2023-02-27T09:35:52Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-02-27T09:35:52Z","file_id":"12691","creator":"dernst","relation":"main_file","file_name":"2023_AnnReviewFluidMech_Avila.pdf"}],"ddc":["530"],"year":"2023","month":"01","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"isi":1,"publication_identifier":{"issn":["0066-4189"]},"article_type":"original","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T13:20:30Z","scopus_import":"1","abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"author":[{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"first_name":"Dwight","full_name":"Barkley, Dwight","last_name":"Barkley"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"status":"public","oa":1,"quality_controlled":"1","date_created":"2023-02-26T23:01:01Z","citation":{"ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. 2023;55:575-602. doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” <i>Annual Review of Fluid Mechanics</i>, vol. 55. Annual Reviews, pp. 575–602, 2023.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","apa":"Avila, M., Barkley, D., &#38; Hof, B. (2023). Transition to turbulence in pipe flow. <i>Annual Review of Fluid Mechanics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>. Annual Reviews, 2023. <a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">https://doi.org/10.1146/annurev-fluid-120720-025957</a>.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” <i>Annual Review of Fluid Mechanics</i>, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:<a href=\"https://doi.org/10.1146/annurev-fluid-120720-025957\">10.1146/annurev-fluid-120720-025957</a>."},"page":"575-602","title":"Transition to turbulence in pipe flow","volume":55,"acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","publication":"Annual Review of Fluid Mechanics","day":"19","date_published":"2023-01-19T00:00:00Z","intvolume":"        55","has_accepted_license":"1","file_date_updated":"2023-02-27T09:35:52Z","doi":"10.1146/annurev-fluid-120720-025957","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-17T12:48:10Z","scopus_import":"1","abstract":[{"text":"We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.","lang":"eng"}],"status":"public","author":[{"first_name":"Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","last_name":"Dubach","full_name":"Dubach, Guillaume","orcid":"0000-0001-6892-8137"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös","orcid":"0000-0001-5366-9603"}],"publisher":"Institute of Mathematical Statistics","external_id":{"arxiv":["2108.13694"],"isi":["000950650200005"]},"publication_status":"published","_id":"12683","type":"journal_article","file":[{"date_created":"2023-02-27T09:43:27Z","file_size":479105,"checksum":"a1c6f0a3e33688fd71309c86a9aad86e","success":1,"date_updated":"2023-02-27T09:43:27Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12692","creator":"dernst","file_name":"2023_ElectCommProbability_Dubach.pdf"}],"oa_version":"Published Version","ddc":["510"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"month":"02","year":"2023","publication_identifier":{"eissn":["1083-589X"]},"isi":1,"article_type":"original","department":[{"_id":"LaEr"}],"publication":"Electronic Communications in Probability","acknowledgement":"G. Dubach gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. L. Erdős is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","day":"08","volume":28,"date_published":"2023-02-08T00:00:00Z","has_accepted_license":"1","intvolume":"        28","file_date_updated":"2023-02-27T09:43:27Z","doi":"10.1214/23-ECP516","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","oa":1,"arxiv":1,"quality_controlled":"1","date_created":"2023-02-26T23:01:01Z","citation":{"ieee":"G. Dubach and L. Erdös, “Dynamics of a rank-one perturbation of a Hermitian matrix,” <i>Electronic Communications in Probability</i>, vol. 28. Institute of Mathematical Statistics, pp. 1–13, 2023.","short":"G. Dubach, L. Erdös, Electronic Communications in Probability 28 (2023) 1–13.","ista":"Dubach G, Erdös L. 2023. Dynamics of a rank-one perturbation of a Hermitian matrix. Electronic Communications in Probability. 28, 1–13.","ama":"Dubach G, Erdös L. Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. 2023;28:1-13. doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>","chicago":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>.","apa":"Dubach, G., &#38; Erdös, L. (2023). Dynamics of a rank-one perturbation of a Hermitian matrix. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-ECP516\">https://doi.org/10.1214/23-ECP516</a>","mla":"Dubach, Guillaume, and László Erdös. “Dynamics of a Rank-One Perturbation of a Hermitian Matrix.” <i>Electronic Communications in Probability</i>, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–13, doi:<a href=\"https://doi.org/10.1214/23-ECP516\">10.1214/23-ECP516</a>."},"page":"1-13","title":"Dynamics of a rank-one perturbation of a Hermitian matrix"},{"department":[{"_id":"SyCr"}],"title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","contributor":[{"last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Sina"},{"last_name":"Kirchner","contributor_type":"data_collector","first_name":"Jessica","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3"},{"first_name":"Anna V","contributor_type":"data_collector","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"}],"month":"02","year":"2023","_id":"12693","oa_version":"Published Version","ddc":["570"],"type":"research_data","file":[{"relation":"main_file","creator":"scremer","file_id":"12694","file_name":"Metzler_ReadMe.pdf","date_created":"2023-02-28T06:34:08Z","file_size":77070,"success":1,"checksum":"c1565d655ca05601acfd84e0d12b8563","date_updated":"2023-02-28T06:34:08Z","content_type":"application/pdf","access_level":"open_access"},{"relation":"main_file","creator":"scremer","file_id":"12695","file_name":"Metzler_RepositoryData.xlsx","date_created":"2023-02-28T06:34:12Z","checksum":"75c4c4948563d6261cb7548f80d909f1","success":1,"file_size":88001,"date_updated":"2023-02-28T06:34:12Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","access_level":"open_access"}],"date_created":"2023-02-28T06:38:37Z","citation":{"ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>.","short":"S. Cremer, (2023).","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>","mla":"Cremer, Sylvia. <i>Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males </i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12693\">10.15479/AT:ISTA:12693</a>.","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>.","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12693\">https://doi.org/10.15479/AT:ISTA:12693</a>"},"oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"status":"public","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"article_processing_charge":"No","file_date_updated":"2023-02-28T06:34:12Z","doi":"10.15479/AT:ISTA:12693","date_published":"2023-02-28T00:00:00Z","related_material":{"record":[{"id":"12696","relation":"used_in_publication","status":"public"}]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"See Readme File for further information."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"28","date_updated":"2023-12-13T11:13:13Z"},{"type":"journal_article","ddc":["570"],"oa_version":"Published Version","file":[{"creator":"dernst","file_id":"14048","relation":"main_file","file_name":"2023_BMCEcology_Metzler.pdf","file_size":2004276,"checksum":"95966dc7d242d2c85bdd4fe14233dbd8","success":1,"date_created":"2023-08-14T07:51:47Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-14T07:51:47Z"}],"_id":"12696","publication_status":"published","external_id":{"isi":["001042643600002"],"pmid":["37550612"]},"publisher":"Springer Nature","department":[{"_id":"SyCr"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["2730-7182"]},"month":"08","year":"2023","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020"}],"abstract":[{"text":"Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.\r\nResults: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk.","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"12693"}]},"scopus_import":"1","date_updated":"2023-12-13T11:13:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina"},{"first_name":"Jessica","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","last_name":"Kirchner","full_name":"Kirchner, Jessica"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_created":"2023-02-28T07:38:17Z","acknowledged_ssus":[{"_id":"LifeSc"}],"citation":{"ista":"Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 23, 37.","ieee":"S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between immunity and competitive ability in fighting ant males,” <i>BMC Ecology and Evolution</i>, vol. 23. Springer Nature, 2023.","short":"S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution 23 (2023).","ama":"Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and competitive ability in fighting ant males. <i>BMC Ecology and Evolution</i>. 2023;23. doi:<a href=\"https://doi.org/10.1186/s12862-023-02137-7\">10.1186/s12862-023-02137-7</a>","mla":"Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” <i>BMC Ecology and Evolution</i>, vol. 23, 37, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s12862-023-02137-7\">10.1186/s12862-023-02137-7</a>.","chicago":"Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” <i>BMC Ecology and Evolution</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s12862-023-02137-7\">https://doi.org/10.1186/s12862-023-02137-7</a>.","apa":"Metzler, S., Kirchner, J., Grasse, A. V., &#38; Cremer, S. (2023). Trade-offs between immunity and competitive ability in fighting ant males. <i>BMC Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12862-023-02137-7\">https://doi.org/10.1186/s12862-023-02137-7</a>"},"quality_controlled":"1","article_number":"37","oa":1,"title":"Trade-offs between immunity and competitive ability in fighting ant males","intvolume":"        23","has_accepted_license":"1","date_published":"2023-08-07T00:00:00Z","volume":23,"acknowledgement":"We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader for sharing the C. obscurior genome data for primer development, the Lab Support Facility of ISTA for general laboratory support and help with the permit approval procedures, and the Finca El Quinto for letting us collect ants on their property. We thank the Social Immunity Team at ISTA for help with ant collection and experimental help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation, and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology Austria (ISTA). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 771402 to SC). ","publication":"BMC Ecology and Evolution","day":"07","pmid":1,"ec_funded":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1186/s12862-023-02137-7","file_date_updated":"2023-08-14T07:51:47Z"},{"date_published":"2023-03-03T00:00:00Z","has_accepted_license":"1","intvolume":"       130","volume":130,"day":"03","acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","publication":"Physical Review Letters","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-02-28T12:37:54Z","doi":"10.1103/physrevlett.130.098202","quality_controlled":"1","arxiv":1,"date_created":"2023-02-28T12:14:46Z","citation":{"ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. <i>Physical Review Letters</i>. 2023;130(9). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.098202\">10.1103/physrevlett.130.098202</a>","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” <i>Physical Review Letters</i>, vol. 130, no. 9. American Physical Society, 2023.","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” <i>Physical Review Letters</i>, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.098202\">10.1103/physrevlett.130.098202</a>.","apa":"Grosjean, G. M., &#38; Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.098202\">https://doi.org/10.1103/physrevlett.130.098202</a>","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.098202\">https://doi.org/10.1103/physrevlett.130.098202</a>."},"article_number":"098202","oa":1,"title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","abstract":[{"text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process.","lang":"eng"}],"keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"8101"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2211.02488"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-22T08:41:32Z","author":[{"orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M","last_name":"Grosjean","first_name":"Galien M","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425"},{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"}],"status":"public","issue":"9","_id":"12697","publication_status":"published","external_id":{"arxiv":["2211.02488"],"isi":["000946178200008"]},"oa_version":"Preprint","type":"journal_article","ddc":["530","537"],"file":[{"checksum":"c4f2f6eea0408811f8f4898e15890355","success":1,"file_size":2301864,"date_created":"2023-02-28T12:20:27Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-02-28T12:20:27Z","file_id":"12698","creator":"ggrosjea","relation":"main_file","file_name":"Main_Preprint.pdf"},{"date_created":"2023-02-28T12:20:55Z","checksum":"6af6ed6c97a977f923de4162294b43c4","success":1,"file_size":1138625,"date_updated":"2023-02-28T12:20:55Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"12699","creator":"ggrosjea","file_name":"Suppl_info.pdf"},{"access_level":"open_access","content_type":"video/mp4","date_updated":"2023-02-28T12:37:54Z","file_size":793449,"success":1,"checksum":"3f20365fb9515bdba3a111d912c8d8b4","date_created":"2023-02-28T12:37:54Z","file_name":"Suppl_vid1.mp4","file_id":"12700","creator":"ggrosjea","relation":"main_file"},{"access_level":"open_access","content_type":"video/mp4","date_updated":"2023-02-28T12:37:54Z","file_size":455925,"success":1,"checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","date_created":"2023-02-28T12:37:54Z","file_name":"Suppl_vid2.mp4","file_id":"12701","creator":"ggrosjea","relation":"main_file"}],"publisher":"American Physical Society","article_type":"original","department":[{"_id":"ScWa"}],"year":"2023","month":"03","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]}},{"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-023-36841-1","file_date_updated":"2023-03-07T10:58:00Z","intvolume":"        14","has_accepted_license":"1","date_published":"2023-02-27T00:00:00Z","volume":14,"publication":"Nature Communications","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","day":"27","pmid":1,"title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","date_created":"2023-03-05T23:01:04Z","citation":{"mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>, vol. 14, 1104, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>.","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>.","apa":"Cheng, B., Hamel, S., &#38; Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>"},"quality_controlled":"1","article_number":"1104","oa":1,"author":[{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Sebastien","full_name":"Hamel, Sebastien","last_name":"Hamel"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","first_name":"Mandy","full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129"}],"status":"public","abstract":[{"lang":"eng","text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution."}],"scopus_import":"1","date_updated":"2023-08-01T13:36:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"BiCh"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"02","year":"2023","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","type":"journal_article","file":[{"relation":"main_file","creator":"cchlebak","file_id":"12713","file_name":"2023_NatComm_Cheng.pdf","date_created":"2023-03-07T10:58:00Z","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","file_size":1946443,"date_updated":"2023-03-07T10:58:00Z","content_type":"application/pdf","access_level":"open_access"}],"ddc":["540"],"_id":"12702","external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"publication_status":"published","publisher":"Springer Nature"},{"oa_version":"Published Version","file":[{"file_size":944052,"checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"date_created":"2023-03-07T12:22:23Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-03-07T12:22:23Z","creator":"cchlebak","file_id":"12714","relation":"main_file","file_name":"2023_IEEERobAutLetters_Lechner.pdf"}],"type":"journal_article","ddc":["000"],"external_id":{"isi":["000936534100012"],"arxiv":["2204.07373"]},"publication_status":"published","_id":"12704","issue":"3","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"ToHe"}],"article_type":"original","publication_identifier":{"eissn":["2377-3766"]},"isi":1,"month":"03","year":"2023","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"11366"}]},"abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"scopus_import":"1","date_updated":"2023-08-01T13:36:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-03-05T23:01:04Z","citation":{"ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. 2023;8(3):1595-1602. doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:<a href=\"https://doi.org/10.1109/LRA.2023.3240930\">10.1109/LRA.2023.3240930</a>.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>IEEE Robotics and Automation Letters</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>.","apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>IEEE Robotics and Automation Letters</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LRA.2023.3240930\">https://doi.org/10.1109/LRA.2023.3240930</a>"},"arxiv":1,"quality_controlled":"1","oa":1,"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","page":"1595-1602","has_accepted_license":"1","intvolume":"         8","date_published":"2023-03-01T00:00:00Z","publication":"IEEE Robotics and Automation Letters","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","day":"01","volume":8,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","doi":"10.1109/LRA.2023.3240930","file_date_updated":"2023-03-07T12:22:23Z"},{"date_published":"2023-02-21T00:00:00Z","intvolume":"       158","pmid":1,"volume":158,"publication":"Journal of Chemical Physics","acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","day":"21","article_processing_charge":"No","doi":"10.1063/5.0134271","quality_controlled":"1","arxiv":1,"date_created":"2023-03-05T23:01:05Z","citation":{"ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. 2023;158(7). doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>","ieee":"V. Sorichetti <i>et al.</i>, “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” <i>Journal of Chemical Physics</i>, vol. 158, no. 7. American Institute of Physics, 2023.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0134271\">10.1063/5.0134271</a>.","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0134271\">https://doi.org/10.1063/5.0134271</a>."},"article_number":"074905","oa":1,"title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","scopus_import":"1","abstract":[{"lang":"eng","text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-03T11:31:51Z","author":[{"first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio","last_name":"Sorichetti"},{"full_name":"Ninarello, Andrea","last_name":"Ninarello","first_name":"Andrea"},{"first_name":"José","full_name":"Ruiz-Franco, José","last_name":"Ruiz-Franco"},{"full_name":"Hugouvieux, Virginie","last_name":"Hugouvieux","first_name":"Virginie"},{"first_name":"Emanuela","full_name":"Zaccarelli, Emanuela","last_name":"Zaccarelli"},{"first_name":"Cristian","last_name":"Micheletti","full_name":"Micheletti, Cristian"},{"full_name":"Kob, Walter","last_name":"Kob","first_name":"Walter"},{"first_name":"Lorenzo","full_name":"Rovigatti, Lorenzo","last_name":"Rovigatti"}],"status":"public","_id":"12705","issue":"7","external_id":{"arxiv":["2211.04810"],"isi":["000936943800002"],"pmid":["36813705"]},"publication_status":"published","type":"journal_article","oa_version":"Preprint","publisher":"American Institute of Physics","article_type":"original","department":[{"_id":"AnSa"}],"year":"2023","month":"02","isi":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]}}]