[{"department":[{"_id":"DaSi"},{"_id":"JoCs"}],"publication_status":"submitted","title":"Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance","status":"public","_id":"8557","acknowledgement":"We thank the following for their contributions: The Drosophila Genomics Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner. B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies, we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for RNA sequencing and analysis and the Life Scientific Service Units at IST Austria for technical support and assistance with microscopy and FACS analysis. We thank C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is supported by an OEAW, DOC fellowship.","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2020-09-23T09:36:47Z","date_updated":"2024-03-28T23:30:25Z","related_material":{"record":[{"id":"10614","status":"public","relation":"later_version"},{"id":"8983","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera","full_name":"Belyaeva, Vera"},{"full_name":"Wachner, Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","first_name":"Stephanie"},{"first_name":"Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor"},{"last_name":"Linder","first_name":"Markus","full_name":"Linder, Markus"},{"full_name":"Emtenani, Shamsi","last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"full_name":"György, Attila","last_name":"György","first_name":"Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Sibilia","full_name":"Sibilia, Maria"},{"last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}],"type":"preprint","ec_funded":1,"abstract":[{"text":"The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638"},{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"},{"name":"Tissue barrier penetration is crucial for immunity and metastasis","grant_number":"24800","_id":"26199CA4-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.301481"}],"citation":{"ieee":"V. Belyaeva et al., “Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv. .","apa":"Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György, A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. https://doi.org/10.1101/2020.09.18.301481","ista":"Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.","ama":"Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv. doi:10.1101/2020.09.18.301481","chicago":"Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481.","short":"V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György, M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).","mla":"Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv, doi:10.1101/2020.09.18.301481."},"oa":1,"publication":"bioRxiv","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1101/2020.09.18.301481","date_published":"2020-09-18T00:00:00Z","article_processing_charge":"No","day":"18","month":"09"},{"file_date_updated":"2020-12-02T10:42:31Z","ec_funded":1,"article_number":"2012.00322","date_updated":"2024-03-28T23:30:27Z","date_created":"2020-12-02T10:42:53Z","author":[{"full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","last_name":"Aggarwal","first_name":"Kushagra"},{"full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87","last_name":"Hofmann","first_name":"Andrea C"},{"full_name":"Jirovec, Daniel","first_name":"Daniel","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez"},{"full_name":"Sammak, Amir","first_name":"Amir","last_name":"Sammak"},{"full_name":"Botifoll, Marc","last_name":"Botifoll","first_name":"Marc"},{"first_name":"Sara","last_name":"Marti-Sanchez","full_name":"Marti-Sanchez, Sara"},{"first_name":"Menno","last_name":"Veldhorst","full_name":"Veldhorst, Menno"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Scappucci","first_name":"Giordano","full_name":"Scappucci, Giordano"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"id":"10559","status":"public","relation":"later_version"},{"id":"8834","status":"public","relation":"research_data"},{"id":"10058","relation":"dissertation_contains","status":"public"}]},"publication_status":"submitted","department":[{"_id":"GeKa"}],"acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","year":"2020","month":"12","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"grant_number":"844511","_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"external_id":{"arxiv":["2012.00322"]},"oa":1,"abstract":[{"lang":"eng","text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip."}],"type":"preprint","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"Superconducting_2D_Ge.pdf","content_type":"application/pdf","file_size":1697939,"creator":"gkatsaro","relation":"main_file","file_id":"8832","checksum":"22a612e206232fa94b138b2c2f957582","date_created":"2020-12-02T10:42:31Z","date_updated":"2020-12-02T10:42:31Z"}],"title":"Enhancement of proximity induced superconductivity in planar Germanium","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8831","day":"02","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-12-02T00:00:00Z","publication":"arXiv","citation":{"ieee":"K. Aggarwal et al., “Enhancement of proximity induced superconductivity in planar Germanium,” arXiv. .","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. arXiv.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, n.d.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.).","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” ArXiv, 2012.00322."}},{"article_number":"6737","file_date_updated":"2020-09-21T14:08:58Z","ec_funded":1,"year":"2020","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","publication_status":"published","publisher":"MDPI","department":[{"_id":"RySh"}],"author":[{"full_name":"Kleindienst, David","last_name":"Kleindienst","first_name":"David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Bhandari, Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","first_name":"Pradeep","last_name":"Bhandari"},{"id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","first_name":"Matthew J","full_name":"Case, Matthew J"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]},"date_created":"2020-09-20T22:01:35Z","date_updated":"2024-03-28T23:30:31Z","volume":21,"month":"09","publication_identifier":{"eissn":["14220067"],"issn":["16616596"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000579945300001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"_id":"25D32BC0-B435-11E9-9278-68D0E5697425","name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus"},{"_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","call_identifier":"H2020"}],"doi":"10.3390/ijms21186737","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"issue":"18","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8532","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","ddc":["570"],"status":"public","intvolume":" 21","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8551","date_created":"2020-09-21T14:08:58Z","date_updated":"2020-09-21T14:08:58Z","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","success":1,"file_name":"2020_JournMolecSciences_Kleindienst.pdf","access_level":"open_access","file_size":5748456,"content_type":"application/pdf","creator":"dernst"}],"scopus_import":"1","day":"14","article_processing_charge":"No","has_accepted_license":"1","publication":"International Journal of Molecular Sciences","citation":{"mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences, vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.","short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” International Journal of Molecular Sciences, vol. 21, no. 18. MDPI, 2020.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21186737"},"article_type":"original","date_published":"2020-09-14T00:00:00Z"},{"file_date_updated":"2020-07-14T12:48:03Z","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2020","date_created":"2020-05-10T22:00:50Z","date_updated":"2024-03-28T23:30:34Z","volume":12075,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"month":"04","publication_identifier":{"issn":["03029743"],"isbn":["9783030449131"],"eissn":["16113349"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000681656800005"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Dublin, Ireland","start_date":"2020-04-25","end_date":"2020-04-30","name":"ESOP: Programming Languages and Systems"},"doi":"10.1007/978-3-030-44914-8_5","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.","lang":"eng"}],"status":"public","title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","ddc":["000"],"intvolume":" 12075","_id":"7810","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_LNCS_Chatterjee.pdf","file_size":651250,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7895","checksum":"8618b80f4cf7b39a60e61a6445ad9807","date_created":"2020-05-26T13:34:48Z","date_updated":"2020-07-14T12:48:03Z"}],"scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","page":"112-140","publication":"European Symposium on Programming","citation":{"short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” European Symposium on Programming, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: European Symposium on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in European Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140."},"date_published":"2020-04-18T00:00:00Z"},{"month":"10","publication_identifier":{"isbn":["9783030591519"],"eissn":["1611-3349"],"eisbn":["9783030591526"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","location":"Hanoi, Vietnam","start_date":"2020-10-19","end_date":"2020-10-23"},"doi":"10.1007/978-3-030-59152-6_14","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000723555700014"]},"file_date_updated":"2020-11-06T07:41:03Z","date_created":"2020-11-06T07:30:05Z","date_updated":"2024-03-28T23:30:34Z","volume":12302,"author":[{"full_name":"Asadi, Ali","first_name":"Ali","last_name":"Asadi"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Kiarash","last_name":"Mohammadi","full_name":"Mohammadi, Kiarash"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2020","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-12T00:00:00Z","page":"253-270","publication":"Automated Technology for Verification and Analysis","citation":{"ama":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In: Automated Technology for Verification and Analysis. Vol 12302. Springer Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14","ieee":"A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis, “Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,” in Automated Technology for Verification and Analysis, Hanoi, Vietnam, 2020, vol. 12302, pp. 253–270.","apa":"Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis, A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. In Automated Technology for Verification and Analysis (Vol. 12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14","ista":"Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020. Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 12302, 253–270.","short":"A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis, in:, Automated Technology for Verification and Analysis, Springer Nature, 2020, pp. 253–270.","mla":"Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” Automated Technology for Verification and Analysis, vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs and MDPs with Small Treewidth.” In Automated Technology for Verification and Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14."},"abstract":[{"text":"Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","file":[{"creator":"dernst","file_size":726648,"content_type":"application/pdf","file_name":"2020_LNCS_ATVA_Asadi_accepted.pdf","access_level":"open_access","date_created":"2020-11-06T07:41:03Z","date_updated":"2020-11-06T07:41:03Z","success":1,"checksum":"ae83f27e5b189d5abc2e7514f1b7e1b5","file_id":"8729","relation":"main_file"}],"oa_version":"Submitted Version","status":"public","ddc":["000"],"title":"Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth","intvolume":" 12302","_id":"8728","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"day":"11","article_processing_charge":"No","scopus_import":"1","date_published":"2020-06-11T00:00:00Z","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 672–87. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385969.","mla":"Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–87, doi:10.1145/3385412.3385969.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 672–687.","ista":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant generation for non-deterministic recursive programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 672–687.","apa":"Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020). Polynomial invariant generation for non-deterministic recursive programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969","ieee":"K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial invariant generation for non-deterministic recursive programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 672–687.","ama":"Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969"},"page":"672-687","abstract":[{"lang":"eng","text":"We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example."}],"type":"conference","oa_version":"Preprint","_id":"8089","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Polynomial invariant generation for non-deterministic recursive programs","status":"public","month":"06","publication_identifier":{"isbn":["9781450376136"]},"conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2020-06-20","location":"London, United Kingdom","start_date":"2020-06-15"},"doi":"10.1145/3385412.3385969","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1902.04373","open_access":"1"}],"external_id":{"arxiv":["1902.04373"],"isi":["000614622300045"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"date_updated":"2024-03-28T23:30:34Z","date_created":"2020-07-05T22:00:45Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}]},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","publication":"Reliability Engineering and System Safety","citation":{"chicago":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.","mla":"Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.","short":"A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020).","ista":"Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665.","ieee":"A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020.","apa":"Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665","ama":"Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665"},"article_type":"original","abstract":[{"lang":"eng","text":"We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem."}],"type":"journal_article","oa_version":"Preprint","_id":"6918","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"An efficient algorithm for computing network reliability in small treewidth","status":"public","intvolume":" 193","month":"01","publication_identifier":{"issn":["09518320"]},"doi":"10.1016/j.ress.2019.106665","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.09692"}],"external_id":{"arxiv":["1712.09692"],"isi":["000501641400050"]},"isi":1,"quality_controlled":"1","project":[{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"article_number":"106665","author":[{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"},{"full_name":"Mohammadi, Fatemeh","first_name":"Fatemeh","last_name":"Mohammadi"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"date_created":"2019-09-29T22:00:44Z","date_updated":"2024-03-28T23:30:34Z","volume":193,"acknowledgement":"We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW).","year":"2020","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}]},{"language":[{"iso":"eng"}],"doi":"10.1007/s10957-019-01616-6","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"oa":1,"external_id":{"isi":["000511805200009"]},"month":"03","publication_identifier":{"issn":["0022-3239"],"eissn":["1573-2878"]},"date_updated":"2023-09-06T11:27:15Z","date_created":"2019-12-09T21:33:44Z","volume":184,"author":[{"full_name":"Shehu, Yekini","first_name":"Yekini","last_name":"Shehu","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139"},{"first_name":"Aviv","last_name":"Gibali","full_name":"Gibali, Aviv"},{"full_name":"Sagratella, Simone","first_name":"Simone","last_name":"Sagratella"}],"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Springer Nature","year":"2020","acknowledgement":"We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST).","file_date_updated":"2021-03-16T23:30:04Z","ec_funded":1,"date_published":"2020-03-01T00:00:00Z","article_type":"original","page":"877–894","publication":"Journal of Optimization Theory and Applications","citation":{"ista":"Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894.","apa":"Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6","ieee":"Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020.","ama":"Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6","chicago":"Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.","mla":"Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.","short":"Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"date_created":"2020-10-12T10:40:27Z","date_updated":"2021-03-16T23:30:04Z","checksum":"9f6dc6c6bf2b48cb3a2091a9ed5feaf2","file_id":"8647","embargo":"2021-03-15","relation":"main_file","creator":"dernst","file_size":332641,"content_type":"application/pdf","file_name":"2020_JourOptimizationTheoryApplic_Shehu.pdf","access_level":"open_access"}],"status":"public","ddc":["518","510","515"],"title":"Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces","intvolume":" 184","_id":"7161","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature."}],"type":"journal_article"},{"author":[{"full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","first_name":"Isabella"},{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok"},{"last_name":"Lagator","first_name":"M.","full_name":"Lagator, M."},{"full_name":"Andersson, A. M. C.","last_name":"Andersson","first_name":"A. M. C."},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"related_material":{"record":[{"id":"8155","relation":"dissertation_contains","status":"public"},{"relation":"research_data","status":"public","id":"7383"},{"id":"7016","relation":"research_data","status":"public"},{"id":"8653","relation":"used_in_publication","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2020-04-08T15:20:53Z","date_updated":"2024-03-28T23:30:37Z","volume":4,"year":"2020","acknowledgement":"We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-10-09T09:56:01Z","doi":"10.1038/s41559-020-1132-7","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000519008300005"]},"quality_controlled":"1","isi":1,"project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2397-334X"]},"oa_version":"Submitted Version","file":[{"success":1,"checksum":"ef3bbf42023e30b2c24a6278025d2040","date_created":"2020-10-09T09:56:01Z","date_updated":"2020-10-09T09:56:01Z","file_id":"8640","relation":"main_file","creator":"dernst","file_size":745242,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_NatureEcolEvo_Tomanek.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7652","status":"public","ddc":["570"],"title":"Gene amplification as a form of population-level gene expression regulation","intvolume":" 4","abstract":[{"text":"Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2020-04-01T00:00:00Z","publication":"Nature Ecology & Evolution","citation":{"mla":"Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no. 4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.","short":"I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik, C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.","chicago":"Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature, 2020. https://doi.org/10.1038/s41559-020-1132-7.","ama":"Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625. doi:10.1038/s41559-020-1132-7","ista":"Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC. 2020. Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. 4(4), 612–625.","ieee":"I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology & Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.","apa":"Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik, G., & Guet, C. C. (2020). Gene amplification as a form of population-level gene expression regulation. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-020-1132-7"},"article_type":"original","page":"612-625","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"date_published":"2020-01-13T00:00:00Z","citation":{"short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","mla":"Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:10.15479/AT:ISTA:7258","apa":"Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria."},"page":"174","day":"13","article_processing_charge":"No","has_accepted_license":"1","oa_version":"None","file":[{"file_id":"7259","relation":"source_file","date_created":"2020-01-12T15:57:14Z","date_updated":"2021-01-13T23:30:05Z","checksum":"4df1ab24e9896635106adde5a54615bf","file_name":"2020_Scarselli_Thesis.zip","embargo_to":"open_access","access_level":"closed","creator":"dscarsel","file_size":26640830,"content_type":"application/zip"},{"relation":"main_file","embargo":"2021-01-12","file_id":"7260","date_updated":"2021-01-13T23:30:05Z","date_created":"2020-01-12T15:56:14Z","checksum":"48659ab98e3414293c7a721385c2fd1c","file_name":"2020_Scarselli_Thesis.pdf","access_level":"open_access","file_size":8515844,"content_type":"application/pdf","creator":"dscarsel"}],"_id":"7258","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["532"],"title":"New approaches to reduce friction in turbulent pipe flow","abstract":[{"lang":"eng","text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:7258","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"},{"call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines","grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425"},{"name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","_id":"25136C54-B435-11E9-9278-68D0E5697425","grant_number":"HO 4393/1-2"}],"month":"01","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Scarselli, Davide","last_name":"Scarselli","first_name":"Davide","orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6228","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6486"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"422"}]},"date_updated":"2023-09-15T12:20:08Z","date_created":"2020-01-12T16:07:26Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BjHo"}],"file_date_updated":"2021-01-13T23:30:05Z","ec_funded":1},{"abstract":[{"text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"embargo_to":"open_access","file_name":"Thesis_ITomanek_final_201016.docx","access_level":"closed","file_size":25131884,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"itomanek","relation":"source_file","file_id":"8666","date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","checksum":"c01d9f59794b4b70528f37637c17ad02"},{"date_created":"2020-10-16T12:14:21Z","date_updated":"2021-10-20T22:30:03Z","checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","relation":"main_file","file_id":"8667","embargo":"2021-10-19","file_size":15405675,"content_type":"application/pdf","creator":"itomanek","file_name":"Thesis_ITomanek_final_201016.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"8653","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"status":"public","title":"The evolution of gene expression by copy number and point mutations","day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"date_published":"2020-10-13T00:00:00Z","citation":{"chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653"},"page":"117","file_date_updated":"2021-10-20T22:30:03Z","author":[{"full_name":"Tomanek, Isabella","last_name":"Tomanek","first_name":"Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"7652","relation":"research_data","status":"public"}]},"date_created":"2020-10-13T13:02:33Z","date_updated":"2023-09-07T13:22:42Z","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"month":"10","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8653","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1},{"publisher":"Cell Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong (Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University), Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing published materials; Jana Riederer for help with cantharidin physiological analysis; David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´ for technical support with tobacco cells; Lucia Strader (Washington University), Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas Mach (BOKU) for helpful discussions; and bioimaging and life science facilities of IST Austria for continuous support. We gratefully acknowledge the Nottingham Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research leading to these results has received funding from the European Union’s Horizon 2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. S.T. was supported by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N. was supported by the Ministry of Education, Youth and Sports of the Czech Republic (European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’ no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no. CZ.2.16/3.1.00/21519). ","year":"2020","volume":30,"date_created":"2020-02-02T23:01:00Z","date_updated":"2024-03-28T23:30:38Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8822"}]},"author":[{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas","first_name":"Melinda F","full_name":"Abas, Melinda F"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub"},{"full_name":"Lasák, Pavel","first_name":"Pavel","last_name":"Lasák"},{"first_name":"Ivan","last_name":"Petřík","full_name":"Petřík, Ivan"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"full_name":"Pospíšil, Jiří","last_name":"Pospíšil","first_name":"Jiří"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"ec_funded":1,"file_date_updated":"2020-09-22T09:51:28Z","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000511287900018"],"pmid":["31956021"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1016/j.cub.2019.11.058","publication_identifier":{"issn":["09609822"]},"month":"02","intvolume":" 30","status":"public","title":"Salicylic acid targets protein phosphatase 2A to attenuate growth in plants","ddc":["580"],"_id":"7427","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":5360135,"content_type":"application/pdf","creator":"dernst","file_name":"2020_CurrentBiology_Tan.pdf","access_level":"open_access","date_created":"2020-09-22T09:51:28Z","date_updated":"2020-09-22T09:51:28Z","checksum":"16f7d51fe28f91c21e4896a2028df40b","success":1,"relation":"main_file","file_id":"8555"}],"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense."}],"page":"381-395.e8","article_type":"original","citation":{"ama":"Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8. doi:10.1016/j.cub.2019.11.058","apa":"Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., … Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058","ieee":"S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8, 2020.","ista":"Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid targets protein phosphatase 2A to attenuate growth in plants. Current Biology. 30(3), 381–395.e8.","short":"S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák, I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current Biology 30 (2020) 381–395.e8.","mla":"Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p. 381–395.e8, doi:10.1016/j.cub.2019.11.058.","chicago":"Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar, Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058."},"publication":"Current Biology","date_published":"2020-02-03T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03"},{"abstract":[{"lang":"eng","text":"Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.\r\nIn the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts."}],"issue":"5","type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"17de728b0205979feb95ce663ba918c2","date_updated":"2020-11-20T09:32:10Z","date_created":"2020-11-20T09:32:10Z","file_id":"8781","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2106888,"access_level":"open_access","file_name":"2020_NewPhytologist_Mazur.pdf"}],"_id":"7500","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["580"],"title":"Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis","intvolume":" 226","day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-06-01T00:00:00Z","publication":"New Phytologist","citation":{"apa":"Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. Wiley. https://doi.org/10.1111/nph.16446","ieee":"E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.","ista":"Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 226(5), 1375–1383.","ama":"Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist. 2020;226(5):1375-1383. doi:10.1111/nph.16446","chicago":"Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.","short":"E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.","mla":"Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley, 2020, pp. 1375–83, doi:10.1111/nph.16446."},"article_type":"original","page":"1375-1383","file_date_updated":"2020-11-20T09:32:10Z","ec_funded":1,"author":[{"last_name":"Mazur","first_name":"E","full_name":"Mazur, E"},{"id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","last_name":"Kulik","first_name":"Ivan","full_name":"Kulik, Ivan"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"record":[{"id":"8822","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:38Z","date_created":"2020-02-18T10:03:47Z","volume":226,"acknowledgement":"We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of CEITEC Masaryk University for help in generating essential data. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 742985) and the Czech Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology. The authors declare no competing interests.","year":"2020","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"month":"06","publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"doi":"10.1111/nph.16446","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31971254"],"isi":["000514939700001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Cell surface receptor complexes for PIN polarity and auxin-mediated development","_id":"2699E3D2-B435-11E9-9278-68D0E5697425","grant_number":"25239"}]},{"publication_identifier":{"issn":["2663-337X"]},"month":"12","doi":"10.15479/AT:ISTA:8822","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file_date_updated":"2021-12-08T23:30:03Z","related_material":{"record":[{"id":"7427","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"id":"7500","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"191"},{"id":"449","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub"}],"date_created":"2020-12-01T12:38:18Z","date_updated":"2023-09-19T10:39:33Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2020-12-01T00:00:00Z","citation":{"mla":"Hajny, Jakub. Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:10.15479/AT:ISTA:8822","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","apa":"Hajny, J. (2020). Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020."},"page":"249","abstract":[{"text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_id":"8919","relation":"source_file","date_created":"2020-12-04T07:27:52Z","date_updated":"2021-07-16T22:30:03Z","checksum":"210a9675af5e4c78b0b56d920ac82866","file_name":"Jakub Hajný IST Austria final_JH.docx","embargo_to":"open_access","access_level":"closed","creator":"jhajny","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":91279806},{"access_level":"open_access","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","content_type":"application/pdf","file_size":68707697,"creator":"jhajny","relation":"main_file","embargo":"2021-12-07","file_id":"8933","checksum":"1781385b4aa73eba89cc76c6172f71d2","date_created":"2020-12-09T15:04:41Z","date_updated":"2021-12-08T23:30:03Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8822","ddc":["580"],"status":"public","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration"},{"doi":"10.15479/AT:ISTA:8350","degree_awarded":"PhD","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa":1,"month":"09","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"}],"related_material":{"record":[{"id":"661","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6508"},{"relation":"part_of_dissertation","status":"public","id":"7001"},{"status":"public","relation":"part_of_dissertation","id":"735"}]},"date_updated":"2023-09-27T14:16:45Z","date_created":"2020-09-09T11:12:10Z","acknowledgement":"I would have had no fish and hence no results without our wonderful fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak. Special thanks to Verena for being always happy to help and dealing with our chaotic schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and EM facilities at IST Austria for supporting us every day. Very special thanks would go to Robert Hauschild for his continuous support on data analysis and also to Jack Merrin for designing and building microfabricated chambers for the project and for the various discussions on making zebrafish extracts.","year":"2020","publication_status":"published","department":[{"_id":"BjHo"},{"_id":"CaHe"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-11T22:30:05Z","date_published":"2020-09-09T00:00:00Z","citation":{"chicago":"Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.","mla":"Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.","short":"S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes , Institute of Science and Technology Austria, 2020.","ista":"Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria.","ieee":"S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes ,” Institute of Science and Technology Austria, 2020.","apa":"Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350","ama":"Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes . 2020. doi:10.15479/AT:ISTA:8350"},"page":"107","day":"09","has_accepted_license":"1","article_processing_charge":"No","oa_version":"None","file":[{"file_name":"Shayan-Thesis-Final.docx","embargo_to":"open_access","access_level":"closed","creator":"sshamip","file_size":65194814,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8351","relation":"source_file","date_updated":"2021-09-11T22:30:05Z","date_created":"2020-09-09T11:06:27Z","checksum":"6e47871c74f85008b9876112eb3fcfa1"},{"content_type":"application/pdf","file_size":23729605,"creator":"sshamip","file_name":"Shayan-Thesis-Final.pdf","access_level":"open_access","date_created":"2020-09-09T11:06:13Z","date_updated":"2021-09-11T22:30:05Z","checksum":"1b44c57f04d7e8a6fe41b1c9c55a52a3","relation":"main_file","embargo":"2021-09-10","file_id":"8352"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8350","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes ","ddc":["570"],"status":"public","abstract":[{"text":"Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood.\r\nIn this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein.\r\nCollectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"article_number":"574382","ec_funded":1,"file_date_updated":"2020-09-28T13:11:17Z","pmid":1,"acknowledgement":"AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.","year":"2020","department":[{"_id":"SiHi"}],"publisher":"Frontiers","publication_status":"published","related_material":{"record":[{"id":"9962","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Hansen, Andi H","last_name":"Hansen","first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"volume":8,"date_updated":"2024-03-28T23:30:41Z","date_created":"2020-09-26T06:11:07Z","publication_identifier":{"issn":["2296-634X"]},"month":"09","external_id":{"pmid":["33102480"],"isi":["000577915900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.3389/fcell.2020.574382","language":[{"iso":"eng"}],"type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8569","intvolume":" 8","status":"public","ddc":["570"],"title":"Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex","oa_version":"Published Version","file":[{"creator":"dernst","file_size":5527139,"content_type":"application/pdf","file_name":"2020_Frontiers_Hansen.pdf","access_level":"open_access","date_created":"2020-09-28T13:11:17Z","date_updated":"2020-09-28T13:11:17Z","success":1,"checksum":"01f731824194c94c81a5da360d997073","file_id":"8584","relation":"main_file"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"25","citation":{"ista":"Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 8(9), 574382.","apa":"Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382","ieee":"A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex,” Frontiers in Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.","ama":"Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental Biology. 2020;8(9). doi:10.3389/fcell.2020.574382","chicago":"Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.","mla":"Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020, doi:10.3389/fcell.2020.574382.","short":"A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology 8 (2020)."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","date_published":"2020-09-25T00:00:00Z"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"author":[{"full_name":"Beattie, Robert J","last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"date_created":"2020-05-11T08:31:20Z","date_updated":"2024-03-28T23:30:42Z","year":"2020","department":[{"_id":"SiHi"}],"publisher":"MyJove Corporation","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","article_number":"e61147","doi":"10.3791/61147","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000546406600043"]},"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"},{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T0101031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1940-087X"]},"month":"05","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-11T08:28:38Z","checksum":"3154ea7f90b9fb45e084cd1c2770597d","file_id":"7816","relation":"main_file","creator":"rbeattie","file_size":1352186,"content_type":"application/pdf","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","access_level":"open_access"}],"_id":"7815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","ddc":["570"],"status":"public","issue":"159","abstract":[{"lang":"eng","text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present."}],"type":"journal_article","date_published":"2020-05-08T00:00:00Z","citation":{"chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147.","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","ieee":"R. J. Beattie et al., “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” Journal of Visual Experiments, no. 159. MyJove Corporation, 2020.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. 2020;(159). doi:10.3791/61147"},"publication":"Journal of Visual Experiments","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1"},{"date_created":"2020-05-29T08:27:32Z","date_updated":"2023-10-18T08:45:16Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6830"},{"status":"public","relation":"dissertation_contains","id":"28"},{"id":"7815","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"SiHi"}],"publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"supervisor":[{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7902","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","file":[{"checksum":"43c172bf006c95b65992d473c7240d13","date_updated":"2021-06-07T22:30:03Z","date_created":"2020-06-05T08:18:08Z","file_id":"7927","relation":"source_file","creator":"xcontreras","file_size":53134142,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"PhDThesis_Contreras.docx","embargo_to":"open_access"},{"embargo":"2021-06-06","file_id":"7928","relation":"main_file","date_created":"2020-06-05T08:18:07Z","date_updated":"2021-06-07T22:30:03Z","checksum":"addfed9128271be05cae3608e03a6ec0","file_name":"PhDThesis_Contreras.pdf","access_level":"open_access","creator":"xcontreras","content_type":"application/pdf","file_size":35117191}],"oa_version":"Published Version","status":"public","title":"Genetic dissection of neural development in health and disease at single cell resolution","ddc":["570"],"_id":"7902","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2020-06-05T00:00:00Z","page":"214","citation":{"mla":"Contreras, Ximena. Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7902.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020.","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7902.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","apa":"Contreras, X. (2020). Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7902"},"has_accepted_license":"1","article_processing_charge":"No","day":"05"},{"author":[{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Huttenlocher, Anna","first_name":"Anna","last_name":"Huttenlocher"}],"volume":219,"date_created":"2020-08-02T22:00:57Z","date_updated":"2023-10-17T10:04:49Z","year":"2020","department":[{"_id":"MiSi"}],"publisher":"Rockefeller University Press","publication_status":"published","file_date_updated":"2021-02-02T23:30:03Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_number":"e202007029","doi":"10.1083/jcb.202007029","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"external_id":{"isi":["000573631000004"]},"isi":1,"publication_identifier":{"eissn":["1540-8140"]},"month":"07","file":[{"file_name":"2020_JCB_Sixt.pdf","access_level":"open_access","file_size":830725,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8200","embargo":"2021-02-01","date_updated":"2021-02-02T23:30:03Z","date_created":"2020-08-04T13:11:52Z","checksum":"30016d778d266b8e17d01094917873b8"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8190","intvolume":" 219","ddc":["570"],"status":"public","title":"Zena Werb (1945-2020): Cell biology in context","issue":"8","type":"journal_article","date_published":"2020-07-22T00:00:00Z","citation":{"ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press, 2020.","apa":"Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202007029","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.","short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” The Journal of Cell Biology. Rockefeller University Press, 2020. https://doi.org/10.1083/jcb.202007029."},"publication":"The Journal of Cell Biology","article_type":"letter_note","article_processing_charge":"No","has_accepted_license":"1","day":"22","scopus_import":"1"},{"article_number":"eabc8895","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2021-01-07T12:44:33Z","publisher":"AAAS","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","year":"2020","volume":6,"date_updated":"2024-03-28T23:30:44Z","date_created":"2021-01-03T23:01:23Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"author":[{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"full_name":"Zhang, Xixi","last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"eissn":["2375-2548"]},"month":"12","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abc8895","type":"journal_article","issue":"50","abstract":[{"lang":"eng","text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants."}],"intvolume":" 6","ddc":["580"],"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8986","oa_version":"Published Version","file":[{"success":1,"checksum":"5ac2500b191c08ef6dab5327f40ff663","date_created":"2021-01-07T12:44:33Z","date_updated":"2021-01-07T12:44:33Z","file_id":"8994","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":10578145,"access_level":"open_access","file_name":"2020_ScienceAdvances_Zhang.pdf"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"11","article_type":"original","citation":{"chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895.","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020.","apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895"},"publication":"Science Advances","date_published":"2020-12-11T00:00:00Z"},{"file":[{"relation":"main_file","file_id":"8292","checksum":"03b039244e6ae80580385fd9f577e2b2","success":1,"date_created":"2020-08-25T09:53:50Z","date_updated":"2020-08-25T09:53:50Z","access_level":"open_access","file_name":"2020_IntMolecSciences_Chen.pdf","file_size":5718755,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","_id":"8283","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling","ddc":["570"],"status":"public","intvolume":" 21","abstract":[{"lang":"eng","text":"Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. "}],"issue":"16","type":"journal_article","date_published":"2020-08-10T00:00:00Z","publication":"International Journal of Molecular Sciences","citation":{"short":"H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X. Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).","mla":"Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.","chicago":"Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada, Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21165727.","ama":"Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727","ieee":"H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling,” International Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.","apa":"Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020). AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21165727","ista":"Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y. 2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling. International Journal of Molecular Sciences. 21(16), 5272."},"article_type":"original","day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"last_name":"Lai","first_name":"Linyi","full_name":"Lai, Linyi"},{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"first_name":"Liping","last_name":"Liu","full_name":"Liu, Liping"},{"last_name":"Jakada","first_name":"Bello Hassan","full_name":"Jakada, Bello Hassan"},{"full_name":"Huang, Youmei","first_name":"Youmei","last_name":"Huang"},{"first_name":"Qing","last_name":"He","full_name":"He, Qing"},{"first_name":"Mengnan","last_name":"Chai","full_name":"Chai, Mengnan"},{"first_name":"Xiaoping","last_name":"Niu","full_name":"Niu, Xiaoping"},{"full_name":"Qin, Yuan","first_name":"Yuan","last_name":"Qin"}],"related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-08-24T06:24:03Z","date_updated":"2024-03-28T23:30:44Z","volume":21,"year":"2020","acknowledgement":"We would like to thank the reviewers for their helpful comments on the original manuscript. ","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"file_date_updated":"2020-08-25T09:53:50Z","article_number":"5272","doi":"10.3390/ijms21165727","language":[{"iso":"eng"}],"external_id":{"pmid":["32785037"],"isi":["000565090300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"08","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]}},{"external_id":{"pmid":["32616560"],"isi":["000561047900021"]},"oa":1,"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1242/jcs.248062","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"08","pmid":1,"year":"2020","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","publisher":"The Company of Biologists","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"author":[{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","first_name":"Nataliia","last_name":"Gnyliukh"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"last_name":"Vert","first_name":"G","full_name":"Vert, G"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"volume":133,"date_updated":"2023-12-01T13:51:07Z","date_created":"2020-07-21T08:58:19Z","article_number":"jcs248062","ec_funded":1,"file_date_updated":"2021-08-08T22:30:03Z","citation":{"short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:10.1242/jcs.248062.","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 2020;133(15). doi:10.1242/jcs.248062","ieee":"A. J. Johnson et al., “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.","apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062."},"publication":"Journal of Cell Science","article_type":"original","date_published":"2020-08-06T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8139","intvolume":" 133","status":"public","ddc":["575"],"title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","file":[{"relation":"main_file","embargo":"2021-08-07","file_id":"8815","date_created":"2020-11-26T17:12:51Z","date_updated":"2021-08-08T22:30:03Z","checksum":"2d11f79a0b4e0a380fb002b933da331a","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","access_level":"open_access","file_size":15150403,"content_type":"application/pdf","creator":"ajohnson"}],"oa_version":"Published Version","type":"journal_article","issue":"15","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}]},{"issue":"3","abstract":[{"text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_PlantComm_Semeradova.pdf","content_type":"application/pdf","file_size":840289,"creator":"dernst","relation":"main_file","file_id":"9161","checksum":"785b266d82a94b007cf40dbbe7c4847e","success":1,"date_updated":"2021-02-18T10:23:59Z","date_created":"2021-02-18T10:23:59Z"}],"oa_version":"Published Version","intvolume":" 1","ddc":["580"],"title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9160","has_accepted_license":"1","article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2020-05-11T00:00:00Z","article_type":"original","citation":{"short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications, vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 2020;1(3). doi:10.1016/j.xplc.2020.100048","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” Plant Communications, vol. 1, no. 3. Elsevier, 2020.","apa":"Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048."},"publication":"Plant Communications","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-02-18T10:23:59Z","article_number":"100048","volume":1,"date_updated":"2024-03-28T23:30:47Z","date_created":"2021-02-18T10:18:43Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10135"}]},"author":[{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana","full_name":"Semeradova, Hana"},{"orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C","full_name":"Montesinos López, Juan C"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","year":"2020","publication_identifier":{"issn":["2590-3462"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2020.100048","project":[{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["33367243"],"isi":["000654052800010"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1},{"publication_identifier":{"issn":["1741-7007"]},"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"external_id":{"pmid":["31640700"]},"oa":1,"quality_controlled":"1","doi":"10.1186/s12915-019-0700-2","language":[{"iso":"eng"}],"article_number":"82","file_date_updated":"2021-11-26T11:37:54Z","extern":"1","pmid":1,"year":"2019","acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"volume":17,"date_updated":"2021-11-26T11:54:29Z","date_created":"2021-11-26T11:25:03Z","scopus_import":"1","keyword":["cell biology"],"article_processing_charge":"No","has_accepted_license":"1","day":"22","citation":{"apa":"Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019.","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2."},"publication":"BMC Biology","article_type":"original","date_published":"2019-10-22T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10354","intvolume":" 17","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"31d8bae55a376d30925f53f7e1a02396","success":1,"date_updated":"2021-11-26T11:37:54Z","date_created":"2021-11-26T11:37:54Z","relation":"main_file","file_id":"10356","content_type":"application/pdf","file_size":1648926,"creator":"cchlebak","access_level":"open_access","file_name":"2019_BMCBio_Harker_Kirschneck.pdf"}]},{"citation":{"ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019.","apa":"Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018."},"publication":"Current Opinion in Structural Biology","page":"43-52","article_type":"original","date_published":"2019-06-18T00:00:00Z","scopus_import":"1","keyword":["molecular biology","structural biology"],"article_processing_charge":"No","day":"18","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10355","intvolume":" 58","status":"public","title":"Minimal coarse-grained models for molecular self-organisation in biology","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}],"external_id":{"pmid":["31226513"]},"oa":1,"quality_controlled":"1","doi":"10.1016/j.sbi.2019.05.018","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-440X"]},"month":"06","pmid":1,"year":"2019","acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","publisher":"Elsevier","publication_status":"published","author":[{"last_name":"Hafner","first_name":"Anne E","full_name":"Hafner, Anne E"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"volume":58,"date_created":"2021-11-26T11:33:21Z","date_updated":"2021-11-26T11:54:25Z","extern":"1"},{"citation":{"mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3.","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3.","ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3","ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","ieee":"H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3"},"publication":"Nature Physics","page":"1011-1016","article_type":"original","date_published":"2019-08-05T00:00:00Z","scopus_import":"1","keyword":["general physics and astronomy"],"article_processing_charge":"No","day":"05","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"10621","intvolume":" 15","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","status":"public","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.00763"}],"external_id":{"arxiv":["1902.00763"]},"quality_controlled":"1","doi":"10.1038/s41567-019-0596-3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"08","year":"2019","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"first_name":"Yuxuan","last_name":"Zhang","full_name":"Zhang, Yuxuan"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"}],"volume":15,"date_updated":"2022-01-20T09:33:38Z","date_created":"2022-01-13T15:00:58Z","extern":"1"},{"intvolume":" 19","status":"public","title":"Manipulating multivortex states in superconducting structures","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"10622","oa_version":"Preprint","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing."}],"page":"5476-5482","article_type":"original","citation":{"ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983.","short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983."},"publication":"Nano Letters","date_published":"2019-06-27T00:00:00Z","keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"scopus_import":"1","article_processing_charge":"No","day":"27","publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","volume":19,"date_updated":"2022-01-13T15:41:24Z","date_created":"2022-01-13T15:11:14Z","author":[{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"extern":"1","quality_controlled":"1","external_id":{"arxiv":["1905.06303"],"pmid":["31246034"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.06303","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.9b01983","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"06"},{"issue":"6431","abstract":[{"text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"10625","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 363","title":"Tuning superconductivity in twisted bilayer graphene","status":"public","article_processing_charge":"No","day":"24","scopus_import":"1","keyword":["multidisciplinary"],"date_published":"2019-01-24T00:00:00Z","citation":{"chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science. American Association for the Advancement of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910.","mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910.","short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.","ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910","ieee":"M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,” Science, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019.","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910"},"publication":"Science","page":"1059-1064","article_type":"original","extern":"1","author":[{"full_name":"Yankowitz, Matthew","last_name":"Yankowitz","first_name":"Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"last_name":"Zhang","first_name":"Yuxuan","full_name":"Zhang, Yuxuan"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"first_name":"David","last_name":"Graf","full_name":"Graf, David"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."},{"full_name":"Dean, Cory R.","last_name":"Dean","first_name":"Cory R."}],"volume":363,"date_created":"2022-01-14T12:14:58Z","date_updated":"2022-01-14T13:48:32Z","pmid":1,"year":"2019","acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","publisher":"American Association for the Advancement of Science (AAAS)","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"01","doi":"10.1126/science.aav1910","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07865"}],"external_id":{"arxiv":["1808.07865"],"pmid":["30679385 "]},"oa":1,"quality_controlled":"1"},{"extern":"1","date_updated":"2022-01-13T15:34:44Z","date_created":"2022-01-13T14:45:16Z","volume":16,"author":[{"full_name":"Zhou, H.","last_name":"Zhou","first_name":"H."},{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"publication_status":"published","publisher":"Springer Nature","acknowledgement":"We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard Foundation and and Alfred. P. Sloan Foundation.","year":"2019","month":"12","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41567-019-0729-8","quality_controlled":"1","abstract":[{"text":"Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"None","title":"Solids of quantum Hall skyrmions in graphene","status":"public","intvolume":" 16","_id":"10620","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","day":"16","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"scopus_import":"1","date_published":"2019-12-16T00:00:00Z","article_type":"original","page":"154-158","publication":"Nature Physics","citation":{"ama":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Solids of quantum Hall skyrmions in graphene. Nature Physics. 2019;16(2):154-158. doi:10.1038/s41567-019-0729-8","ieee":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Solids of quantum Hall skyrmions in graphene,” Nature Physics, vol. 16, no. 2. Springer Nature, pp. 154–158, 2019.","apa":"Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., & Young, A. F. (2019). Solids of quantum Hall skyrmions in graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0729-8","ista":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2019. Solids of quantum Hall skyrmions in graphene. Nature Physics. 16(2), 154–158.","short":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics 16 (2019) 154–158.","mla":"Zhou, H., et al. “Solids of Quantum Hall Skyrmions in Graphene.” Nature Physics, vol. 16, no. 2, Springer Nature, 2019, pp. 154–58, doi:10.1038/s41567-019-0729-8.","chicago":"Zhou, H., Hryhoriy Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young. “Solids of Quantum Hall Skyrmions in Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0729-8."}},{"type":"journal_article","abstract":[{"text":"Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream\r\nof experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points.","lang":"eng"}],"publisher":"Simons Foundation ; University of California, Riverside","intvolume":" 3","publication_status":"published","title":"New correlated phenomena in magic-angle twisted bilayer graphene/s","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10664","year":"2019","oa_version":"Published Version","volume":"03","date_updated":"2022-01-25T15:56:39Z","date_created":"2022-01-25T15:09:58Z","author":[{"last_name":"Yankowitz","first_name":"Mathew","full_name":"Yankowitz, Mathew"},{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"full_name":"Graf, David","last_name":"Graf","first_name":"David"},{"last_name":"Young","first_name":"Andrea F.","full_name":"Young, Andrea F."},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."},{"full_name":"Sharpe, Aaron L.","last_name":"Sharpe","first_name":"Aaron L."},{"last_name":"Fox","first_name":"E.J.","full_name":"Fox, E.J."},{"first_name":"A.W.","last_name":"Barnard","full_name":"Barnard, A.W."},{"last_name":"Finney","first_name":"Joe","full_name":"Finney, Joe"}],"article_processing_charge":"No","month":"02","day":"28","quality_controlled":"1","article_type":"original","main_file_link":[{"url":"https://www.condmatjclub.org/?p=3541","open_access":"1"}],"oa":1,"citation":{"mla":"Yankowitz, Mathew, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics, vol. 03, Simons Foundation ; University of California, Riverside, 2019, doi:10.36471/jccm_february_2019_03.","short":"M. Yankowitz, S. Chen, H. Polshyn, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, A.L. Sharpe, E.J. Fox, A.W. Barnard, J. Finney, Journal Club for Condensed Matter Physics 03 (2019).","chicago":"Yankowitz, Mathew, Shaowen Chen, Hryhoriy Polshyn, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, et al. “New Correlated Phenomena in Magic-Angle Twisted Bilayer Graphene/S.” Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside, 2019. https://doi.org/10.36471/jccm_february_2019_03.","ama":"Yankowitz M, Chen S, Polshyn H, et al. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 2019;03. doi:10.36471/jccm_february_2019_03","ista":"Yankowitz M, Chen S, Polshyn H, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR, Sharpe AL, Fox EJ, Barnard AW, Finney J. 2019. New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. 03.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D., … Finney, J. (2019). New correlated phenomena in magic-angle twisted bilayer graphene/s. Journal Club for Condensed Matter Physics. Simons Foundation ; University of California, Riverside. https://doi.org/10.36471/jccm_february_2019_03","ieee":"M. Yankowitz et al., “New correlated phenomena in magic-angle twisted bilayer graphene/s,” Journal Club for Condensed Matter Physics, vol. 03. Simons Foundation ; University of California, Riverside, 2019."},"publication":"Journal Club for Condensed Matter Physics","language":[{"iso":"eng"}],"doi":"10.36471/jccm_february_2019_03","date_published":"2019-02-28T00:00:00Z"},{"extern":"1","year":"2019","acknowledgement":"The authors acknowledge discussions with A. Macdonald, Y. Saito, and M. Zaletel.","pmid":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","author":[{"last_name":"Serlin","first_name":"M.","full_name":"Serlin, M."},{"full_name":"Tschirhart, C. L.","first_name":"C. L.","last_name":"Tschirhart"},{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Y.","first_name":"Y.","last_name":"Zhang"},{"first_name":"J.","last_name":"Zhu","full_name":"Zhu, J."},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"last_name":"Balents","first_name":"L.","full_name":"Balents, L."},{"first_name":"A. F.","last_name":"Young","full_name":"Young, A. F."}],"related_material":{"record":[{"status":"public","relation":"other","id":"10697"},{"id":"10698","status":"public","relation":"other"},{"relation":"other","status":"public","id":"10699"}]},"date_updated":"2023-02-21T16:00:09Z","date_created":"2022-01-13T14:21:32Z","volume":367,"month":"12","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"oa":1,"external_id":{"pmid":["31857492"],"arxiv":["1907.00261"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.00261","open_access":"1"}],"quality_controlled":"1","doi":"10.1126/science.aay5533","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory."}],"issue":"6480","_id":"10619","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure","status":"public","intvolume":" 367","oa_version":"Preprint","scopus_import":"1","keyword":["multidisciplinary"],"day":"19","article_processing_charge":"No","publication":"Science","citation":{"ama":"Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 2019;367(6480):900-903. doi:10.1126/science.aay5533","ieee":"M. Serlin et al., “Intrinsic quantized anomalous Hall effect in a moiré heterostructure,” Science, vol. 367, no. 6480. American Association for the Advancement of Science, pp. 900–903, 2019.","apa":"Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K., … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aay5533","ista":"Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 367(6480), 900–903.","short":"M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.","mla":"Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science, vol. 367, no. 6480, American Association for the Advancement of Science, 2019, pp. 900–03, doi:10.1126/science.aay5533.","chicago":"Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aay5533."},"article_type":"original","page":"900-903","date_published":"2019-12-19T00:00:00Z"},{"oa_version":"Published Version","title":"Normal state transport in superconducting twisted bilayer graphene","status":"public","intvolume":" 64","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10724","abstract":[{"text":"Twisted bilayer graphene (tBLG) near the flat band condition is a versatile new platform for the study of correlated physics in 2D. Resistive states have been observed at several commensurate fillings of the flat miniband, along with superconducting states near half filling. To better understand the electronic structure of this system, we study electronic transport of graphite gated superconducting tBLG devices in the normal regime. At high magnetic fields, we observe full lifting of the spin and valley degeneracy. The transitions in the splitting of this four-fold degeneracy as a function of carrier density indicate Landau level (LL) crossings, which tilted field measurements show occur between LLs with different valley polarization. Similar LL structure measured in two devices, one with twist angle θ=1.08° at ambient pressure and one at θ=1.27° and 1.33GPa, suggests that the dimensionless combination of twist angle and interlayer coupling controls the relevant details of the band structure. In addition, we find that the temperature dependence of the resistance at B=0 shows linear growth at several hundred Ohm/K in a broad range of temperatures. We discuss the implications for modeling the scattering processes in this system.","lang":"eng"}],"issue":"2","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","date_published":"2019-03-01T00:00:00Z","publication":"APS March Meeting 2019","citation":{"short":"H. Polshyn, Y. Zhang, M. Yankowitz, S. Chen, T. Taniguchi, K. Watanabe, D.E. Graf, C.R. Dean, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","mla":"Polshyn, Hryhoriy, et al. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” APS March Meeting 2019, vol. 64, no. 2, V14.00008, American Physical Society, 2019.","chicago":"Polshyn, Hryhoriy, Yuxuan Zhang, Matthew Yankowitz, Shaowen Chen, Takashi Taniguchi, Kenji Watanabe, David E. Graf, Cory R. Dean, and Andrea Young. “Normal State Transport in Superconducting Twisted Bilayer Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019.","ama":"Polshyn H, Zhang Y, Yankowitz M, et al. Normal state transport in superconducting twisted bilayer graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","apa":"Polshyn, H., Zhang, Y., Yankowitz, M., Chen, S., Taniguchi, T., Watanabe, K., … Young, A. (2019). Normal state transport in superconducting twisted bilayer graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"H. Polshyn et al., “Normal state transport in superconducting twisted bilayer graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ista":"Polshyn H, Zhang Y, Yankowitz M, Chen S, Taniguchi T, Watanabe K, Graf DE, Dean CR, Young A. 2019. Normal state transport in superconducting twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, V14.00008."},"day":"01","article_processing_charge":"No","date_created":"2022-02-04T12:25:04Z","date_updated":"2022-02-08T10:23:13Z","volume":64,"author":[{"first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Yuxuan","first_name":"Yuxuan","last_name":"Zhang"},{"first_name":"Matthew","last_name":"Yankowitz","full_name":"Yankowitz, Matthew"},{"full_name":"Chen, Shaowen","last_name":"Chen","first_name":"Shaowen"},{"last_name":"Taniguchi","first_name":"Takashi","full_name":"Taniguchi, Takashi"},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"full_name":"Graf, David E.","last_name":"Graf","first_name":"David E."},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}],"publication_status":"published","publisher":"American Physical Society","year":"2019","extern":"1","article_number":"V14.00008","language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","location":"Boston, MA, United States","start_date":"2019-03-04","end_date":"2019-03-08"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/V14.8"}],"oa":1,"month":"03","publication_identifier":{"issn":["0003-0503"]}},{"oa_version":"Published Version","status":"public","title":"Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy","intvolume":" 64","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10722","abstract":[{"lang":"eng","text":"Bilayer graphene, rotationally faulted to ~1.1 degree misalignment, has recently been shown to host superconducting and resistive states associated with the formation of a flat electronic band. While numerous theories exist for the origins of both states, direct validation of these theories remains an outstanding experimental problem. Here, we focus on the resistive states occurring at commensurate filling (1/2, 1/4, and 3/4) of the two lowest superlattice bands. We test theoretical proposals that these states arise due to broken spin—and/or valley—symmetry by performing direct magnetic imaging with nanoscale SQUID-on-tip microscopy. This technique provides single-spin resolved magnetometry on sub-100nm length scales. I will present imaging data from our 4.2K nSOT microscope on graphite-gated twisted bilayers near the flat band condition and discuss the implications for the physics of the commensurate resistive states."}],"issue":"2","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","date_published":"2019-03-01T00:00:00Z","publication":"APS March Meeting 2019","citation":{"ama":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","apa":"Serlin, M., Tschirhart, C., Polshyn, H., Zhu, J., Huber, M. E., & Young, A. (2019). Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M. E. Huber, and A. Young, “Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ista":"Serlin M, Tschirhart C, Polshyn H, Zhu J, Huber ME, Young A. 2019. Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, L14.00006.","short":"M. Serlin, C. Tschirhart, H. Polshyn, J. Zhu, M.E. Huber, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019.","mla":"Serlin, Marec, et al. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” APS March Meeting 2019, vol. 64, no. 2, L14.00006, American Physical Society, 2019.","chicago":"Serlin, Marec, Charles Tschirhart, Hryhoriy Polshyn, Jiacheng Zhu, Martin E. Huber, and Andrea Young. “Direct Imaging of Magnetic Structure in Twisted Bilayer Graphene with Scanning NanoSQUID-On-Tip Microscopy.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019."},"day":"01","article_processing_charge":"No","date_created":"2022-02-04T11:54:21Z","date_updated":"2022-02-08T10:25:30Z","volume":64,"author":[{"full_name":"Serlin, Marec","last_name":"Serlin","first_name":"Marec"},{"full_name":"Tschirhart, Charles","last_name":"Tschirhart","first_name":"Charles"},{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhu, Jiacheng","first_name":"Jiacheng","last_name":"Zhu"},{"last_name":"Huber","first_name":"Martin E.","full_name":"Huber, Martin E."},{"last_name":"Young","first_name":"Andrea","full_name":"Young, Andrea"}],"publication_status":"published","publisher":"American Physical Society","year":"2019","extern":"1","article_number":"L14.00006","language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","end_date":"2019-03-08","location":"Boston, MA, United States","start_date":"2019-03-04"},"quality_controlled":"1","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR19/Session/L14.6","open_access":"1"}],"oa":1,"month":"03","publication_identifier":{"issn":["0003-0503"]}},{"type":"conference","alternative_title":["Bulletin of the American Physical Society"],"abstract":[{"lang":"eng","text":"Bilayer graphene with ~ 1.1 degrees twist mismatch between the layers hosts a low energy flat band in which the Coulomb interaction is large relative to the bandwidth, promoting correlated insulating states at half band filling, and superconducting (SC) phases with dome-like structure neighboring correlated insulating states. Here we show measurements of a dual-graphite-gated twisted bilayer graphene device, which minimizes charge inhomogeneity. We observe new correlated phases, including for the first time a SC pocket near half-filling of the electron-doped band and resistive states at quarter-filling of both bands that emerge in a magnetic field. Changing the layer polarization with vertical electric field reveals an unexpected competition between SC and correlated insulator phases, which we interpret to result from differences in disorder of each graphene layer and underscores the spatial inhomogeneity like twist angle as a significant source of disorder in these devices [1]."}],"issue":"2","_id":"10725","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Correlated insulating and superconducting phases in twisted bilayer graphene","status":"public","intvolume":" 64","oa_version":"Published Version","day":"01","article_processing_charge":"No","publication":"APS March Meeting 2019","citation":{"short":"S. Chen, M. Yankowitz, H. Polshyn, K. Watanabe, T. Taniguchi, D.E. Graf, A. Young, C.R. Dean, in:, APS March Meeting 2019, American Physical Society, 2019.","mla":"Chen, Shaowen, et al. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” APS March Meeting 2019, vol. 64, no. 2, R14.00004, American Physical Society, 2019.","chicago":"Chen, Shaowen, Matthew Yankowitz, Hryhoriy Polshyn, Kenji Watanabe, Takashi Taniguchi, David E. Graf, Andrea Young, and Cory R. Dean. “Correlated Insulating and Superconducting Phases in Twisted Bilayer Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019.","ama":"Chen S, Yankowitz M, Polshyn H, et al. Correlated insulating and superconducting phases in twisted bilayer graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","apa":"Chen, S., Yankowitz, M., Polshyn, H., Watanabe, K., Taniguchi, T., Graf, D. E., … Dean, C. R. (2019). Correlated insulating and superconducting phases in twisted bilayer graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"S. Chen et al., “Correlated insulating and superconducting phases in twisted bilayer graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ista":"Chen S, Yankowitz M, Polshyn H, Watanabe K, Taniguchi T, Graf DE, Young A, Dean CR. 2019. Correlated insulating and superconducting phases in twisted bilayer graphene. APS March Meeting 2019. APS: American Physical Society, Bulletin of the American Physical Society, vol. 64, R14.00004."},"date_published":"2019-03-01T00:00:00Z","article_number":"R14.00004","extern":"1","year":"2019","publication_status":"published","publisher":"American Physical Society","author":[{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn"},{"last_name":"Watanabe","first_name":"Kenji","full_name":"Watanabe, Kenji"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"first_name":"David E.","last_name":"Graf","full_name":"Graf, David E."},{"full_name":"Young, Andrea","last_name":"Young","first_name":"Andrea"},{"full_name":"Dean, Cory R.","last_name":"Dean","first_name":"Cory R."}],"related_material":{"link":[{"url":"https://arxiv.org/abs/1808.07865","relation":"used_in_publication"}]},"date_updated":"2022-02-08T10:24:13Z","date_created":"2022-02-04T13:48:04Z","volume":64,"month":"03","publication_identifier":{"issn":["0003-0503"]},"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/R14.4"}],"oa":1,"quality_controlled":"1","conference":{"start_date":"2019-03-04","location":"Boston, MA, United States","end_date":"2019-03-08","name":"APS: American Physical Society"},"language":[{"iso":"eng"}]},{"intvolume":" 64","publisher":"American Physical Society","status":"public","publication_status":"published","title":"Spin wave transport through electron solids and fractional quantum Hall liquids in graphene","year":"2019","_id":"10723","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","volume":64,"date_created":"2022-02-04T12:14:02Z","date_updated":"2022-02-04T13:59:47Z","author":[{"full_name":"Zhou, Haoxin","last_name":"Zhou","first_name":"Haoxin"},{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"full_name":"Tanaguchi, Takashi","first_name":"Takashi","last_name":"Tanaguchi"},{"full_name":"Watanabe, Kenji","last_name":"Watanabe","first_name":"Kenji"},{"first_name":"Andrea","last_name":"Young","full_name":"Young, Andrea"}],"type":"conference","article_number":"P01.00004","extern":"1","issue":"2","abstract":[{"lang":"eng","text":"In monolayer graphene, the interplay of electronic correlations with the internal spin- and valley- degrees of freedom leads to a complex phase diagram of isospin symmetry breaking at high magnetic fields. Recently, Wei et al. (Science (2018)) demonstrated that spin waves can be electrically generated and detected in graphene heterojunctions, allowing direct experiment access to the spin degree of freedom. Here, we apply this technique to high quality graphite-gated graphene devices showing robust fractional quantum Hall phases and isospin phase transitions. We use an edgeless Corbino geometry to eliminate the contributions of edge states to the spin-wave mediated nonlocal voltage, allowing unambiguous identification of spin wave transport signatures. Our data reveal two phases within the ν = 1 plateau. For exactly ν=1, charge is localized but spin waves propagate freely while small carrier doping completely quenches the low-energy spin-wave transport, even as those charges remain localized. We identify this new phase as a spin textured electron solid. We also find that spin-wave transport is modulated by phase transitions in the valley order that preserve spin polarization, suggesting that this technique is sensitive to both spin and valley order."}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR19/Session/P01.4"}],"oa":1,"citation":{"ista":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. 2019. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. APS March Meeting 2019. APS: American Physical Society vol. 64, P01.00004.","apa":"Zhou, H., Polshyn, H., Tanaguchi, T., Watanabe, K., & Young, A. (2019). Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In APS March Meeting 2019 (Vol. 64). Boston, MA, United States: American Physical Society.","ieee":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, and A. Young, “Spin wave transport through electron solids and fractional quantum Hall liquids in graphene,” in APS March Meeting 2019, Boston, MA, United States, 2019, vol. 64, no. 2.","ama":"Zhou H, Polshyn H, Tanaguchi T, Watanabe K, Young A. Spin wave transport through electron solids and fractional quantum Hall liquids in graphene. In: APS March Meeting 2019. Vol 64. American Physical Society; 2019.","chicago":"Zhou, Haoxin, Hryhoriy Polshyn, Takashi Tanaguchi, Kenji Watanabe, and Andrea Young. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” In APS March Meeting 2019, Vol. 64. American Physical Society, 2019.","mla":"Zhou, Haoxin, et al. “Spin Wave Transport through Electron Solids and Fractional Quantum Hall Liquids in Graphene.” APS March Meeting 2019, vol. 64, no. 2, P01.00004, American Physical Society, 2019.","short":"H. Zhou, H. Polshyn, T. Tanaguchi, K. Watanabe, A. Young, in:, APS March Meeting 2019, American Physical Society, 2019."},"publication":"APS March Meeting 2019","language":[{"iso":"eng"}],"date_published":"2019-03-01T00:00:00Z","conference":{"name":"APS: American Physical Society","location":"Boston, MA, United States","start_date":"2019-03-04","end_date":"2019-03-08"},"article_processing_charge":"No","publication_identifier":{"issn":["0003-0503"]},"day":"01","month":"03"},{"date_published":"2019-05-25T00:00:00Z","citation":{"ama":"Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn","ista":"Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series in Computing, vol. 61, 1–13.","ieee":"G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol. 61, pp. 1–13.","apa":"Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella, E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13). Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn","mla":"Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.","short":"G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe, A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G. Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.","chicago":"Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn."},"publication":"ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems","page":"1-13","has_accepted_license":"1","article_processing_charge":"No","day":"25","scopus_import":"1","file":[{"relation":"main_file","file_id":"11391","checksum":"4b92e333db7b4e2349501a804dfede69","success":1,"date_updated":"2022-05-17T06:55:49Z","date_created":"2022-05-17T06:55:49Z","access_level":"open_access","file_name":"2019_EPiCs_Frehse.pdf","content_type":"application/pdf","file_size":346415,"creator":"dernst"}],"oa_version":"Published Version","_id":"10877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 61","ddc":["000"],"status":"public","title":"ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics","abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.","lang":"eng"}],"type":"conference","alternative_title":["EPiC Series in Computing"],"doi":"10.29007/rjwn","conference":{"end_date":"2019-04-15","location":"Montreal, Canada","start_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["2398-7340"]},"month":"05","author":[{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Abate, Alessandro","last_name":"Abate","first_name":"Alessandro"},{"full_name":"Adzkiya, Dieky","first_name":"Dieky","last_name":"Adzkiya"},{"full_name":"Becchi, Anna","last_name":"Becchi","first_name":"Anna"},{"first_name":"Lei","last_name":"Bu","full_name":"Bu, Lei"},{"last_name":"Cimatti","first_name":"Alessandro","full_name":"Cimatti, Alessandro"},{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe"},{"full_name":"Griggio, Alberto","first_name":"Alberto","last_name":"Griggio"},{"full_name":"Mover, Sergio","first_name":"Sergio","last_name":"Mover"},{"full_name":"Mufid, Muhammad Syifa'ul","last_name":"Mufid","first_name":"Muhammad Syifa'ul"},{"last_name":"Riouak","first_name":"Idriss","full_name":"Riouak, Idriss"},{"last_name":"Tonetta","first_name":"Stefano","full_name":"Tonetta, Stefano"},{"last_name":"Zaffanella","first_name":"Enea","full_name":"Zaffanella, Enea"}],"volume":61,"date_updated":"2022-05-17T07:09:47Z","date_created":"2022-03-18T12:29:23Z","year":"2019","acknowledgement":"The authors gratefully acknowledge \fnancial support by the European Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported by the National Natural Science\r\nFoundation of China (No.61572249).","editor":[{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"full_name":"Althoff, Matthias","first_name":"Matthias","last_name":"Althoff"}],"department":[{"_id":"ToHe"}],"publisher":"EasyChair","publication_status":"published","file_date_updated":"2022-05-17T06:55:49Z"},{"extern":"1","file_date_updated":"2022-04-08T08:26:32Z","date_updated":"2022-07-18T08:31:52Z","date_created":"2022-04-07T07:45:11Z","volume":218,"author":[{"full_name":"Toyama, Brandon H.","last_name":"Toyama","first_name":"Brandon H."},{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"full_name":"Lev-Ram, Varda","last_name":"Lev-Ram","first_name":"Varda"},{"first_name":"Ranjan","last_name":"Ramachandra","full_name":"Ramachandra, Ranjan"},{"full_name":"Deerinck, Thomas J.","first_name":"Thomas J.","last_name":"Deerinck"},{"last_name":"Lechene","first_name":"Claude","full_name":"Lechene, Claude"},{"full_name":"Ellisman, Mark H.","last_name":"Ellisman","first_name":"Mark H."},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}],"publication_status":"published","publisher":"Rockefeller University Press","year":"2019","pmid":1,"month":"02","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"doi":"10.1083/jcb.201809123","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"pmid":["30552100"]},"abstract":[{"text":"Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2503838,"file_name":"2019_JCB_Toyama.pdf","access_level":"open_access","date_updated":"2022-04-08T08:26:32Z","date_created":"2022-04-08T08:26:32Z","success":1,"checksum":"7964ebbf833b0b35f9fba840eea9531d","file_id":"11139","relation":"main_file"}],"ddc":["570"],"status":"public","title":"Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells","intvolume":" 218","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11061","day":"04","article_processing_charge":"No","has_accepted_license":"1","keyword":["Cell Biology"],"scopus_import":"1","date_published":"2019-02-04T00:00:00Z","article_type":"original","page":"433-444","publication":"Journal of Cell Biology","citation":{"ista":"Toyama BH, Arrojo e Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer M. 2019. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 218(2), 433–444.","apa":"Toyama, B. H., Arrojo e Drigo, R., Lev-Ram, V., Ramachandra, R., Deerinck, T. J., Lechene, C., … Hetzer, M. (2019). Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201809123","ieee":"B. H. Toyama et al., “Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells,” Journal of Cell Biology, vol. 218, no. 2. Rockefeller University Press, pp. 433–444, 2019.","ama":"Toyama BH, Arrojo e Drigo R, Lev-Ram V, et al. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 2019;218(2):433-444. doi:10.1083/jcb.201809123","chicago":"Toyama, Brandon H., Rafael Arrojo e Drigo, Varda Lev-Ram, Ranjan Ramachandra, Thomas J. Deerinck, Claude Lechene, Mark H. Ellisman, and Martin Hetzer. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology. Rockefeller University Press, 2019. https://doi.org/10.1083/jcb.201809123.","mla":"Toyama, Brandon H., et al. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology, vol. 218, no. 2, Rockefeller University Press, 2019, pp. 433–44, doi:10.1083/jcb.201809123.","short":"B.H. Toyama, R. Arrojo e Drigo, V. Lev-Ram, R. Ramachandra, T.J. Deerinck, C. Lechene, M.H. Ellisman, M. Hetzer, Journal of Cell Biology 218 (2019) 433–444."}},{"article_type":"original","page":"343-351.e3","publication":"Cell Metabolism","citation":{"ista":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.","apa":"Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. Cell Metabolism. Elsevier. https://doi.org/10.1016/j.cmet.2019.05.010","ieee":"R. Arrojo e Drigo et al., “Age mosaicism across multiple scales in adult tissues,” Cell Metabolism, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019.","ama":"Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 2019;30(2):343-351.e3. doi:10.1016/j.cmet.2019.05.010","chicago":"Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism. Elsevier, 2019. https://doi.org/10.1016/j.cmet.2019.05.010.","mla":"Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:10.1016/j.cmet.2019.05.010.","short":"R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3."},"date_published":"2019-08-06T00:00:00Z","keyword":["Cell Biology","Molecular Biology","Physiology"],"scopus_import":"1","day":"06","article_processing_charge":"No","status":"public","title":"Age mosaicism across multiple scales in adult tissues","intvolume":" 30","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11062","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization."}],"issue":"2","quality_controlled":"1","external_id":{"pmid":["31178361"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cmet.2019.05.010","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.cmet.2019.05.010","month":"08","publication_identifier":{"issn":["1550-4131"]},"publication_status":"published","publisher":"Elsevier","year":"2019","pmid":1,"date_updated":"2022-07-18T08:32:30Z","date_created":"2022-04-07T07:45:21Z","volume":30,"author":[{"first_name":"Rafael","last_name":"Arrojo e Drigo","full_name":"Arrojo e Drigo, Rafael"},{"full_name":"Lev-Ram, Varda","last_name":"Lev-Ram","first_name":"Varda"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"full_name":"Ramachandra, Ranjan","last_name":"Ramachandra","first_name":"Ranjan"},{"full_name":"Deerinck, Thomas","first_name":"Thomas","last_name":"Deerinck"},{"full_name":"Bushong, Eric","last_name":"Bushong","first_name":"Eric"},{"last_name":"Phan","first_name":"Sebastien","full_name":"Phan, Sebastien"},{"last_name":"Orphan","first_name":"Victoria","full_name":"Orphan, Victoria"},{"full_name":"Lechene, Claude","last_name":"Lechene","first_name":"Claude"},{"full_name":"Ellisman, Mark H.","first_name":"Mark H.","last_name":"Ellisman"},{"orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W"}],"extern":"1"},{"intvolume":" 20","status":"public","title":"Coaching from the sidelines: The nuclear periphery in genome regulation","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11059","oa_version":"None","type":"journal_article","issue":"1","abstract":[{"text":"The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing.","lang":"eng"}],"page":"39-50","article_type":"review","citation":{"ista":"Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.","apa":"Buchwalter, A., Kaneshiro, J. M., & Hetzer, M. (2019). Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. Springer Nature. https://doi.org/10.1038/s41576-018-0063-5","ieee":"A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines: The nuclear periphery in genome regulation,” Nature Reviews Genetics, vol. 20, no. 1. Springer Nature, pp. 39–50, 2019.","ama":"Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 2019;20(1):39-50. doi:10.1038/s41576-018-0063-5","chicago":"Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” Nature Reviews Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41576-018-0063-5.","mla":"Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” Nature Reviews Genetics, vol. 20, no. 1, Springer Nature, 2019, pp. 39–50, doi:10.1038/s41576-018-0063-5.","short":"A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019) 39–50."},"publication":"Nature Reviews Genetics","date_published":"2019-01-01T00:00:00Z","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"scopus_import":"1","article_processing_charge":"No","day":"01","publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","volume":20,"date_created":"2022-04-07T07:44:45Z","date_updated":"2022-07-18T08:31:42Z","author":[{"full_name":"Buchwalter, Abigail","first_name":"Abigail","last_name":"Buchwalter"},{"last_name":"Kaneshiro","first_name":"Jeanae M.","full_name":"Kaneshiro, Jeanae M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W"}],"extern":"1","quality_controlled":"1","external_id":{"pmid":["30356165"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41576-018-0063-5","publication_identifier":{"issn":["1471-0056"],"eissn":["1471-0064"]},"month":"01"},{"month":"04","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.05960"}],"oa":1,"external_id":{"arxiv":["1902.05960"]},"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834565","article_number":"A89","extern":"1","publication_status":"published","publisher":"EDP Sciences","acknowledgement":"The authors wish to thank the referee for constructive comments that improved the paper substantially. We thank the BPASS team for making the stellar population models available. We thank Elizabeth Stanway, Claus Leitherer, Daniel Schaerer, Jorick Vink, and Nell Byler for insightful discussions. We thank the Lorentz Centre and the scientific organizers of the Characterizing galaxies with spectroscopy with a view for JWST workshop held at the Lorentz Centre in 2017 October, which promoted useful discussions in the wider community. TN, JB, and RB acknowledges the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) top grant TOP1.16.057. AF acknowledges support from the ERC via an Advanced Grant under grant agreement no. 339659-MUSICOS. JB acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003, and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). JR acknowledges support from the ERC Starting grant 336736 (CALENDS). This research made use of astropy (http://www.astropy.org) a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018) and pandas (McKinney 2010). Figures were generated using matplotlib (Hunter 2007) and seaborn (https://seaborn.pydata.org). Facilities: VLT (MUSE).","year":"2019","date_updated":"2022-07-19T09:36:08Z","date_created":"2022-07-06T09:07:06Z","volume":648,"author":[{"full_name":"Nanayakkara, Themiya","first_name":"Themiya","last_name":"Nanayakkara"},{"full_name":"Brinchmann, Jarle","first_name":"Jarle","last_name":"Brinchmann"},{"first_name":"Leindert","last_name":"Boogaard","full_name":"Boogaard, Leindert"},{"last_name":"Bouwens","first_name":"Rychard","full_name":"Bouwens, Rychard"},{"full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo","first_name":"Sebastiano"},{"full_name":"Feltre, Anna","first_name":"Anna","last_name":"Feltre"},{"last_name":"Kollatschny","first_name":"Wolfram","full_name":"Kollatschny, Wolfram"},{"full_name":"Marino, Raffaella Anna","last_name":"Marino","first_name":"Raffaella Anna"},{"full_name":"Maseda, Michael","first_name":"Michael","last_name":"Maseda"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"},{"full_name":"Paalvast, Mieke","first_name":"Mieke","last_name":"Paalvast"},{"last_name":"Richard","first_name":"Johan","full_name":"Richard, Johan"},{"full_name":"Verhamme, Anne","last_name":"Verhamme","first_name":"Anne"}],"related_material":{"link":[{"url":"https://doi.org/10.1051/0004-6361/201834565e","relation":"erratum"}]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: ISM / galaxies: star formation / galaxies: evolution / galaxies: high-redshift"],"scopus_import":"1","day":"16","article_processing_charge":"No","article_type":"original","publication":"Astronomy & Astrophysics","citation":{"ama":"Nanayakkara T, Brinchmann J, Boogaard L, et al. Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. 2019;648. doi:10.1051/0004-6361/201834565","apa":"Nanayakkara, T., Brinchmann, J., Boogaard, L., Bouwens, R., Cantalupo, S., Feltre, A., … Verhamme, A. (2019). Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834565","ieee":"T. Nanayakkara et al., “Exploring He II λ1640 emission line properties at z ∼2−4,” Astronomy & Astrophysics, vol. 648. EDP Sciences, 2019.","ista":"Nanayakkara T, Brinchmann J, Boogaard L, Bouwens R, Cantalupo S, Feltre A, Kollatschny W, Marino RA, Maseda M, Matthee JJ, Paalvast M, Richard J, Verhamme A. 2019. Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy & Astrophysics. 648, A89.","short":"T. Nanayakkara, J. Brinchmann, L. Boogaard, R. Bouwens, S. Cantalupo, A. Feltre, W. Kollatschny, R.A. Marino, M. Maseda, J.J. Matthee, M. Paalvast, J. Richard, A. Verhamme, Astronomy & Astrophysics 648 (2019).","mla":"Nanayakkara, Themiya, et al. “Exploring He II Λ1640 Emission Line Properties at z ∼2−4.” Astronomy & Astrophysics, vol. 648, A89, EDP Sciences, 2019, doi:10.1051/0004-6361/201834565.","chicago":"Nanayakkara, Themiya, Jarle Brinchmann, Leindert Boogaard, Rychard Bouwens, Sebastiano Cantalupo, Anna Feltre, Wolfram Kollatschny, et al. “Exploring He II Λ1640 Emission Line Properties at z ∼2−4.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834565."},"date_published":"2019-04-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Deep optical spectroscopic surveys of galaxies provide a unique opportunity to investigate rest-frame ultra-violet (UV) emission line properties of galaxies at z ∼ 2 − 4.5. Here we combine VLT/MUSE Guaranteed Time Observations of the Hubble Deep Field South, Ultra Deep Field, COSMOS, and several quasar fields with other publicly available data from VLT/VIMOS and VLT/FORS2 to construct a catalogue of He II λ1640 emitters at z ≳ 2. The deepest areas of our MUSE pointings reach a 3σ line flux limit of 3.1 × 10−19 erg s−1 cm−2. After discarding broad-line active galactic nuclei, we find 13 He II λ1640 detections from MUSE with a median MUV = −20.1 and 21 tentative He II λ1640 detections from other public surveys. Excluding Lyα, all except two galaxies in our sample show at least one other rest-UV emission line, with C III] λ1907, λ1909 being the most prominent. We use multi-wavelength data available in the Hubble legacy fields to derive basic galaxy properties of our sample through spectral energy distribution fitting techniques. Taking advantage of the high-quality spectra obtained by MUSE (∼10 − 30 h of exposure time per pointing), we use photo-ionisation models to study the rest-UV emission line diagnostics of the He II λ1640 emitters. Line ratios of our sample can be reproduced by moderately sub-solar photo-ionisation models, however, we find that including effects of binary stars lead to degeneracies in most free parameters. Even after considering extra ionising photons produced by extreme sub-solar metallicity binary stellar models, photo-ionisation models are unable to reproduce rest-frame He II λ1640 equivalent widths (∼0.2 − 10 Å), thus additional mechanisms are necessary in models to match the observed He II λ1640 properties."}],"status":"public","title":"Exploring He II λ1640 emission line properties at z ∼2−4","intvolume":" 648","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11499","oa_version":"Published Version"},{"type":"journal_article","abstract":[{"text":"Contact. This paper presents the results obtained with the Multi-Unit Spectroscopic Explorer (MUSE) at the ESO Very Large Telescope on the faint end of the Lyman-alpha luminosity function (LF) based on deep observations of four lensing clusters. The goal of our project is to set strong constraints on the relative contribution of the Lyman-alpha emitter (LAE) population to cosmic reionization.\r\n\r\nAims. The precise aim of the present study is to further constrain the abundance of LAEs by taking advantage of the magnification provided by lensing clusters to build a blindly selected sample of galaxies which is less biased than current blank field samples in redshift and luminosity. By construction, this sample of LAEs is complementary to those built from deep blank fields, whether observed by MUSE or by other facilities, and makes it possible to determine the shape of the LF at fainter levels, as well as its evolution with redshift.\r\n\r\nMethods. We selected a sample of 156 LAEs with redshifts between 2.9 ≤ z ≤ 6.7 and magnification-corrected luminosities in the range 39 ≲ log LLyα [erg s−1] ≲43. To properly take into account the individual differences in detection conditions between the LAEs when computing the LF, including lensing configurations, and spatial and spectral morphologies, the non-parametric 1/Vmax method was adopted. The price to pay to benefit from magnification is a reduction of the effective volume of the survey, together with a more complex analysis procedure to properly determine the effective volume Vmax for each galaxy. In this paper we present a complete procedure for the determination of the LF based on IFU detections in lensing clusters. This procedure, including some new methods for masking, effective volume integration and (individual) completeness determinations, has been fully automated when possible, and it can be easily generalized to the analysis of IFU observations in blank fields.\r\n\r\nResults. As a result of this analysis, the Lyman-alpha LF has been obtained in four different redshift bins: 2.9 < z < 6, 7, 2.9 < z < 4.0, 4.0 < z < 5.0, and 5.0 < z < 6.7 with constraints down to log LLyα = 40.5. From our data only, no significant evolution of LF mean slope can be found. When performing a Schechter analysis also including data from the literature to complete the present sample towards the brightest luminosities, a steep faint end slope was measured varying from α = −1.69−0.08+0.08 to α = −1.87−0.12+0.12 between the lowest and the highest redshift bins.\r\n\r\nConclusions. The contribution of the LAE population to the star formation rate density at z ∼ 6 is ≲50% depending on the luminosity limit considered, which is of the same order as the Lyman-break galaxy (LBG) contribution. The evolution of the LAE contribution with redshift depends on the assumed escape fraction of Lyman-alpha photons, and appears to slightly increase with increasing redshift when this fraction is conservatively set to one. Depending on the intersection between the LAE/LBG populations, the contribution of the observed galaxies to the ionizing flux may suffice to keep the universe ionized at z ∼ 6.","lang":"eng"}],"title":"Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE","status":"public","intvolume":" 628","_id":"11505","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","keyword":["Space and Planetary Science","Astronomy and Astrophysics","gravitational lensing: strong / galaxies: high-redshift / dark ages","reionization","first stars / galaxies: clusters: general / galaxies: luminosity function","mass function"],"scopus_import":"1","day":"25","article_processing_charge":"No","article_type":"original","publication":"Astronomy & Astrophysics","citation":{"ama":"de La Vieuville G, Bina D, Pello R, et al. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. 2019;628. doi:10.1051/0004-6361/201834471","ieee":"G. de La Vieuville et al., “Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE,” Astronomy & Astrophysics, vol. 628. EDP Sciences, 2019.","apa":"de La Vieuville, G., Bina, D., Pello, R., Mahler, G., Richard, J., Drake, A. B., … Soucail, G. (2019). Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834471","ista":"de La Vieuville G, Bina D, Pello R, Mahler G, Richard J, Drake AB, Herenz EC, Bauer FE, Clément B, Lagattuta D, Laporte N, Martinez J, Patrício V, Wisotzki L, Zabl J, Bouwens RJ, Contini T, Garel T, Guiderdoni B, Marino RA, Maseda MV, Matthee JJ, Schaye J, Soucail G. 2019. Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy & Astrophysics. 628, A3.","short":"G. de La Vieuville, D. Bina, R. Pello, G. Mahler, J. Richard, A.B. Drake, E.C. Herenz, F.E. Bauer, B. Clément, D. Lagattuta, N. Laporte, J. Martinez, V. Patrício, L. Wisotzki, J. Zabl, R.J. Bouwens, T. Contini, T. Garel, B. Guiderdoni, R.A. Marino, M.V. Maseda, J.J. Matthee, J. Schaye, G. Soucail, Astronomy & Astrophysics 628 (2019).","mla":"de La Vieuville, G., et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” Astronomy & Astrophysics, vol. 628, A3, EDP Sciences, 2019, doi:10.1051/0004-6361/201834471.","chicago":"La Vieuville, G. de, D. Bina, R. Pello, G. Mahler, J. Richard, A. B. Drake, E. C. Herenz, et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834471."},"date_published":"2019-07-25T00:00:00Z","article_number":"A3","extern":"1","publication_status":"published","publisher":"EDP Sciences","year":"2019","acknowledgement":"We thank the anonymous referee for their critical review and useful suggestions. This work has been carried out thanks to the support of the OCEVU Labex (ANR-11-LABX-0060) and the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the “Investissements d’Avenir” French government programme managed by the ANR. Partially funded by the ERC starting grant CALENDS (JR, VP, BC, JM), the Agence Nationale de la recherche bearing the reference ANR-13-BS05-0010-02 (FOGHAR), and the “Programme National de Cosmologie and Galaxies” (PNCG) of CNRS/INSU, France. GdV, RP, JR, GM, JM, BC, and VP also acknowledge support by the Programa de Cooperacion Cientifica – ECOS SUD Program C16U02. NL acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 669253), ABD acknowledges support from the ERC advanced grant “Cosmic Gas”. LW acknowledges support by the Competitive Fund of the Leibniz Association through grant SAW-2015-AIP-2, and TG acknowledges support from the European Research Council under grant agreement ERC-stg-757258 (TRIPLE).. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 060.A-9345, 094.A-0115, 095.A-0181, 096.A-0710, 097.A0269, 100.A-0249, and 294.A-5032. Also based on observations obtained with the NASA/ESA Hubble Space Telescope, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. This research made use of Astropy, a community-developed core Python package for Astronomy (Astropy Collaboration 2013). All plots in this paper were created using Matplotlib (Hunter 2007).","date_updated":"2022-07-19T09:36:31Z","date_created":"2022-07-06T10:09:36Z","volume":628,"author":[{"full_name":"de La Vieuville, G.","first_name":"G.","last_name":"de La Vieuville"},{"full_name":"Bina, D.","last_name":"Bina","first_name":"D."},{"first_name":"R.","last_name":"Pello","full_name":"Pello, R."},{"first_name":"G.","last_name":"Mahler","full_name":"Mahler, G."},{"full_name":"Richard, J.","first_name":"J.","last_name":"Richard"},{"first_name":"A. B.","last_name":"Drake","full_name":"Drake, A. B."},{"full_name":"Herenz, E. C.","last_name":"Herenz","first_name":"E. C."},{"first_name":"F. E.","last_name":"Bauer","full_name":"Bauer, F. E."},{"full_name":"Clément, B.","first_name":"B.","last_name":"Clément"},{"last_name":"Lagattuta","first_name":"D.","full_name":"Lagattuta, D."},{"last_name":"Laporte","first_name":"N.","full_name":"Laporte, N."},{"first_name":"J.","last_name":"Martinez","full_name":"Martinez, J."},{"first_name":"V.","last_name":"Patrício","full_name":"Patrício, V."},{"first_name":"L.","last_name":"Wisotzki","full_name":"Wisotzki, L."},{"last_name":"Zabl","first_name":"J.","full_name":"Zabl, J."},{"full_name":"Bouwens, R. J.","first_name":"R. J.","last_name":"Bouwens"},{"full_name":"Contini, T.","first_name":"T.","last_name":"Contini"},{"full_name":"Garel, T.","first_name":"T.","last_name":"Garel"},{"first_name":"B.","last_name":"Guiderdoni","full_name":"Guiderdoni, B."},{"full_name":"Marino, R. A.","last_name":"Marino","first_name":"R. A."},{"first_name":"M. V.","last_name":"Maseda","full_name":"Maseda, M. V."},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"full_name":"Schaye, J.","last_name":"Schaye","first_name":"J."},{"full_name":"Soucail, G.","first_name":"G.","last_name":"Soucail"}],"month":"07","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"quality_controlled":"1","external_id":{"arxiv":["1905.13696"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13696"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834471"},{"month":"03","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"oa":1,"external_id":{"arxiv":["1803.08923"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08923"}],"quality_controlled":"1","doi":"10.1051/0004-6361/201833075","language":[{"iso":"eng"}],"article_number":"A157","extern":"1","year":"2019","acknowledgement":"We thank the anonymous referees for multiple comments and suggestions which have improved the manuscript. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt et al. 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration 2013) packages, and the TOPCAT analysis program (Taylor 2013). The results and samples of LAEs used for this paper are publicly available (see e.g. Sobral et al. 2017, 2018a) and we also provide the toy model used as a PYTHON script.","publication_status":"published","publisher":"EDP Sciences","author":[{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"}],"date_created":"2022-07-06T11:08:16Z","date_updated":"2022-07-19T09:37:20Z","volume":623,"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: star formation / galaxies: statistics / galaxies: evolution / galaxies: formation / galaxies: ISM"],"day":"26","article_processing_charge":"No","publication":"Astronomy & Astrophysics","citation":{"chicago":"Sobral, David, and Jorryt J Matthee. “Predicting Lyα Escape Fractions with a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation Rate Indicator.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833075.","mla":"Sobral, David, and Jorryt J. Matthee. “Predicting Lyα Escape Fractions with a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation Rate Indicator.” Astronomy & Astrophysics, vol. 623, A157, EDP Sciences, 2019, doi:10.1051/0004-6361/201833075.","short":"D. Sobral, J.J. Matthee, Astronomy & Astrophysics 623 (2019).","ista":"Sobral D, Matthee JJ. 2019. Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. 623, A157.","apa":"Sobral, D., & Matthee, J. J. (2019). Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833075","ieee":"D. Sobral and J. J. Matthee, “Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019.","ama":"Sobral D, Matthee JJ. Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201833075"},"article_type":"original","date_published":"2019-03-26T00:00:00Z","type":"journal_article","abstract":[{"text":"Lyman-α (Lyα) is intrinsically the brightest line emitted from active galaxies. While it originates from many physical processes, for star-forming galaxies the intrinsic Lyα luminosity is a direct tracer of the Lyman-continuum (LyC) radiation produced by the most massive O- and early-type B-stars (M⋆ ≳ 10 M⊙) with lifetimes of a few Myrs. As such, Lyα luminosity should be an excellent instantaneous star formation rate (SFR) indicator. However, its resonant nature and susceptibility to dust as a rest-frame UV photon makes Lyα very hard to interpret due to the uncertain Lyα escape fraction, fesc, Lyα. Here we explore results from the CAlibrating LYMan-α with Hα (CALYMHA) survey at z = 2.2, follow-up of Lyα emitters (LAEs) at z = 2.2 − 2.6 and a z ∼ 0−0.3 compilation of LAEs to directly measure fesc, Lyα with Hα. We derive a simple empirical relation that robustly retrieves fesc, Lyα as a function of Lyα rest-frame EW (EW0): fesc,Lyα = 0.0048 EW0[Å] ± 0.05 and we show that it constrains a well-defined anti-correlation between ionisation efficiency (ξion) and dust extinction in LAEs. Observed Lyα luminosities and EW0 are easy measurable quantities at high redshift, thus making our relation a practical tool to estimate intrinsic Lyα and LyC luminosities under well controlled and simple assumptions. Our results allow observed Lyα luminosities to be used to compute SFRs for LAEs at z ∼ 0−2.6 within ±0.2 dex of the Hα dust corrected SFRs. We apply our empirical SFR(Lyα,EW0) calibration to several sources at z ≥ 2.6 to find that star-forming LAEs have SFRs typically ranging from 0.1 to 20 M⊙ yr−1 and that our calibration might be even applicable for the most luminous LAEs within the epoch of re-ionisation. Our results imply high ionisation efficiencies (log10[ξion/Hz erg−1] = 25.4−25.6) and low dust content in LAEs across cosmic time, and will be easily tested with future observations with JWST which can obtain Hα and Hβ measurements for high-redshift LAEs.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11507","title":"Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator","status":"public","intvolume":" 623","oa_version":"Published Version"},{"date_published":"2019-09-11T00:00:00Z","article_type":"original","citation":{"ama":"Boogaard LA, Decarli R, González-López J, et al. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. 2019;882(2). doi:10.3847/1538-4357/ab3102","ista":"Boogaard LA, Decarli R, González-López J, van der Werf P, Walter F, Bouwens R, Aravena M, Carilli C, Bauer FE, Brinchmann J, Contini T, Cox P, da Cunha E, Daddi E, Díaz-Santos T, Hodge J, Inami H, Ivison R, Maseda M, Matthee JJ, Oesch P, Popping G, Riechers D, Schaye J, Schouws S, Smail I, Weiss A, Wisotzki L, Bacon R, Cortes PC, Rix H-W, Somerville RS, Swinbank M, Wagg J. 2019. The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. 882(2), 140.","apa":"Boogaard, L. A., Decarli, R., González-López, J., van der Werf, P., Walter, F., Bouwens, R., … Wagg, J. (2019). The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab3102","ieee":"L. A. Boogaard et al., “The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy,” The Astrophysical Journal, vol. 882, no. 2. IOP Publishing, 2019.","mla":"Boogaard, Leindert A., et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” The Astrophysical Journal, vol. 882, no. 2, 140, IOP Publishing, 2019, doi:10.3847/1538-4357/ab3102.","short":"L.A. Boogaard, R. Decarli, J. González-López, P. van der Werf, F. Walter, R. Bouwens, M. Aravena, C. Carilli, F.E. Bauer, J. Brinchmann, T. Contini, P. Cox, E. da Cunha, E. Daddi, T. Díaz-Santos, J. Hodge, H. Inami, R. Ivison, M. Maseda, J.J. Matthee, P. Oesch, G. Popping, D. Riechers, J. Schaye, S. Schouws, I. Smail, A. Weiss, L. Wisotzki, R. Bacon, P.C. Cortes, H.-W. Rix, R.S. Somerville, M. Swinbank, J. Wagg, The Astrophysical Journal 882 (2019).","chicago":"Boogaard, Leindert A., Roberto Decarli, Jorge González-López, Paul van der Werf, Fabian Walter, Rychard Bouwens, Manuel Aravena, et al. “The ALMA Spectroscopic Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab3102."},"publication":"The Astrophysical Journal","article_processing_charge":"No","day":"11","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","oa_version":"Preprint","intvolume":" 882","title":"The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy","status":"public","_id":"11514","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"text":"We discuss the nature and physical properties of gas-mass selected galaxies in the ALMA spectroscopic survey (ASPECS) of the Hubble Ultra Deep Field (HUDF). We capitalize on the deep optical integral-field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) HUDF Survey and multiwavelength data to uniquely associate all 16 line emitters, detected in the ALMA data without preselection, with rotational transitions of carbon monoxide (CO). We identify 10 as CO(2–1) at 1 < z < 2, 5 as CO(3–2) at 2 < z < 3, and 1 as CO(4–3) at z = 3.6. Using the MUSE data as a prior, we identify two additional CO(2–1) emitters, increasing the total sample size to 18. We infer metallicities consistent with (super-)solar for the CO-detected galaxies at z ≤ 1.5, motivating our choice of a Galactic conversion factor between CO luminosity and molecular gas mass for these galaxies. Using deep Chandra imaging of the HUDF, we determine an X-ray AGN fraction of 20% and 60% among the CO emitters at z ∼ 1.4 and z ∼ 2.6, respectively. Being a CO-flux-limited survey, ASPECS-LP detects molecular gas in galaxies on, above, and below the main sequence (MS) at z ∼ 1.4. For stellar masses ≥1010 (1010.5) ${M}_{\\odot }$, we detect about 40% (50%) of all galaxies in the HUDF at 1 < z < 2 (2 < z < 3). The combination of ALMA and MUSE integral-field spectroscopy thus enables an unprecedented view of MS galaxies during the peak of galaxy formation.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ab3102","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09167"}],"external_id":{"arxiv":["1903.09167"]},"oa":1,"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"09","volume":882,"date_updated":"2022-07-19T09:50:55Z","date_created":"2022-07-06T13:31:35Z","author":[{"last_name":"Boogaard","first_name":"Leindert A.","full_name":"Boogaard, Leindert A."},{"full_name":"Decarli, Roberto","first_name":"Roberto","last_name":"Decarli"},{"full_name":"González-López, Jorge","last_name":"González-López","first_name":"Jorge"},{"last_name":"van der Werf","first_name":"Paul","full_name":"van der Werf, Paul"},{"full_name":"Walter, Fabian","first_name":"Fabian","last_name":"Walter"},{"full_name":"Bouwens, Rychard","last_name":"Bouwens","first_name":"Rychard"},{"last_name":"Aravena","first_name":"Manuel","full_name":"Aravena, Manuel"},{"full_name":"Carilli, Chris","last_name":"Carilli","first_name":"Chris"},{"last_name":"Bauer","first_name":"Franz Erik","full_name":"Bauer, Franz Erik"},{"full_name":"Brinchmann, Jarle","first_name":"Jarle","last_name":"Brinchmann"},{"full_name":"Contini, Thierry","first_name":"Thierry","last_name":"Contini"},{"full_name":"Cox, Pierre","last_name":"Cox","first_name":"Pierre"},{"last_name":"da Cunha","first_name":"Elisabete","full_name":"da Cunha, Elisabete"},{"full_name":"Daddi, Emanuele","first_name":"Emanuele","last_name":"Daddi"},{"full_name":"Díaz-Santos, Tanio","first_name":"Tanio","last_name":"Díaz-Santos"},{"full_name":"Hodge, Jacqueline","first_name":"Jacqueline","last_name":"Hodge"},{"full_name":"Inami, Hanae","first_name":"Hanae","last_name":"Inami"},{"full_name":"Ivison, Rob","last_name":"Ivison","first_name":"Rob"},{"first_name":"Michael","last_name":"Maseda","full_name":"Maseda, Michael"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"first_name":"Pascal","last_name":"Oesch","full_name":"Oesch, Pascal"},{"last_name":"Popping","first_name":"Gergö","full_name":"Popping, Gergö"},{"full_name":"Riechers, Dominik","last_name":"Riechers","first_name":"Dominik"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"},{"full_name":"Schouws, Sander","first_name":"Sander","last_name":"Schouws"},{"last_name":"Smail","first_name":"Ian","full_name":"Smail, Ian"},{"last_name":"Weiss","first_name":"Axel","full_name":"Weiss, Axel"},{"first_name":"Lutz","last_name":"Wisotzki","full_name":"Wisotzki, Lutz"},{"full_name":"Bacon, Roland","first_name":"Roland","last_name":"Bacon"},{"full_name":"Cortes, Paulo C.","last_name":"Cortes","first_name":"Paulo C."},{"full_name":"Rix, Hans-Walter","first_name":"Hans-Walter","last_name":"Rix"},{"full_name":"Somerville, Rachel S.","last_name":"Somerville","first_name":"Rachel S."},{"full_name":"Swinbank, Mark","first_name":"Mark","last_name":"Swinbank"},{"first_name":"Jeff","last_name":"Wagg","full_name":"Wagg, Jeff"}],"publisher":"IOP Publishing","publication_status":"published","year":"2019","acknowledgement":"We are grateful to the referee for providing a constructive report. L.A.B. wants to thank Madusha L.P. Gunawardhana for her help with platefit. Based on observations collected at the European Southern Observatory under ESO programme(s): 094.A-2089(B), 095.A-0010(A), 096.A-0045(A), and 096.A-0045(B). This paper makes use of the following ALMA data: ADS/JAO.ALMA#2016.1.00324.L. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada), NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities, Inc.\r\n\r\n\"Este trabajo contó con el apoyo de CONICYT+Programa de Astronomía+ Fondo CHINA-CONICYT\" J.G-L. acknowledges partial support from ALMA-CONICYT project 31160033. F.E.B. acknowledges support from CONICYT grant Basal AFB-170002 (FEB), and the Ministry of Economy, Development, and Tourism's Millennium Science Initiative through grant IC120009, awarded to The Millennium Institute of Astrophysics, MAS (FEB). J.B. acknowledges support by Fundação para a Ciência e a Tecnologia (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003., and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). T.D-S. acknowledges support from ALMA-CONYCIT project 31130005 and FONDECYT project 1151239. J.H. acknowledges support of the VIDI research programme with project number 639.042.611, which is (partly) financed by the Netherlands Organization for Scientific Research (NWO). D.R. acknowledges support from the National Science Foundation under grant No. AST-1614213. I.R.S. acknowledges support from the ERC Advanced Grant DUSTYGAL (321334) and STFC (ST/P000541/1)\r\n\r\nWork on Gnuastro has been funded by the Japanese MEXT scholarship and its Grant-in-Aid for Scientific Research (21244012, 24253003), the ERC advanced grant 339659-MUSICOS, European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No. 721463 to the SUNDIAL ITN, and from the Spanish MINECO under grant No. AYA2016-76219-P.","extern":"1","article_number":"140"},{"citation":{"mla":"Marino, Raffaella Anna, et al. “A Giant Lyα Nebula and a Small-Scale Clumpy Outflow in the System of the Exotic Quasar J0952+0114 Unveiled by MUSE.” The Astrophysical Journal, vol. 880, no. 1, 47, IOP Publishing, 2019, doi:10.3847/1538-4357/ab2881.","short":"R.A. Marino, S. Cantalupo, G. Pezzulli, S.J. Lilly, S. Gallego, R. Mackenzie, J.J. Matthee, J. Brinchmann, N. Bouché, A. Feltre, S. Muzahid, I. Schroetter, S.D. Johnson, T. Nanayakkara, The Astrophysical Journal 880 (2019).","chicago":"Marino, Raffaella Anna, Sebastiano Cantalupo, Gabriele Pezzulli, Simon J. Lilly, Sofia Gallego, Ruari Mackenzie, Jorryt J Matthee, et al. “A Giant Lyα Nebula and a Small-Scale Clumpy Outflow in the System of the Exotic Quasar J0952+0114 Unveiled by MUSE.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab2881.","ama":"Marino RA, Cantalupo S, Pezzulli G, et al. A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. 2019;880(1). doi:10.3847/1538-4357/ab2881","ista":"Marino RA, Cantalupo S, Pezzulli G, Lilly SJ, Gallego S, Mackenzie R, Matthee JJ, Brinchmann J, Bouché N, Feltre A, Muzahid S, Schroetter I, Johnson SD, Nanayakkara T. 2019. A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. 880(1), 47.","apa":"Marino, R. A., Cantalupo, S., Pezzulli, G., Lilly, S. J., Gallego, S., Mackenzie, R., … Nanayakkara, T. (2019). A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab2881","ieee":"R. A. Marino et al., “A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE,” The Astrophysical Journal, vol. 880, no. 1. IOP Publishing, 2019."},"publication":"The Astrophysical Journal","article_type":"original","date_published":"2019-07-24T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_processing_charge":"No","day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11516","intvolume":" 880","title":"A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE","status":"public","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"The well-known quasar SDSS J095253.83+011421.9 (J0952+0114) at z = 3.02 has one of the most peculiar spectra discovered so far, showing the presence of narrow Lyα and broad metal emission lines. Although recent studies have suggested that a proximate damped Lyα absorption (PDLA) system causes this peculiar spectrum, the origin of the gas associated with the PDLA is unknown. Here we report the results of observations with the Multi Unit Spectroscopic Explorer (MUSE) that reveal a new giant (≈100 physical kpc) Lyα nebula. The detailed analysis of the Lyα velocity, velocity dispersion, and surface brightness profiles suggests that the J0952+0114 Lyα nebula shares similar properties with other QSO nebulae previously detected with MUSE, implying that the PDLA in J0952+0144 is covering only a small fraction of the solid angle of the QSO emission. We also detected bright and spectrally narrow C iv λ1550 and He ii λ1640 extended emission around J0952+0114 with velocity centroids similar to the peak of the extended and central narrow Lyα emission. The presence of a peculiarly bright, unresolved, and relatively broad He ii λ1640 emission in the central region at exactly the same PDLA redshift hints at the possibility that the PDLA originates in a clumpy outflow with a bulk velocity of about 500 km s−1. The smaller velocity dispersion of the large-scale Lyα emission suggests that the high-speed outflow is confined to the central region. Lastly, the derived spatially resolved He ii/Lyα and C iv/Lyα maps show a positive gradient with the distance to the QSO, hinting at a non-homogeneous distribution of the ionization parameter.","lang":"eng"}],"external_id":{"arxiv":["1906.06347"]},"main_file_link":[{"url":"https://arxiv.org/abs/1906.06347","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.3847/1538-4357/ab2881","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"07","year":"2019","acknowledgement":"We thank Lutz Wisotzki for stimulating discussions. This work is based on observations taken at ESO/VLT in Paranal and we would like to thank the ESO staff for their assistance and support during the MUSE GTO campaigns. This work was supported by the Swiss National Science Foundation. This research made use of Astropy, a community-developed core PYTHON package for astronomy (Astropy Collaboration et al. 2013), NumPy and SciPy (Oliphant 2007), Matplotlib (Hunter 2007), IPython (Perez & Granger 2007), and of the NASA Astrophysics Data System Bibliographic Services. S.C. and G.P. gratefully acknowledge support from Swiss National Science Foundation grant PP00P2−163824. A.F. acknowledges support from the ERC via Advanced Grant under grants agreement no. 339659-MUSICOS. J.B. acknowledges support by FCT/MCTES through national funds by grant UID/FIS/04434/2019 and through Investigador FCT Contract No. IF/01654/2014/CP1215/CT0003. S.D.J. is supported by a NASA Hubble Fellowship (HST-HF2-51375.001-A). T.N. acknowledges the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) top grant TOP1.16.057.","publisher":"IOP Publishing","publication_status":"published","author":[{"first_name":"Raffaella Anna","last_name":"Marino","full_name":"Marino, Raffaella Anna"},{"full_name":"Cantalupo, Sebastiano","last_name":"Cantalupo","first_name":"Sebastiano"},{"full_name":"Pezzulli, Gabriele","last_name":"Pezzulli","first_name":"Gabriele"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"full_name":"Gallego, Sofia","first_name":"Sofia","last_name":"Gallego"},{"first_name":"Ruari","last_name":"Mackenzie","full_name":"Mackenzie, Ruari"},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"last_name":"Brinchmann","first_name":"Jarle","full_name":"Brinchmann, Jarle"},{"last_name":"Bouché","first_name":"Nicolas","full_name":"Bouché, Nicolas"},{"last_name":"Feltre","first_name":"Anna","full_name":"Feltre, Anna"},{"full_name":"Muzahid, Sowgat","last_name":"Muzahid","first_name":"Sowgat"},{"last_name":"Schroetter","first_name":"Ilane","full_name":"Schroetter, Ilane"},{"full_name":"Johnson, Sean D.","first_name":"Sean D.","last_name":"Johnson"},{"full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara","first_name":"Themiya"}],"volume":880,"date_updated":"2022-08-18T10:20:18Z","date_created":"2022-07-06T13:50:33Z","article_number":"47","extern":"1"},{"_id":"11515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization","status":"public","intvolume":" 881","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present new deep ALMA and Hubble Space Telescope (HST)/WFC3 observations of MASOSA and VR7, two luminous Lyα emitters (LAEs) at z = 6.5, for which the UV continuum levels differ by a factor of four. No IR dust continuum emission is detected in either, indicating little amounts of obscured star formation and/or high dust temperatures. MASOSA, with a UV luminosity M1500 = −20.9, compact size, and very high Lyα ${\\mathrm{EW}}_{0}\\approx 145\\,\\mathring{\\rm A} $, is undetected in [C ii] to a limit of L[C ii] < 2.2 × 107 L⊙, implying a metallicity Z ≲ 0.07 Z⊙. Intriguingly, our HST data indicate a red UV slope β = −1.1 ± 0.7, at odds with the low dust content. VR7, which is a bright (M1500 = −22.4) galaxy with moderate color (β = −1.4 ± 0.3) and Lyα EW0 = 34 Å, is clearly detected in [C ii] emission (S/N = 15). VR7's rest-frame UV morphology can be described by two components separated by ≈1.5 kpc and is globally more compact than the [C ii] emission. The global [C ii]/UV ratio indicates Z ≈ 0.2 Z⊙, but there are large variations in the UV/[C ii] ratio on kiloparsec scales. We also identify diffuse, possibly outflowing, [C ii]-emitting gas at ≈100 km s−1 with respect to the peak. VR7 appears to be assembling its components at a slightly more evolved stage than other luminous LAEs, with outflows already shaping its direct environment at z ∼ 7. Our results further indicate that the global [C ii]−UV relation steepens at SFR < 30 M⊙ yr−1, naturally explaining why the [C ii]/UV ratio is anticorrelated with Lyα EW in many, but not all, observed LAEs."}],"issue":"2","publication":"The Astrophysical Journal","citation":{"ama":"Matthee JJ, Sobral D, Boogaard LA, et al. Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. 2019;881(2). doi:10.3847/1538-4357/ab2f81","ista":"Matthee JJ, Sobral D, Boogaard LA, Röttgering H, Vallini L, Ferrara A, Paulino-Afonso A, Boone F, Schaerer D, Mobasher B. 2019. Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. 881(2), 124.","ieee":"J. J. Matthee et al., “Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization,” The Astrophysical Journal, vol. 881, no. 2. IOP Publishing, 2019.","apa":"Matthee, J. J., Sobral, D., Boogaard, L. A., Röttgering, H., Vallini, L., Ferrara, A., … Mobasher, B. (2019). Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab2f81","mla":"Matthee, Jorryt J., et al. “Resolved UV and [C Ii] Structures of Luminous Galaxies within the Epoch of Reionization.” The Astrophysical Journal, vol. 881, no. 2, 124, IOP Publishing, 2019, doi:10.3847/1538-4357/ab2f81.","short":"J.J. Matthee, D. Sobral, L.A. Boogaard, H. Röttgering, L. Vallini, A. Ferrara, A. Paulino-Afonso, F. Boone, D. Schaerer, B. Mobasher, The Astrophysical Journal 881 (2019).","chicago":"Matthee, Jorryt J, D. Sobral, L. A. Boogaard, H. Röttgering, L. Vallini, A. Ferrara, A. Paulino-Afonso, F. Boone, D. Schaerer, and B. Mobasher. “Resolved UV and [C Ii] Structures of Luminous Galaxies within the Epoch of Reionization.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab2f81."},"article_type":"original","date_published":"2019-08-21T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"21","article_processing_charge":"No","year":"2019","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We thank Max Gronke for comments on an earlier version of this paper. L.V. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 746119. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada), NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. Based on observations obtained with the Very Large Telescope, programs 294.A-5018, 097.A-0943, and 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained (from the Data Archive) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program No. 14699.","publication_status":"published","publisher":"IOP Publishing","author":[{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"first_name":"D.","last_name":"Sobral","full_name":"Sobral, D."},{"full_name":"Boogaard, L. A.","first_name":"L. A.","last_name":"Boogaard"},{"full_name":"Röttgering, H.","first_name":"H.","last_name":"Röttgering"},{"last_name":"Vallini","first_name":"L.","full_name":"Vallini, L."},{"full_name":"Ferrara, A.","last_name":"Ferrara","first_name":"A."},{"full_name":"Paulino-Afonso, A.","first_name":"A.","last_name":"Paulino-Afonso"},{"full_name":"Boone, F.","first_name":"F.","last_name":"Boone"},{"last_name":"Schaerer","first_name":"D.","full_name":"Schaerer, D."},{"first_name":"B.","last_name":"Mobasher","full_name":"Mobasher, B."}],"date_created":"2022-07-06T13:38:15Z","date_updated":"2022-08-18T10:19:48Z","volume":881,"article_number":"124","extern":"1","external_id":{"arxiv":["1903.08171"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1903.08171","open_access":"1"}],"quality_controlled":"1","doi":"10.3847/1538-4357/ab2f81","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]}},{"citation":{"chicago":"Wang, Enci, Simon J. Lilly, Gabriele Pezzulli, and Jorryt J Matthee. “On the Elevation and Suppression of Star Formation within Galaxies.” The Astrophysical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-4357/ab1c5b.","short":"E. Wang, S.J. Lilly, G. Pezzulli, J.J. Matthee, The Astrophysical Journal 877 (2019).","mla":"Wang, Enci, et al. “On the Elevation and Suppression of Star Formation within Galaxies.” The Astrophysical Journal, vol. 877, no. 2, 132, IOP Publishing, 2019, doi:10.3847/1538-4357/ab1c5b.","ieee":"E. Wang, S. J. Lilly, G. Pezzulli, and J. J. Matthee, “On the elevation and suppression of star formation within galaxies,” The Astrophysical Journal, vol. 877, no. 2. IOP Publishing, 2019.","apa":"Wang, E., Lilly, S. J., Pezzulli, G., & Matthee, J. J. (2019). On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ab1c5b","ista":"Wang E, Lilly SJ, Pezzulli G, Matthee JJ. 2019. On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. 877(2), 132.","ama":"Wang E, Lilly SJ, Pezzulli G, Matthee JJ. On the elevation and suppression of star formation within galaxies. The Astrophysical Journal. 2019;877(2). doi:10.3847/1538-4357/ab1c5b"},"publication":"The Astrophysical Journal","article_type":"original","date_published":"2019-06-04T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"article_processing_charge":"No","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11517","intvolume":" 877","status":"public","title":"On the elevation and suppression of star formation within galaxies","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"text":"To understand star formation in galaxies, we investigate the star formation rate (SFR) surface density (ΣSFR) profiles for galaxies, based on a well-defined sample of 976 star-forming MaNGA galaxies. We find that the typical ΣSFR profiles within 1.5Re of normal SF galaxies can be well described by an exponential function for different stellar mass intervals, while the sSFR profile shows positive gradients, especially for more massive SF galaxies. This is due to the more pronounced central cores or bulges rather than the onset of a `quenching' process. While galaxies that lie significantly above (or below) the star formation main sequence (SFMS) show overall an elevation (or suppression) of ΣSFR at all radii, this central elevation (or suppression) is more pronounced in more massive galaxies. The degree of central enhancement and suppression is quite symmetric, suggesting that both the elevation and suppression of star formation are following the same physical processes. Furthermore, we find that the dispersion in ΣSFR within and across the population is found to be tightly correlated with the inferred gas depletion time, whether based on the stellar surface mass density or the orbital dynamical time. This suggests that we are seeing the response of a simple gas-regulator system to variations in the accretion rate. This is explored using a heuristic model that can quantitatively explain the dependence of σ(ΣSFR) on gas depletion timescale. Variations in accretion rate are progressively more damped out in regions of low star-formation efficiency leading to a reduced amplitude of variations in star-formation.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10276"}],"oa":1,"external_id":{"arxiv":["1901.10276"]},"quality_controlled":"1","doi":"10.3847/1538-4357/ab1c5b","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"06","year":"2019","acknowledgement":"We are grateful to the anonymous referee for their thoughtful and constructive review of the paper and their several suggestions (including the analysis of Section 3.4), which have improved the paper. This research has been supported by the Swiss National Science Foundation.\r\n\r\nFunding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High-Performance Computing at the University of Utah. The SDSS website is www.sdss.org.\r\n\r\nSDSS-IV is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration, including the Brazilian Participation Group, the Carnegie Institution for Science, Carnegie Mellon University, the Chilean Participation Group, the French Participation Group, Harvard-Smithsonian Center for Astrophysics, Instituto de Astrofísica de Canarias, the Johns Hopkins University, Kavli Institute for the Physics and Mathematics of the Universe (IPMU)/University of Tokyo, Lawrence Berkeley National Laboratory, Leibniz Institut für Astrophysik Potsdam (AIP), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Max-Planck-Institut für Astrophysik (MPA Garching), Max-Planck-Institut für Extraterrestrische Physik (MPE), National Astronomical Observatory of China, New Mexico State University, New York University, University of Notre Dame, Observatário Nacional/MCTI, the Ohio State University, Pennsylvania State University, Shanghai Astronomical Observatory, United Kingdom Participation Group, Universidad Nacional Autónoma de México, University of Arizona, University of Colorado Boulder, University of Oxford, University of Portsmouth, University of Utah, University of Virginia, University of Washington, University of Wisconsin, Vanderbilt University, and Yale University","publisher":"IOP Publishing","publication_status":"published","author":[{"full_name":"Wang, Enci","first_name":"Enci","last_name":"Wang"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"full_name":"Pezzulli, Gabriele","first_name":"Gabriele","last_name":"Pezzulli"},{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"}],"volume":877,"date_created":"2022-07-07T08:38:24Z","date_updated":"2022-08-18T10:19:08Z","article_number":"132","extern":"1"},{"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1811.00556","open_access":"1"}],"external_id":{"arxiv":["1811.00556"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stz2149","month":"10","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that helped improve this study. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. JM acknowledges support from the ETH Zwicky fellowship. RKC acknowledges funding from STFC via a studentship. APA acknowledges support from the Fundac¸ao para a Ci ˜ encia e a Tecnologia FCT through the fellowship PD/BD/52706/2014 and the research grant UID/FIS/04434/2013. JC and SS both acknowledge their support from the Lancaster University PhD Fellowship. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, SCIPY, MATPLOTLIB, SCIKIT-LEARN, and ASTROPY packages, as well as the TOPCAT analysis program. The SC4K samples used in this paper are all publicly available for use by the community (Sobral et al. 2018a). The catalogue is also available on the COSMOS IPAC website (https://irsa.ipac.caltech.edu/data/COSMOS/overview.html).","year":"2019","date_created":"2022-07-07T13:01:03Z","date_updated":"2022-08-19T06:38:42Z","volume":489,"author":[{"last_name":"Khostovan","first_name":"A A","full_name":"Khostovan, A A"},{"full_name":"Sobral, D","last_name":"Sobral","first_name":"D"},{"first_name":"B","last_name":"Mobasher","full_name":"Mobasher, B"},{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"last_name":"Cochrane","first_name":"R K","full_name":"Cochrane, R K"},{"last_name":"Chartab","first_name":"N","full_name":"Chartab, N"},{"last_name":"Jafariyazani","first_name":"M","full_name":"Jafariyazani, M"},{"full_name":"Paulino-Afonso, A","last_name":"Paulino-Afonso","first_name":"A"},{"full_name":"Santos, S","first_name":"S","last_name":"Santos"},{"first_name":"J","last_name":"Calhau","full_name":"Calhau, J"}],"extern":"1","article_type":"original","page":"555-573","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"short":"A.A. Khostovan, D. Sobral, B. Mobasher, J.J. Matthee, R.K. Cochrane, N. Chartab, M. Jafariyazani, A. Paulino-Afonso, S. Santos, J. Calhau, Monthly Notices of the Royal Astronomical Society 489 (2019) 555–573.","mla":"Khostovan, A. A., et al. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” Monthly Notices of the Royal Astronomical Society, vol. 489, no. 1, Oxford University Press, 2019, pp. 555–73, doi:10.1093/mnras/stz2149.","chicago":"Khostovan, A A, D Sobral, B Mobasher, Jorryt J Matthee, R K Cochrane, N Chartab, M Jafariyazani, A Paulino-Afonso, S Santos, and J Calhau. “The Clustering of Typical Ly α Emitters from z ∼ 2.5–6: Host Halo Masses Depend on Ly α and UV Luminosities.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2149.","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. 2019;489(1):555-573. doi:10.1093/mnras/stz2149","ieee":"A. A. Khostovan et al., “The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities,” Monthly Notices of the Royal Astronomical Society, vol. 489, no. 1. Oxford University Press, pp. 555–573, 2019.","apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Matthee, J. J., Cochrane, R. K., Chartab, N., … Calhau, J. (2019). The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2149","ista":"Khostovan AA, Sobral D, Mobasher B, Matthee JJ, Cochrane RK, Chartab N, Jafariyazani M, Paulino-Afonso A, Santos S, Calhau J. 2019. The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities. Monthly Notices of the Royal Astronomical Society. 489(1), 555–573."},"date_published":"2019-10-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities","intvolume":" 489","_id":"11535","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the clustering and halo properties of ∼5000 Ly α-selected emission-line galaxies (LAEs) from the Slicing COSMOS 4K (SC4K) and from archival NB497 imaging of SA22 split in 15 discrete redshift slices between z ∼ 2.5 and 6. We measure clustering lengths of r0 ∼ 3–6 h−1 Mpc and typical halo masses of ∼1011 M⊙ for our narrowband-selected LAEs with typical LLy α ∼ 1042–43 erg s−1. The intermediate-band-selected LAEs are observed to have r0 ∼ 3.5–15 h−1 Mpc with typical halo masses of ∼1011–12 M⊙ and typical LLy α ∼ 1043–43.6 erg s−1. We find a strong, redshift-independent correlation between halo mass and Ly α luminosity normalized by the characteristic Ly α luminosity, L⋆(z). The faintest LAEs (L ∼ 0.1 L⋆(z)) typically identified by deep narrowband surveys are found in 1010 M⊙ haloes and the brightest LAEs (L ∼ 7 L⋆(z)) are found in ∼5 × 1012 M⊙ haloes. A dependency on the rest-frame 1500 Å UV luminosity, MUV, is also observed where the halo masses increase from 1011 to 1013 M⊙ for MUV ∼ −19 to −23.5 mag. Halo mass is also observed to increase from 109.8 to 1012 M⊙ for dust-corrected UV star formation rates from ∼0.6 to 10 M⊙ yr−1 and continues to increase up to 1013 M⊙ in halo mass, where the majority of those sources are active galactic nuclei. All the trends we observe are found to be redshift independent. Our results reveal that LAEs are the likely progenitors of a wide range of galaxies depending on their luminosity, from dwarf-like, to Milky Way-type, to bright cluster galaxies. LAEs therefore provide unique insight into the early formation and evolution of the galaxies we observe in the local Universe."}],"issue":"1"},{"article_type":"original","page":"2422-2441","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"short":"D. Sobral, J.J. Matthee, G. Brammer, A. Ferrara, L. Alegre, H. Röttgering, D. Schaerer, B. Mobasher, B. Darvish, Monthly Notices of the Royal Astronomical Society 482 (2019) 2422–2441.","mla":"Sobral, David, et al. “On the Nature and Physical Conditions of the Luminous Ly α Emitter CR7 and Its Rest-Frame UV Components.” Monthly Notices of the Royal Astronomical Society, vol. 482, no. 2, Oxford University Press, 2019, pp. 2422–41, doi:10.1093/mnras/sty2779.","chicago":"Sobral, David, Jorryt J Matthee, Gabriel Brammer, Andrea Ferrara, Lara Alegre, Huub Röttgering, Daniel Schaerer, Bahram Mobasher, and Behnam Darvish. “On the Nature and Physical Conditions of the Luminous Ly α Emitter CR7 and Its Rest-Frame UV Components.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/sty2779.","ama":"Sobral D, Matthee JJ, Brammer G, et al. On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. 2019;482(2):2422-2441. doi:10.1093/mnras/sty2779","apa":"Sobral, D., Matthee, J. J., Brammer, G., Ferrara, A., Alegre, L., Röttgering, H., … Darvish, B. (2019). On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty2779","ieee":"D. Sobral et al., “On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components,” Monthly Notices of the Royal Astronomical Society, vol. 482, no. 2. Oxford University Press, pp. 2422–2441, 2019.","ista":"Sobral D, Matthee JJ, Brammer G, Ferrara A, Alegre L, Röttgering H, Schaerer D, Mobasher B, Darvish B. 2019. On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components. Monthly Notices of the Royal Astronomical Society. 482(2), 2422–2441."},"date_published":"2019-01-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","cosmology: observations","dark ages","reionization","first stars","early Universe"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components","intvolume":" 482","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11541","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We present new Hubble Space Telescope (HST)/WFC3 observations and re-analyse VLT data to unveil the continuum, variability, and rest-frame ultraviolet (UV) lines of the multiple UV clumps of the most luminous Lyα emitter at z = 6.6, CR7 (COSMOS Redshift 7). Our re-reduced, flux-calibrated X-SHOOTER spectra of CR7 reveal an He II emission line in observations obtained along the major axis of Lyα emission with the best seeing conditions. He II is spatially offset by ≈+0.8 arcsec from the peak of Lyα emission, and it is found towards clump B. Our WFC3 grism spectra detects the UV continuum of CR7’s clump A, yielding a power law with β=−2.5+0.6−0.7 and MUV=−21.87+0.25−0.20. No significant variability is found for any of the UV clumps on their own, but there is tentative (≈2.2 σ) brightening of CR7 in F110W as a whole from 2012 to 2017. HST grism data fail to robustly detect rest-frame UV lines in any of the clumps, implying fluxes ≲2×10−17 erg s−1 cm−2 (3σ). We perform CLOUDY modelling to constrain the metallicity and the ionizing nature of CR7. CR7 seems to be actively forming stars without any clear active galactic nucleus activity in clump A, consistent with a metallicity of ∼0.05–0.2 Z⊙. Component C or an interclump component between B and C may host a high ionization source. Our results highlight the need for spatially resolved information to study the formation and assembly of early galaxies.","lang":"eng"}],"issue":"2","quality_controlled":"1","external_id":{"arxiv":["1710.08422"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1710.08422","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/mnras/sty2779","month":"01","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We thank the anonymous reviewer for the numerous detailed comments that led us to greatly improve the quality, extent, and statistical robustness of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific research through a Veni fellowship. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program, grant number NNX12AE20G and the National Science Foundation, grant number 1716907. We are thankful for several discussions and constructive comments from Johannes Zabl, Eros Vanzella, Bo Milvang-Jensen, Henry McCracken, Max Gronke, Mark Dijkstra, Richard Ellis, and Nicolas Laporte. We also thank Umar Burhanudin and Izzy Garland for taking part in the XGAL internship in Lancaster and for exploring the HST grism data independently. Based on observations obtained with HST/WFC3 programs 12578, 14495, and 14596. Based on observations of the National Japanese Observatory with the Suprime-Cam on the Subaru telescope (S14A-086) on the big island of Hawaii. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France–Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A 0786, 093.A-0561, 097.A0043, 097.A-0943, 098.A-0819, 298.A-5012, and 179.A-2005, and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. The authors acknowledge the award of service time (SW2014b20) on the William Herschel Telescope (WHT). WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This research was supported by the Munich Institute for Astro- and Particle Physics of the DFG cluster of excellence ‘Origin and Structure of the Universe’. We have benefitted immensely from the public available programming language PYTHON, including NUMPY and SCIPY (Jones et al. 2001; Van Der Walt, Colbert & Varoquaux 2011), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France. All data used for this paper are publicly available, and we make all reduced data available with the refereed paper.","year":"2019","date_updated":"2022-08-19T06:49:36Z","date_created":"2022-07-08T10:40:05Z","volume":482,"author":[{"last_name":"Sobral","first_name":"David","full_name":"Sobral, David"},{"full_name":"Matthee, Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J"},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"full_name":"Ferrara, Andrea","last_name":"Ferrara","first_name":"Andrea"},{"last_name":"Alegre","first_name":"Lara","full_name":"Alegre, Lara"},{"first_name":"Huub","last_name":"Röttgering","full_name":"Röttgering, Huub"},{"last_name":"Schaerer","first_name":"Daniel","full_name":"Schaerer, Daniel"},{"full_name":"Mobasher, Bahram","first_name":"Bahram","last_name":"Mobasher"},{"full_name":"Darvish, Behnam","last_name":"Darvish","first_name":"Behnam"}],"extern":"1"},{"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics : galaxies: evolution","galaxies: formation","galaxies: star formation","cosmology: theory"],"day":"01","article_processing_charge":"No","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Matthee JJ, Schaye J. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 2019;484(1):915-932. doi:10.1093/mnras/stz030","ista":"Matthee JJ, Schaye J. 2019. The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. 484(1), 915–932.","ieee":"J. J. Matthee and J. Schaye, “The origin of scatter in the star formation rate–stellar mass relation,” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1. Oxford University Press, pp. 915–932, 2019.","apa":"Matthee, J. J., & Schaye, J. (2019). The origin of scatter in the star formation rate–stellar mass relation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz030","mla":"Matthee, Jorryt J., and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 1, Oxford University Press, 2019, pp. 915–32, doi:10.1093/mnras/stz030.","short":"J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society 484 (2019) 915–932.","chicago":"Matthee, Jorryt J, and Joop Schaye. “The Origin of Scatter in the Star Formation Rate–Stellar Mass Relation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz030."},"article_type":"original","page":"915-932","date_published":"2019-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Observations have revealed that the star formation rate (SFR) and stellar mass (Mstar) of star-forming galaxies follow a tight relation known as the galaxy main sequence. However, what physical information is encoded in this relation is under debate. Here, we use the EAGLE cosmological hydrodynamical simulation to study the mass dependence, evolution, and origin of scatter in the SFR–Mstar relation. At z = 0, we find that the scatter decreases slightly with stellar mass from 0.35 dex at Mstar ≈ 109 M⊙ to 0.30 dex at Mstar ≳ 1010.5 M⊙. The scatter decreases from z = 0 to z = 5 by 0.05 dex at Mstar ≳ 1010 M⊙ and by 0.15 dex for lower masses. We show that the scatter at z = 0.1 originates from a combination of fluctuations on short time-scales (ranging from 0.2–2 Gyr) that are presumably associated with self-regulation from cooling, star formation, and outflows, but is dominated by long time-scale (∼10 Gyr) variations related to differences in halo formation times. Shorter time-scale fluctuations are relatively more important for lower mass galaxies. At high masses, differences in black hole formation efficiency cause additional scatter, but also diminish the scatter caused by different halo formation times. While individual galaxies cross the main sequence multiple times during their evolution, they fluctuate around tracks associated with their halo properties, i.e. galaxies above/below the main sequence at z = 0.1 tend to have been above/below the main sequence for ≫1 Gyr."}],"issue":"1","_id":"11540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The origin of scatter in the star formation rate–stellar mass relation","intvolume":" 484","oa_version":"Preprint","month":"03","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"oa":1,"external_id":{"arxiv":["1805.05956"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.05956"}],"quality_controlled":"1","doi":"10.1093/mnras/stz030","language":[{"iso":"eng"}],"extern":"1","year":"2019","acknowledgement":"JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Camila Correa for help analysing snipshot merger trees. We thank the anonymous referee for constructive comments. We also thank Jarle Brinchmann, Rob Crain, Antonios Katsianis, Paola Popesso, and David Sobral for discussions and suggestions. We also thank the participants of the Lorentz Center workshop ‘A Decade of the Star-Forming Main Sequence’ held on 2017 September 4–8, for discussions and ideas. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, and SCIPY (Hunter 2007) packages and the TOPCAT analysis tool (Taylor 2013).","publication_status":"published","publisher":"Oxford University Press","author":[{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"}],"date_created":"2022-07-08T07:48:31Z","date_updated":"2022-08-19T06:42:43Z","volume":484},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.01643"}],"external_id":{"arxiv":["1901.01643"]},"oa":1,"quality_controlled":"1","doi":"10.3847/1538-3881/ab1488","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["0004-6256"]},"acknowledgement":"The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the indigenous Hawai'ian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We thank Andrei Tokovinin for helpful information on the Speckle observations obtained with SOAR. D.H. acknowledges support by the National Aeronautics and Space Administration through the TESS Guest Investigator Program (80NSSC18K1585) and by the National Science Foundation (AST-1717000). A.C. acknowledges support by the National Science Foundation under the Graduate Research Fellowship Program. W.J.C., W.H.B., A.M., O.J.H., and G.R.D. acknowledge support from the Science and Technology Facilities Council and UK Space Agency. H.K. and F.G. acknowledge support from the European Social Fund via the Lithuanian Science Council grant No. 09.3.3-LMT-K-712-01-0103. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (grant DNRF106). A.J. acknowledges support from FONDECYT project 1171208, CONICYT project BASAL AFB-170002, and by the Ministry for the Economy, Development, and Tourism's Programa Iniciativa Científica Milenio through grant IC 120009, awarded to the Millennium Institute of Astrophysics (MAS). R.B. acknowledges support from FONDECYT Post-doctoral Fellowship Project 3180246, and from the Millennium Institute of Astrophysics (MAS). A.M.S. is supported by grants ESP2017-82674-R (MINECO) and SGR2017-1131 (AGAUR). R.A.G. and L.B. acknowledge the support of the PLATO grant from the CNES. The research leading to the presented results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP72007-2013)ERC grant agreement No. 338251 (StellarAges). S.M. acknowledges support from the European Research Council through the SPIRE grant 647383. This work was also supported by FCT (Portugal) through national funds and by FEDER through COMPETE2020 by these grants: UID/FIS/04434/2013 and POCI-01-0145-FEDER-007672, PTDC/FIS-AST/30389/2017, and POCI-01-0145-FEDER-030389. T.L.C. acknowledges support from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 792848 (PULSATION). E.C. is funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 664931. V.S.A. acknowledges support from the Independent Research Fund Denmark (Research grant 7027-00096B). D.S. acknowledges support from the Australian Research Council. S.B. acknowledges NASA grant NNX16AI09G and NSF grant AST-1514676. T.R.W. acknowledges support from the Australian Research Council through grant DP150100250. A.M. acknowledges support from the ERC Consolidator Grant funding scheme (project ASTEROCHRONOMETRY, G.A. n. 772293). S.M. acknowledges support from the Ramon y Cajal fellowship number RYC-2015-17697. M.S.L. is supported by the Carlsberg Foundation (grant agreement No. CF17-0760). A.M. and P.R. acknowledge support from the HBCSE-NIUS programme. J.K.T. and J.T. acknowledge that support for this work was provided by NASA through Hubble Fellowship grants HST-HF2-51399.001 and HST-HF2-51424.001 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. T.S.R. acknowledges financial support from Premiale 2015 MITiC (PI B. Garilli). This project has been supported by the NKFIH K-115709 grant and the Lendület Program of the Hungarian Academy of Sciences, project No. LP2018-7/2018.\r\n\r\nBased on observations made with the Hertzsprung SONG telescope operated on the Spanish Observatorio del Teide on the island of Tenerife by the Aarhus and Copenhagen Universities and by the Instituto de Astrofísica de Canarias. Funding for the TESS mission is provided by NASA's Science Mission directorate. We acknowledge the use of public TESS Alert data from pipelines at the TESS Science Office and at the TESS Science Processing Operations Center. This research has made use of the Exoplanet Follow-up Observation Program website, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program. This paper includes data collected by the TESS mission, which are publicly available from the Mikulski Archive for Space Telescopes (MAST).\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2018), Matplotlib (Hunter 2007), DIAMONDS (Corsaro & De Ridder 2014), isoclassify (Huber et al. 2017), EXOFASTv2 (Eastman 2017), ktransit (Barclay 2018).","year":"2019","publication_status":"published","publisher":"IOP Publishing","author":[{"full_name":"Huber, Daniel","last_name":"Huber","first_name":"Daniel"},{"full_name":"Chaplin, William J.","first_name":"William J.","last_name":"Chaplin"},{"full_name":"Chontos, Ashley","first_name":"Ashley","last_name":"Chontos"},{"full_name":"Kjeldsen, Hans","last_name":"Kjeldsen","first_name":"Hans"},{"first_name":"Jørgen","last_name":"Christensen-Dalsgaard","full_name":"Christensen-Dalsgaard, Jørgen"},{"first_name":"Timothy R.","last_name":"Bedding","full_name":"Bedding, Timothy R."},{"first_name":"Warrick","last_name":"Ball","full_name":"Ball, Warrick"},{"full_name":"Brahm, Rafael","first_name":"Rafael","last_name":"Brahm"},{"full_name":"Espinoza, Nestor","first_name":"Nestor","last_name":"Espinoza"},{"full_name":"Henning, Thomas","first_name":"Thomas","last_name":"Henning"},{"full_name":"Jordán, Andrés","last_name":"Jordán","first_name":"Andrés"},{"full_name":"Sarkis, Paula","first_name":"Paula","last_name":"Sarkis"},{"first_name":"Emil","last_name":"Knudstrup","full_name":"Knudstrup, Emil"},{"first_name":"Simon","last_name":"Albrecht","full_name":"Albrecht, Simon"},{"last_name":"Grundahl","first_name":"Frank","full_name":"Grundahl, Frank"},{"full_name":"Andersen, Mads Fredslund","last_name":"Andersen","first_name":"Mads Fredslund"},{"full_name":"Pallé, Pere L.","last_name":"Pallé","first_name":"Pere L."},{"full_name":"Crossfield, Ian","first_name":"Ian","last_name":"Crossfield"},{"last_name":"Fulton","first_name":"Benjamin","full_name":"Fulton, Benjamin"},{"full_name":"Howard, Andrew W.","last_name":"Howard","first_name":"Andrew W."},{"full_name":"Isaacson, Howard T.","first_name":"Howard T.","last_name":"Isaacson"},{"first_name":"Lauren M.","last_name":"Weiss","full_name":"Weiss, Lauren M."},{"last_name":"Handberg","first_name":"Rasmus","full_name":"Handberg, Rasmus"},{"last_name":"Lund","first_name":"Mikkel N.","full_name":"Lund, Mikkel N."},{"full_name":"Serenelli, Aldo M.","first_name":"Aldo M.","last_name":"Serenelli"},{"full_name":"Rørsted Mosumgaard, Jakob","first_name":"Jakob","last_name":"Rørsted Mosumgaard"},{"full_name":"Stokholm, Amalie","first_name":"Amalie","last_name":"Stokholm"},{"full_name":"Bieryla, Allyson","first_name":"Allyson","last_name":"Bieryla"},{"last_name":"Buchhave","first_name":"Lars A.","full_name":"Buchhave, Lars A."},{"full_name":"Latham, David W.","first_name":"David W.","last_name":"Latham"},{"full_name":"Quinn, Samuel N.","first_name":"Samuel N.","last_name":"Quinn"},{"last_name":"Gaidos","first_name":"Eric","full_name":"Gaidos, Eric"},{"first_name":"Teruyuki","last_name":"Hirano","full_name":"Hirano, Teruyuki"},{"full_name":"Ricker, George R.","last_name":"Ricker","first_name":"George R."},{"first_name":"Roland K.","last_name":"Vanderspek","full_name":"Vanderspek, Roland K."},{"full_name":"Seager, Sara","first_name":"Sara","last_name":"Seager"},{"full_name":"Jenkins, Jon M.","first_name":"Jon M.","last_name":"Jenkins"},{"full_name":"Winn, Joshua N.","last_name":"Winn","first_name":"Joshua N."},{"full_name":"Antia, H. M.","last_name":"Antia","first_name":"H. M."},{"last_name":"Appourchaux","first_name":"Thierry","full_name":"Appourchaux, Thierry"},{"last_name":"Basu","first_name":"Sarbani","full_name":"Basu, Sarbani"},{"first_name":"Keaton J.","last_name":"Bell","full_name":"Bell, Keaton J."},{"full_name":"Benomar, Othman","last_name":"Benomar","first_name":"Othman"},{"last_name":"Bonanno","first_name":"Alfio","full_name":"Bonanno, Alfio"},{"full_name":"Buzasi, Derek L.","first_name":"Derek L.","last_name":"Buzasi"},{"full_name":"Campante, Tiago L.","first_name":"Tiago L.","last_name":"Campante"},{"last_name":"Çelik Orhan","first_name":"Z.","full_name":"Çelik Orhan, Z."},{"first_name":"Enrico","last_name":"Corsaro","full_name":"Corsaro, Enrico"},{"full_name":"Cunha, Margarida S.","last_name":"Cunha","first_name":"Margarida S."},{"full_name":"Davies, Guy R.","last_name":"Davies","first_name":"Guy R."},{"first_name":"Sebastien","last_name":"Deheuvels","full_name":"Deheuvels, Sebastien"},{"first_name":"Samuel K.","last_name":"Grunblatt","full_name":"Grunblatt, Samuel K."},{"full_name":"Hasanzadeh, Amir","last_name":"Hasanzadeh","first_name":"Amir"},{"last_name":"Di Mauro","first_name":"Maria Pia","full_name":"Di Mauro, Maria Pia"},{"last_name":"A. García","first_name":"Rafael","full_name":"A. García, Rafael"},{"full_name":"Gaulme, Patrick","last_name":"Gaulme","first_name":"Patrick"},{"full_name":"Girardi, Léo","first_name":"Léo","last_name":"Girardi"},{"last_name":"Guzik","first_name":"Joyce A.","full_name":"Guzik, Joyce A."},{"full_name":"Hon, Marc","last_name":"Hon","first_name":"Marc"},{"full_name":"Jiang, Chen","last_name":"Jiang","first_name":"Chen"},{"full_name":"Kallinger, Thomas","first_name":"Thomas","last_name":"Kallinger"},{"first_name":"Steven D.","last_name":"Kawaler","full_name":"Kawaler, Steven D."},{"last_name":"Kuszlewicz","first_name":"James S.","full_name":"Kuszlewicz, James S."},{"full_name":"Lebreton, Yveline","first_name":"Yveline","last_name":"Lebreton"},{"last_name":"Li","first_name":"Tanda","full_name":"Li, Tanda"},{"full_name":"Lucas, Miles","first_name":"Miles","last_name":"Lucas"},{"first_name":"Mia S.","last_name":"Lundkvist","full_name":"Lundkvist, Mia S."},{"full_name":"Mann, Andrew W.","first_name":"Andrew W.","last_name":"Mann"},{"first_name":"Stéphane","last_name":"Mathis","full_name":"Mathis, Stéphane"},{"first_name":"Savita","last_name":"Mathur","full_name":"Mathur, Savita"},{"last_name":"Mazumdar","first_name":"Anwesh","full_name":"Mazumdar, Anwesh"},{"full_name":"Metcalfe, Travis S.","first_name":"Travis S.","last_name":"Metcalfe"},{"full_name":"Miglio, Andrea","first_name":"Andrea","last_name":"Miglio"},{"first_name":"Mário J. P.","last_name":"F. G. Monteiro","full_name":"F. G. Monteiro, Mário J. 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G.","last_name":"Tinney","full_name":"Tinney, C. G."},{"full_name":"Teske, Johanna","first_name":"Johanna","last_name":"Teske"},{"first_name":"Alexandra","last_name":"Thomas","full_name":"Thomas, Alexandra"},{"full_name":"Trampedach, Regner","first_name":"Regner","last_name":"Trampedach"},{"full_name":"Wright, Duncan","first_name":"Duncan","last_name":"Wright"},{"first_name":"Thomas T.","last_name":"Yuan","full_name":"Yuan, Thomas T."},{"full_name":"Zohrabi, Farzaneh","first_name":"Farzaneh","last_name":"Zohrabi"}],"date_updated":"2022-08-22T07:38:34Z","date_created":"2022-07-18T14:29:07Z","volume":157,"article_number":"245","extern":"1","publication":"The Astronomical Journal","citation":{"chicago":"Huber, Daniel, William J. Chaplin, Ashley Chontos, Hans Kjeldsen, Jørgen Christensen-Dalsgaard, Timothy R. Bedding, Warrick Ball, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal. IOP Publishing, 2019. https://doi.org/10.3847/1538-3881/ab1488.","mla":"Huber, Daniel, et al. “A Hot Saturn Orbiting an Oscillating Late Subgiant Discovered by TESS.” The Astronomical Journal, vol. 157, no. 6, 245, IOP Publishing, 2019, doi:10.3847/1538-3881/ab1488.","short":"D. Huber, W.J. Chaplin, A. Chontos, H. Kjeldsen, J. Christensen-Dalsgaard, T.R. Bedding, W. Ball, R. Brahm, N. Espinoza, T. Henning, A. Jordán, P. Sarkis, E. Knudstrup, S. Albrecht, F. Grundahl, M.F. Andersen, P.L. Pallé, I. Crossfield, B. Fulton, A.W. Howard, H.T. Isaacson, L.M. Weiss, R. Handberg, M.N. Lund, A.M. Serenelli, J. Rørsted Mosumgaard, A. Stokholm, A. Bieryla, L.A. Buchhave, D.W. Latham, S.N. Quinn, E. Gaidos, T. Hirano, G.R. Ricker, R.K. Vanderspek, S. Seager, J.M. Jenkins, J.N. Winn, H.M. Antia, T. Appourchaux, S. Basu, K.J. Bell, O. Benomar, A. Bonanno, D.L. Buzasi, T.L. Campante, Z. Çelik Orhan, E. Corsaro, M.S. Cunha, G.R. Davies, S. Deheuvels, S.K. Grunblatt, A. Hasanzadeh, M.P. Di Mauro, R. A. García, P. Gaulme, L. Girardi, J.A. Guzik, M. Hon, C. Jiang, T. Kallinger, S.D. Kawaler, J.S. Kuszlewicz, Y. Lebreton, T. Li, M. Lucas, M.S. Lundkvist, A.W. Mann, S. Mathis, S. Mathur, A. Mazumdar, T.S. Metcalfe, A. Miglio, M.J.P. F. G. Monteiro, B. Mosser, A. Noll, B. Nsamba, J.M. Joel Ong, S. Örtel, F. Pereira, P. Ranadive, C. Régulo, T.S. Rodrigues, I.W. Roxburgh, V.S. Aguirre, B. Smalley, M. Schofield, S.G. Sousa, K.G. Stassun, D. Stello, J. Tayar, T.R. White, K. Verma, M. Vrard, M. Yıldız, D. Baker, M. Bazot, C. Beichmann, C. Bergmann, L.A. Bugnet, B. Cale, R. Carlino, S.M. Cartwright, J.L. Christiansen, D.R. Ciardi, O. Creevey, J.A. Dittmann, J.-D.D. Nascimento, V.V. Eylen, G. Fürész, J. Gagné, P. Gao, K. Gazeas, F. Giddens, O.J. Hall, S. Hekker, M.J. Ireland, N. Latouf, D. LeBrun, A.M. Levine, W. Matzko, E. Natinsky, E. Page, P. Plavchan, M. Mansouri-Samani, S. McCauliff, S.E. Mullally, B. Orenstein, A.G. Soto, M. Paegert, J.L. van Saders, C. Schnaible, D.R. Soderblom, R. Szabó, A. Tanner, C.G. Tinney, J. Teske, A. Thomas, R. Trampedach, D. Wright, T.T. Yuan, F. Zohrabi, The Astronomical Journal 157 (2019).","ista":"Huber D et al. 2019. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 157(6), 245.","apa":"Huber, D., Chaplin, W. J., Chontos, A., Kjeldsen, H., Christensen-Dalsgaard, J., Bedding, T. R., … Zohrabi, F. (2019). A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. IOP Publishing. https://doi.org/10.3847/1538-3881/ab1488","ieee":"D. Huber et al., “A hot Saturn orbiting an oscillating late subgiant discovered by TESS,” The Astronomical Journal, vol. 157, no. 6. IOP Publishing, 2019.","ama":"Huber D, Chaplin WJ, Chontos A, et al. A hot Saturn orbiting an oscillating late subgiant discovered by TESS. The Astronomical Journal. 2019;157(6). doi:10.3847/1538-3881/ab1488"},"article_type":"original","date_published":"2019-05-30T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"30","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11616","status":"public","title":"A hot Saturn orbiting an oscillating late subgiant discovered by TESS","intvolume":" 157","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We present the discovery of HD 221416 b, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. HD 221416 b (HIP 116158, TOI-197) is a bright (V = 8.2 mag), spectroscopically classified subgiant that oscillates with an average frequency of about 430 μHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2 minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (R⋆ = 2.943 ± 0.064 R⊙), mass (M⋆ = 1.212 ± 0.074 M⊙), and age (4.9 ± 1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a \"hot Saturn\" (Rp = 9.17 ± 0.33 R⊕) with an orbital period of ∼14.3 days, irradiance of F = 343 ± 24 F⊕, and moderate mass (Mp = 60.5 ± 5.7 M⊕) and density (ρp = 0.431 ± 0.062 g cm−3). The properties of HD 221416 b show that the host-star metallicity–planet mass correlation found in sub-Saturns (4–8 R⊕) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ∼15%, HD 221416 b is one of the best characterized Saturn-size planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology.","lang":"eng"}],"issue":"6"}]