[{"pmid":1,"year":"2017","acknowledgement":"M.S. and G.A.V. acknowledge their research reported in this publication as being supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01-GM063796. Computational resources were provided to M.S. and G.A.V. by the National Science Foundation through XSEDE (Grant TG-MCA94P017, supercomputers Stampede and Gordon), and also by the Blue Waters computing project at the National Center for Supercomputing Applications (University of Illinois at Urbana–Champaign, NSF Awards OCI-0725070 and ACI-1238993). A.Š. acknowledges support from the Human Frontier Science Program and Royal Society. J.M.H. and K.Y.C.L. acknowledge the support from the National Science Foundation (Grant MCB-1413613) and the NSF-supported MRSEC program at the University of Chicago (Grant DMR-1420709). We are grateful to Carsten Mim and Vinzenz Unger of Northwestern University for generously providing us with the protein. We thank all the members of the Voth group for fruitful discussions, especially John M. A. Grime.","publisher":"American Chemical Society","publication_status":"published","author":[{"first_name":"Mijo","last_name":"Simunovic","full_name":"Simunovic, Mijo"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Henderson, J. Michael","first_name":"J. Michael","last_name":"Henderson"},{"full_name":"Lee, Ka Yee C.","first_name":"Ka Yee C.","last_name":"Lee"},{"full_name":"Voth, Gregory A.","last_name":"Voth","first_name":"Gregory A."}],"volume":3,"date_updated":"2021-11-29T09:28:06Z","date_created":"2021-11-29T08:49:50Z","file_date_updated":"2021-11-29T09:00:40Z","license":"https://creativecommons.org/licenses/by/4.0/","extern":"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":["29296664"]},"main_file_link":[{"open_access":"1","url":"https://pubs.acs.org/doi/10.1021/acscentsci.7b00392"}],"oa":1,"quality_controlled":"1","doi":"10.1021/acscentsci.7b00392","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2374-7943"],"eissn":["2374-7951"]},"month":"11","_id":"10369","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 3","ddc":["540"],"title":"Long-range organization of membrane-curving proteins","status":"public","file":[{"date_updated":"2021-11-29T09:00:40Z","date_created":"2021-11-29T09:00:40Z","success":1,"checksum":"1cf3e5e5342f2d728f47560acc3ec560","file_id":"10371","relation":"main_file","creator":"cchlebak","file_size":2635263,"content_type":"application/pdf","file_name":"2017_ACSCentSci_Simunovic.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell.","lang":"eng"}],"citation":{"ama":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-range organization of membrane-curving proteins. ACS Central Science. 2017;3(12):1246-1253. doi:10.1021/acscentsci.7b00392","ieee":"M. Simunovic, A. Šarić, J. M. Henderson, K. Y. C. Lee, and G. A. Voth, “Long-range organization of membrane-curving proteins,” ACS Central Science, vol. 3, no. 12. American Chemical Society, pp. 1246–1253, 2017.","apa":"Simunovic, M., Šarić, A., Henderson, J. M., Lee, K. Y. C., & Voth, G. A. (2017). Long-range organization of membrane-curving proteins. ACS Central Science. American Chemical Society. https://doi.org/10.1021/acscentsci.7b00392","ista":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. 2017. Long-range organization of membrane-curving proteins. ACS Central Science. 3(12), 1246–1253.","short":"M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central Science 3 (2017) 1246–1253.","mla":"Simunovic, Mijo, et al. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science, vol. 3, no. 12, American Chemical Society, 2017, pp. 1246–53, doi:10.1021/acscentsci.7b00392.","chicago":"Simunovic, Mijo, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and Gregory A. Voth. “Long-Range Organization of Membrane-Curving Proteins.” ACS Central Science. American Chemical Society, 2017. https://doi.org/10.1021/acscentsci.7b00392."},"publication":"ACS Central Science","page":"1246-1253","article_type":"original","date_published":"2017-11-21T00:00:00Z","scopus_import":"1","keyword":["general chemical engineering","general chemistry"],"article_processing_charge":"No","has_accepted_license":"1","day":"21"},{"day":"24","article_processing_charge":"No","scopus_import":"1","keyword":["multidisciplinary"],"date_published":"2017-04-24T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"ieee":"P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel, “Numerical evidence for thermally induced monopoles,” Proceedings of the National Academy of Sciences, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914, 2017.","apa":"Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., & Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1621494114","ista":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 114(19), 4911–4914.","ama":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 2017;114(19):4911-4914. doi:10.1073/pnas.1621494114","chicago":"Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621494114.","short":"P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel, Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.","mla":"Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.” Proceedings of the National Academy of Sciences, vol. 114, no. 19, National Academy of Sciences, 2017, pp. 4911–14, doi:10.1073/pnas.1621494114."},"article_type":"original","page":"4911-4914","abstract":[{"lang":"eng","text":"Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis."}],"issue":"19","type":"journal_article","oa_version":"Published Version","_id":"10373","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Numerical evidence for thermally induced monopoles","status":"public","intvolume":" 114","month":"04","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"doi":"10.1073/pnas.1621494114","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28439003"],"arxiv":["1610.06840"]},"main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/114/19/4911"}],"quality_controlled":"1","extern":"1","author":[{"first_name":"Peter","last_name":"Wirnsberger","full_name":"Wirnsberger, Peter"},{"full_name":"Fijan, Domagoj","last_name":"Fijan","first_name":"Domagoj"},{"full_name":"Lightwood, Roger A.","first_name":"Roger A.","last_name":"Lightwood"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Dellago","first_name":"Christoph","full_name":"Dellago, Christoph"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"}],"date_created":"2021-11-29T09:28:24Z","date_updated":"2021-11-29T09:59:12Z","volume":114,"acknowledgement":"P.W. acknowledges many invaluable discussions with Martin Neumann, Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge financial support from the Austrian Academy of Sciences through a doctoral (DOC) fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results presented here have been achieved in part using the Vienna Scientific Cluster.","year":"2017","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences"},{"article_processing_charge":"No","day":"31","scopus_import":"1","keyword":["general chemistry"],"date_published":"2017-08-31T00:00:00Z","citation":{"mla":"Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science, vol. 8, no. 10, Royal Society of Chemistry, 2017, pp. 7087–97, doi:10.1039/c7sc01965c.","short":"G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand, A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Chemical Science 8 (2017) 7087–7097.","chicago":"Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” Chemical Science. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sc01965c.","ama":"Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 2017;8(10):7087-7097. doi:10.1039/c7sc01965c","ista":"Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10), 7087–7097.","apa":"Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand, E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c7sc01965c","ieee":"G. Meisl et al., “Scaling behaviour and rate-determining steps in filamentous self-assembly,” Chemical Science, vol. 8, no. 10. Royal Society of Chemistry, pp. 7087–7097, 2017."},"publication":"Chemical Science","page":"7087-7097","article_type":"original","issue":"10","abstract":[{"lang":"eng","text":"The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly."}],"type":"journal_article","oa_version":"Published Version","_id":"10374","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 8","status":"public","title":"Scaling behaviour and rate-determining steps in filamentous self-assembly","ddc":["540"],"publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"month":"08","doi":"10.1039/c7sc01965c","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png"},"oa":1,"external_id":{"pmid":["29147538"]},"quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc/3.0/","extern":"1","author":[{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Rajah, Luke","last_name":"Rajah","first_name":"Luke"},{"first_name":"Samuel A. I.","last_name":"Cohen","full_name":"Cohen, Samuel A. I."},{"full_name":"Pfammatter, Manuela","last_name":"Pfammatter","first_name":"Manuela"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Hellstrand, Erik","first_name":"Erik","last_name":"Hellstrand"},{"full_name":"Buell, Alexander K.","last_name":"Buell","first_name":"Alexander K."},{"full_name":"Aguzzi, Adriano","last_name":"Aguzzi","first_name":"Adriano"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"volume":8,"date_updated":"2021-11-29T10:00:00Z","date_created":"2021-11-29T09:29:31Z","pmid":1,"year":"2017","acknowledgement":"The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (SL, TPJK), Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation (TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ), and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV).","publisher":"Royal Society of Chemistry","publication_status":"published"},{"author":[{"full_name":"Vahid, Afshin","last_name":"Vahid","first_name":"Afshin"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"}],"date_updated":"2021-11-29T10:33:36Z","date_created":"2021-11-29T10:00:39Z","volume":13,"year":"2017","acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program.","pmid":1,"publication_status":"published","publisher":"Royal Society of Chemistry","license":"https://creativecommons.org/licenses/by/3.0/","extern":"1","doi":"10.1039/c7sm00433h","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H","open_access":"1"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1703.00776"],"pmid":["28677712"]},"quality_controlled":"1","month":"06","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10375","title":"Curvature variation controls particle aggregation on fluid vesicles","status":"public","intvolume":" 13","abstract":[{"text":"Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts.","lang":"eng"}],"issue":"28","type":"journal_article","date_published":"2017-06-15T00:00:00Z","publication":"Soft Matter","citation":{"ama":"Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 2017;13(28):4924-4930. doi:10.1039/c7sm00433h","ista":"Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930.","apa":"Vahid, A., Šarić, A., & Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c7sm00433h","ieee":"A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” Soft Matter, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017.","mla":"Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:10.1039/c7sm00433h.","short":"A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.","chicago":"Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” Soft Matter. Royal Society of Chemistry, 2017. https://doi.org/10.1039/c7sm00433h."},"article_type":"original","page":"4924-4930","day":"15","article_processing_charge":"No","scopus_import":"1","keyword":["condensed matter physics","general chemistry"]},{"article_number":"33","year":"2017","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Mciver, Annabelle","first_name":"Annabelle","last_name":"Mciver"},{"full_name":"Morgan, Carroll","last_name":"Morgan","first_name":"Carroll"},{"full_name":"Kaminski, Benjamin Lucien","last_name":"Kaminski","first_name":"Benjamin Lucien"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"}],"volume":2,"date_updated":"2021-12-07T08:04:14Z","date_created":"2021-12-05T23:01:49Z","publication_identifier":{"eissn":["2475-1421"]},"month":"12","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"external_id":{"arxiv":["1711.03588"]},"oa":1,"quality_controlled":"1","doi":"10.1145/3158121","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","start_date":"2018-01-07","location":"Los Angeles, CA, United States"},"language":[{"iso":"eng"}],"type":"journal_article","issue":"POPL","abstract":[{"lang":"eng","text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10418","intvolume":" 2","status":"public","title":"A new proof rule for almost-sure termination","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"07","citation":{"ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2017-12-07T00:00:00Z"},{"abstract":[{"lang":"eng","text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures."}],"extern":"1","type":"dissertation","alternative_title":["Graduate Dissertations and Theses at Illinois"],"author":[{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"}],"date_updated":"2022-01-25T15:00:26Z","date_created":"2022-01-25T14:54:14Z","oa_version":"Published Version","year":"2017","_id":"10663","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","status":"public","title":"Magnetic force microscopy studies of mesoscopic superconducting structures","publisher":"University of Illinois at Urbana-Champaign","month":"09","day":"18","article_processing_charge":"No","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"date_published":"2017-09-18T00:00:00Z","supervisor":[{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"citation":{"mla":"Polshyn, Hryhoriy. Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures. University of Illinois at Urbana-Champaign, 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","apa":"Polshyn, H. (2017). Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/2142/99178"}],"page":"103"},{"publication":"APS March Meeting 2017","citation":{"ama":"Polshyn H, Naibert T, Budakian R. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: APS March Meeting 2017. Vol 62. American Physical Society; 2017.","ista":"Polshyn H, Naibert T, Budakian R. 2017. Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in APS March Meeting 2017, New Orleans, LA, United States, 2017, vol. 62, no. 4.","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2017). Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In APS March Meeting 2017 (Vol. 62). New Orleans, LA, United States: American Physical Society.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” APS March Meeting 2017, vol. 62, no. 4, P39.00011, American Physical Society, 2017.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In APS March Meeting 2017, Vol. 62. American Physical Society, 2017."},"date_published":"2017-03-01T00:00:00Z","day":"01","article_processing_charge":"No","status":"public","title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","intvolume":" 62","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10745","oa_version":"Published Version","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","abstract":[{"lang":"eng","text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures"}],"issue":"4","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"APS: American Physical Society","end_date":"2017-03-17","location":"New Orleans, LA, United States","start_date":"2017-03-13"},"month":"03","publication_identifier":{"issn":["0003-0503"]},"publication_status":"published","publisher":"American Physical Society","year":"2017","date_created":"2022-02-08T09:49:17Z","date_updated":"2022-02-08T10:44:35Z","volume":62,"author":[{"last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"full_name":"Naibert, Tyler","first_name":"Tyler","last_name":"Naibert"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"article_number":"P39.00011","extern":"1"},{"day":"01","has_accepted_license":"1","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","citation":{"ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier",” in Austria and America: 20th-Century Cross-Cultural Encounters, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In J. Parker & R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier" In: Parker J, Poole R, eds. Austria and America: 20th-Century Cross-Cultural Encounters. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on "The Vienna Frontier"” In Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.","short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on "The Vienna Frontier"” Austria and America: 20th-Century Cross-Cultural Encounters, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80."},"page":"73 - 80","date_published":"2017-02-01T00:00:00Z","type":"book_chapter","alternative_title":["American Studies in Austria"],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"1075","title":"An American in Allied-occupied Austria: John Dos Passos Reports on "The Vienna Frontier"","status":"public","ddc":["001"],"intvolume":" 15","oa_version":"None","file":[{"file_id":"4666","relation":"main_file","date_updated":"2018-12-12T10:08:06Z","date_created":"2018-12-12T10:08:06Z","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":380624}],"month":"02","publication_identifier":{"isbn":["978-3643908124"]},"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:08:06Z","publist_id":"6306","extern":"1","year":"2017","publication_status":"published","editor":[{"first_name":"Joshua","last_name":"Parker","full_name":"Parker, Joshua"},{"first_name":"Ralph","last_name":"Poole","full_name":"Poole, Ralph"}],"publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","author":[{"first_name":"Bernhard","last_name":"Wenzl","id":"479E9046-F248-11E8-B48F-1D18A9856A87","full_name":"Wenzl, Bernhard"}],"date_updated":"2021-01-12T06:48:06Z","date_created":"2018-12-11T11:50:00Z","volume":15},{"abstract":[{"lang":"eng","text":"Recent studies have shown that a subset of nucleoporins (Nups) can detach from the nuclear pore complex and move into the nuclear interior to regulate transcription. One such dynamic Nup, called Nup98, has been implicated in gene activation in healthy cells and has been shown to drive leukemogenesis when mutated in patients with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS (complex of proteins associated with Set1) complex, which is required for deposition of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98 or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3 at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation of associated genes. Our findings establish a function of Nup98 in hematopoietic gene activation and provide mechanistic insight into which Nup98 leukemic fusion proteins promote AML."}],"issue":"22","type":"journal_article","oa_version":"Published Version","_id":"11066","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","title":"Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells","intvolume":" 31","day":"21","article_processing_charge":"No","scopus_import":"1","keyword":["Developmental Biology","Genetics"],"date_published":"2017-12-21T00:00:00Z","publication":"Genes & Development","citation":{"apa":"Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., & Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117","ieee":"T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M. Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development, vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017.","ista":"Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234.","ama":"Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234. doi:10.1101/gad.306753.117","chicago":"Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117.","short":"T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer, Genes & Development 31 (2017) 2222–2234.","mla":"Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.” Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory, 2017, pp. 2222–34, doi:10.1101/gad.306753.117."},"article_type":"original","page":"2222-2234","extern":"1","author":[{"full_name":"Franks, Tobias M.","last_name":"Franks","first_name":"Tobias M."},{"full_name":"McCloskey, Asako","first_name":"Asako","last_name":"McCloskey"},{"full_name":"Shokhirev, Maxim Nikolaievich","first_name":"Maxim Nikolaievich","last_name":"Shokhirev"},{"full_name":"Benner, Chris","first_name":"Chris","last_name":"Benner"},{"first_name":"Annie","last_name":"Rathore","full_name":"Rathore, Annie"},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"date_updated":"2022-07-18T08:33:05Z","date_created":"2022-04-07T07:45:59Z","volume":31,"year":"2017","pmid":1,"publication_status":"published","publisher":"Cold Spring Harbor Laboratory","month":"12","publication_identifier":{"issn":["0890-9369","1549-5477"]},"doi":"10.1101/gad.306753.117","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.306753.117"}],"oa":1,"external_id":{"pmid":["29269482"]},"quality_controlled":"1"},{"type":"journal_article","issue":"5","abstract":[{"text":"Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate.","lang":"eng"}],"intvolume":" 21","status":"public","title":"Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11067","oa_version":"Published Version","keyword":["Cell Biology","Genetics","Molecular Medicine"],"scopus_import":"1","article_processing_charge":"No","day":"02","page":"618-634.e7","article_type":"original","citation":{"apa":"Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., … Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012","ieee":"T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells,” Cell Stem Cell, vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017.","ista":"Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7.","ama":"Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance of neural progenitor cells. Cell Stem Cell. 2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012","chicago":"Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer, Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012.","short":"T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto, M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7.","mla":"Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no. 5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012."},"publication":"Cell Stem Cell","date_published":"2017-11-02T00:00:00Z","extern":"1","publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2017","volume":21,"date_created":"2022-04-07T07:46:12Z","date_updated":"2022-07-18T08:33:07Z","author":[{"first_name":"Tomohisa","last_name":"Toda","full_name":"Toda, Tomohisa"},{"full_name":"Hsu, Jonathan Y.","first_name":"Jonathan Y.","last_name":"Hsu"},{"last_name":"Linker","first_name":"Sara B.","full_name":"Linker, Sara B."},{"first_name":"Lauren","last_name":"Hu","full_name":"Hu, Lauren"},{"first_name":"Simon T.","last_name":"Schafer","full_name":"Schafer, Simon T."},{"last_name":"Mertens","first_name":"Jerome","full_name":"Mertens, Jerome"},{"first_name":"Filipe V.","last_name":"Jacinto","full_name":"Jacinto, Filipe V."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","full_name":"HETZER, Martin W"},{"last_name":"Gage","first_name":"Fred H.","full_name":"Gage, Fred H."}],"publication_identifier":{"issn":["1934-5909"]},"month":"11","quality_controlled":"1","external_id":{"pmid":["28919367"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.stem.2017.08.012","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.stem.2017.08.012"},{"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"scopus_import":"1","article_processing_charge":"No","day":"30","article_type":"original","citation":{"ama":"Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z","ista":"Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. 8, 328.","ieee":"A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.","apa":"Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein translation in premature aging. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-017-00322-z","mla":"Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer Nature, 2017, doi:10.1038/s41467-017-00322-z.","short":"A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).","chicago":"Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein Translation in Premature Aging.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z."},"publication":"Nature Communications","date_published":"2017-08-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Premature aging disorders provide an opportunity to study the mechanisms that drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins. We sought to investigate protein homeostasis in this disease. Here, we report a widespread increase in protein turnover in HGPS-derived cells compared to normal cells. We determine that global protein synthesis is elevated as a consequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts. Depleting normal lamin A or inducing mutant lamin A expression are each sufficient to drive nucleolar expansion. We further show that nucleolar size correlates with donor age in primary fibroblasts derived from healthy individuals and that ribosomal RNA production increases with age, indicating that nucleolar size and activity can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan in several systems, we show that increased ribosome biogenesis and activity are a hallmark of premature aging."}],"intvolume":" 8","status":"public","title":"Nucleolar expansion and elevated protein translation in premature aging","_id":"11065","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"month":"08","quality_controlled":"1","external_id":{"pmid":["28855503"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-017-00322-z"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-00322-z","article_number":"328","extern":"1","publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2017","volume":8,"date_created":"2022-04-07T07:45:50Z","date_updated":"2022-07-18T08:33:03Z","author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W"}]},{"external_id":{"arxiv":["1709.06569"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.06569"}],"oa":1,"quality_controlled":"1","doi":"10.3847/1538-4357/aa9931","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"12","year":"2017","acknowledgement":"We thank the referee for their constructive comments, which have helped improve the quality and clarity of this work. We thank Raffaella Schneider for comments on an earlier version of this paper. We thank Leindert Boogaard, Steven Bos, Rychard Bouwens, and Renske Smit for discussions. J.M. acknowledges the support of a Huygens PhD fellowship from Leiden University. D.S. acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. A.F. acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120. B.D. acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 294.A-5018. This paper makes use of the following ALMA data: ADS/JAO.ALMA#2015.1.00122.S. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada) and 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.","publisher":"IOP Publishing","publication_status":"published","author":[{"last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J"},{"full_name":"Sobral, D.","first_name":"D.","last_name":"Sobral"},{"full_name":"Boone, F.","last_name":"Boone","first_name":"F."},{"full_name":"Röttgering, H.","first_name":"H.","last_name":"Röttgering"},{"first_name":"D.","last_name":"Schaerer","full_name":"Schaerer, D."},{"full_name":"Girard, M.","first_name":"M.","last_name":"Girard"},{"full_name":"Pallottini, A.","first_name":"A.","last_name":"Pallottini"},{"full_name":"Vallini, L.","first_name":"L.","last_name":"Vallini"},{"full_name":"Ferrara, A.","last_name":"Ferrara","first_name":"A."},{"first_name":"B.","last_name":"Darvish","full_name":"Darvish, B."},{"first_name":"B.","last_name":"Mobasher","full_name":"Mobasher, B."}],"volume":851,"date_updated":"2022-08-18T10:23:35Z","date_created":"2022-07-07T08:48:04Z","article_number":"145","extern":"1","citation":{"short":"J.J. Matthee, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, L. Vallini, A. Ferrara, B. Darvish, B. Mobasher, The Astrophysical Journal 851 (2017).","mla":"Matthee, Jorryt J., et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal, vol. 851, no. 2, 145, IOP Publishing, 2017, doi:10.3847/1538-4357/aa9931.","chicago":"Matthee, Jorryt J, D. Sobral, F. Boone, H. Röttgering, D. Schaerer, M. Girard, A. Pallottini, et al. “ALMA Reveals Metals yet No Dust within Multiple Components in CR7.” The Astrophysical Journal. IOP Publishing, 2017. https://doi.org/10.3847/1538-4357/aa9931.","ama":"Matthee JJ, Sobral D, Boone F, et al. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 2017;851(2). doi:10.3847/1538-4357/aa9931","ieee":"J. J. Matthee et al., “ALMA reveals metals yet no dust within multiple components in CR7,” The Astrophysical Journal, vol. 851, no. 2. IOP Publishing, 2017.","apa":"Matthee, J. J., Sobral, D., Boone, F., Röttgering, H., Schaerer, D., Girard, M., … Mobasher, B. (2017). ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/aa9931","ista":"Matthee JJ, Sobral D, Boone F, Röttgering H, Schaerer D, Girard M, Pallottini A, Vallini L, Ferrara A, Darvish B, Mobasher B. 2017. ALMA reveals metals yet no dust within multiple components in CR7. The Astrophysical Journal. 851(2), 145."},"publication":"The Astrophysical Journal","article_type":"original","date_published":"2017-12-21T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","dark ages","reionization","first stars – galaxies: formation – galaxies: high-redshift – galaxies: ISM – galaxies: kinematics and dynamics"],"article_processing_charge":"No","day":"21","_id":"11518","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 851","title":"ALMA reveals metals yet no dust within multiple components in CR7","status":"public","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"text":"We present spectroscopic follow-up observations of CR7 with ALMA, targeted at constraining the infrared (IR) continuum and [C II]158 mm line-emission at high spatial resolution matched to the HST/WFC3 imaging. CR7 is a luminous Lyα emitting galaxy at z = 6.6 that consists of three separated UV-continuum components. Our observations reveal several well-separated components of [C II] emission. The two most luminous components in [C II] coincide with the brightest UV components (A and B), blueshifted by »150 km s−1 with respect to the\r\npeak of Lyα emission. Other [C II] components are observed close to UV clumps B and C and are blueshifted by »300 and ≈80 km s−1 with respect to the systemic redshift. We do not detect FIR continuum emission due to dust with a 3σ limiting luminosity LIR T L d 35 K 3.1 10 = <´ 10 ( ) . This allows us to mitigate uncertainties in the dust-corrected SFR and derive SFRs for the three UV clumps A, B, and C of 28, 5, and 7 M yr−1. All clumps have [C II] luminosities consistent within the scatter observed in the local relation between SFR and L[ ] C II , implying that strong Lyα emission does not necessarily anti-correlate with [C II] luminosity. Combining\r\nour measurements with the literature, we show that galaxies with blue UV slopes have weaker [C II] emission at fixed SFR, potentially due to their lower metallicities and/or higher photoionization. Comparison with hydrodynamical simulations suggests that CR7ʼs clumps have metallicities of 0.1 Z Z 0.2 < < . The observed ISM structure of CR7 indicates that we are likely witnessing the build up of a central galaxy in the early universe through complex accretion of satellites.","lang":"eng"}]},{"day":"01","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics","cosmology: observations"],"scopus_import":"1","date_published":"2017-04-01T00:00:00Z","article_type":"original","page":"1242-1258","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Sobral D, Matthee JJ, Best P, et al. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 2017;466(1):1242-1258. doi:10.1093/mnras/stw3090","ista":"Sobral D, Matthee JJ, Best P, Stroe A, Röttgering H, Oteo I, Smail I, Morabito L, Paulino-Afonso A. 2017. The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. 466(1), 1242–1258.","ieee":"D. Sobral et al., “The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23,” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1. Oxford University Press, pp. 1242–1258, 2017.","apa":"Sobral, D., Matthee, J. J., Best, P., Stroe, A., Röttgering, H., Oteo, I., … Paulino-Afonso, A. (2017). The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw3090","mla":"Sobral, David, et al. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society, vol. 466, no. 1, Oxford University Press, 2017, pp. 1242–58, doi:10.1093/mnras/stw3090.","short":"D. Sobral, J.J. Matthee, P. Best, A. Stroe, H. Röttgering, I. Oteo, I. Smail, L. Morabito, A. Paulino-Afonso, Monthly Notices of the Royal Astronomical Society 466 (2017) 1242–1258.","chicago":"Sobral, David, Jorryt J Matthee, Philip Best, Andra Stroe, Huub Röttgering, Iván Oteo, Ian Smail, Leah Morabito, and Ana Paulino-Afonso. “The CALYMHA Survey: Lyα Luminosity Function and Global Escape Fraction of Lyα Photons at z = 2.23.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw3090."},"abstract":[{"lang":"eng","text":"We present the CAlibrating LYMan-α with Hα (CALYMHA) pilot survey and new results on Lyman α (Lyα) selected galaxies at z ∼ 2. We use a custom-built Lyα narrow-band filter at the Isaac Newton Telescope, designed to provide a matched volume coverage to the z = 2.23 Hα HiZELS survey. Here, we present the first results for the COSMOS and UDS fields. Our survey currently reaches a 3σ line flux limit of ∼4 × 10−17 erg s−1 cm−2, and a Lyα luminosity limit of ∼1042.3 erg s−1. We find 188 Lyα emitters over 7.3 × 105 Mpc3, but also find significant numbers of other line-emitting sources corresponding to He II, C III] and C IV emission lines. These sources are important contaminants, and we carefully remove them, unlike most previous studies. We find that the Lyα luminosity function at z = 2.23 is very well described by a Schechter function up to LLy α ≈ 1043 erg s−1 with L∗=1042.59+0.16−0.08 erg s−1, ϕ∗=10−3.09+0.14−0.34 Mpc−3 and α = −1.75 ± 0.25. Above LLy α ≈ 1043 erg s−1, the Lyα luminosity function becomes power-law like, driven by X-ray AGN. We find that Lyα-selected emitters have a high escape fraction of 37 ± 7 per cent, anticorrelated with Lyα luminosity and correlated with Lyα equivalent width. Lyα emitters have ubiquitous large (≈40 kpc) Lyα haloes, ∼2 times larger than their Hα extents. By directly comparing our Lyα and Hα luminosity functions, we find that the global/overall escape fraction of Lyα photons (within a 13 kpc radius) from the full population of star-forming galaxies is 5.1 ± 0.2 per cent at the peak of the star formation history. An extra 3.3 ± 0.3 per cent of Lyα photons likely still escape, but at larger radii."}],"issue":"1","type":"journal_article","oa_version":"Preprint","title":"The CALYMHA survey: Lyα luminosity function and global escape fraction of Lyα photons at z = 2.23","status":"public","intvolume":" 466","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11562","month":"04","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stw3090","quality_controlled":"1","external_id":{"arxiv":["1609.05897"]},"main_file_link":[{"url":"https://arxiv.org/abs/1609.05897","open_access":"1"}],"oa":1,"extern":"1","date_updated":"2022-08-19T07:18:20Z","date_created":"2022-07-12T12:04:16Z","volume":466,"author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"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":"Best, Philip","last_name":"Best","first_name":"Philip"},{"last_name":"Stroe","first_name":"Andra","full_name":"Stroe, Andra"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"},{"first_name":"Iván","last_name":"Oteo","full_name":"Oteo, Iván"},{"first_name":"Ian","last_name":"Smail","full_name":"Smail, Ian"},{"full_name":"Morabito, Leah","last_name":"Morabito","first_name":"Leah"},{"full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso","first_name":"Ana"}],"publication_status":"published","publisher":"Oxford University Press","year":"2017","acknowledgement":"We thank the reviewer for his/her helpful comments and suggestions that have greatly improved this work. DS and JM acknowledge financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship. DS also acknowledges funding from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson merit award. We thank Matthew Hayes, Ryan Trainor, Kimihiko Nakajima and Anne Verhamme for many helpful discussions and Ana Sobral, Carolina Duarte and Miguel Domingos for taking part in observations with the NB392 filter. We also thank Sergio Santos for helpful comments. This research is based on observations obtained on the Isaac Newton Telescope (INT), programs: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B & I15AN008. The authors acknowledge the award of time from programmes: I13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008 on the INT. INT is 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. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 098.A 0819. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP (Bertin & Arnouts 1996; Bertin 2010), SCAMP (Bertin 2006) and TOPCAT (Taylor 2005). Dedicated to the memory of M. L. Nicolau and M. C. Serrano."},{"article_type":"original","page":"2558-2574","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"mla":"Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2558–74, doi:10.1093/mnras/stx1712.","short":"A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2558–2574.","chicago":"Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, Morphologies and Equivalent Widths .” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1712.","ama":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 2017;471(3):2558-2574. doi:10.1093/mnras/stx1712","ista":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. 471(3), 2558–2574.","ieee":"A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2558–2574, 2017.","apa":"Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths . Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1712"},"date_published":"2017-11-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high-redshift","quasars: emission lines","galaxies: star formation","cosmology: observations"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – I. Nature, morphologies and equivalent widths ","intvolume":" 471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11566","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"While traditionally associated with active galactic nuclei (AGN), the properties of the C II] (λ = 2326 Å), C III] (λ, λ = 1907, 1909 Å) and C IV (λ, λ = 1549, 1551 Å) emission lines are still uncertain as large, unbiased samples of sources are scarce. We present the first blind, statistical study of C II], C III] and C IV emitters at z ∼ 0.68, 1.05, 1.53, respectively, uniformly selected down to a flux limit of ∼4 × 10−17 erg s−1 cm−1 through a narrow-band survey covering an area of ∼1.4 deg2 over COSMOS and UDS. We detect 16 C II], 35 C III] and 17 C IV emitters, whose nature we investigate using optical colours as well as Hubble Space Telescope (HST), X-ray, radio and far-infrared data. We find that z ∼ 0.7 C II] emitters are consistent with a mixture of blue (UV slope β = −2.0 ± 0.4) star-forming (SF) galaxies with discy HST structure and AGN with Seyfert-like morphologies. Bright C II] emitters have individual X-ray detections as well as high average black hole accretion rates (BHARs) of ∼0.1 M⊙ yr−1. C III] emitters at z ∼ 1.05 trace a general population of SF galaxies, with β = −0.8 ± 1.1, a variety of optical morphologies, including isolated and interacting galaxies and low BHAR (<0.02 M⊙ yr−1). Our C IV emitters at z ∼ 1.5 are consistent with young, blue quasars (β ∼ −1.9) with point-like optical morphologies, bright X-ray counterparts and large BHAR (0.8 M⊙ yr−1). We also find some surprising C II], C III] and C IV emitters with rest-frame equivalent widths (EWs) that could be as large as 50–100 Å. AGN or spatial offsets between the UV continuum stellar disc and the line-emitting regions may explain the large EW. These bright C II], C III] and C IV emitters are ideal candidates for spectroscopic follow-up to fully unveil their nature.","lang":"eng"}],"issue":"3","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.10169","open_access":"1"}],"external_id":{"arxiv":["1703.10169"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stx1712","month":"11","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"publication_status":"published","publisher":"Oxford University Press","acknowledgement":"We would like to thank the anonymous referee for her/his valuable input that helped improve the clarity and interpretation of our results. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO), through a Veni fellowship. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. CALYMHA data are based on observations made with the Isaac Newton Telescope (proposals 13AN002, I14AN002, 088-INT7/14A, I14BN006, 118-INT13/14B, I15AN008) 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 Astrofísica de Canarias. Also based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 098.A-0819 and 179.A-2005. We are grateful to E. L. Wright and J. Schombert for their cosmology calculator. We would like to thank the authors of NUMPY (van der Walt et al. 2011), SCIPY (Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration et al. 2013) for making these packages publicly available. This research has made use of the NASA/IPAC Extragalactic Database (NED), which is ","year":"2017","date_created":"2022-07-12T12:33:16Z","date_updated":"2022-08-19T07:59:57Z","volume":471,"author":[{"full_name":"Stroe, Andra","first_name":"Andra","last_name":"Stroe"},{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"full_name":"Calhau, João","last_name":"Calhau","first_name":"João"},{"first_name":"Ivan","last_name":"Oteo","full_name":"Oteo, Ivan"}],"extern":"1"},{"oa_version":"Preprint","intvolume":" 465","title":"The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution","status":"public","_id":"11564","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"We study the production rate of ionizing photons of a sample of 588 Hα emitters (HAEs) and 160 Lyman-α emitters (LAEs) at z = 2.2 in the COSMOS field in order to assess the implied emissivity from galaxies, based on their ultraviolet (UV) luminosity. By exploring the rest-frame Lyman Continuum (LyC) with GALEX/NUV data, we find fesc < 2.8 (6.4) per cent through median (mean) stacking. By combining the Hα luminosity density with intergalactic medium emissivity measurements from absorption studies, we find a globally averaged 〈fesc〉 of 5.9+14.5−4.2 per cent at z = 2.2 if we assume HAEs are the only source of ionizing photons. We find similarly low values of the global 〈fesc〉 at z ≈ 3–5, also ruling out a high 〈fesc〉 at z < 5. These low escape fractions allow us to measure ξion, the number of produced ionizing photons per unit UV luminosity, and investigate how this depends on galaxy properties. We find a typical ξion ≈ 1024.77 ± 0.04 Hz erg−1 for HAEs and ξion ≈ 1025.14 ± 0.09 Hz erg−1 for LAEs. LAEs and low-mass HAEs at z = 2.2 show similar values of ξion as typically assumed in the reionization era, while the typical HAE is three times less ionizing. Due to an increasing ξion with increasing EW(Hα), ξion likely increases with redshift. This evolution alone is fully in line with the observed evolution of ξion between z ≈ 2 and 5, indicating a typical value of ξion ≈ 1025.4 Hz erg−1 in the reionization era."}],"type":"journal_article","date_published":"2017-03-01T00:00:00Z","page":"3637-3655","article_type":"original","citation":{"mla":"Matthee, Jorryt J., et al. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3, Oxford University Press, 2017, pp. 3637–55, doi:10.1093/mnras/stw2973.","short":"J.J. Matthee, D. Sobral, P. Best, A.A. Khostovan, I. Oteo, R. Bouwens, H. Röttgering, Monthly Notices of the Royal Astronomical Society 465 (2017) 3637–3655.","chicago":"Matthee, Jorryt J, David Sobral, Philip Best, Ali Ahmad Khostovan, Iván Oteo, Rychard Bouwens, and Huub Röttgering. “The Production and Escape of Lyman-Continuum Radiation from Star-Forming Galaxies at z ∼ 2 and Their Redshift Evolution.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2973.","ama":"Matthee JJ, Sobral D, Best P, et al. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 2017;465(3):3637-3655. doi:10.1093/mnras/stw2973","ista":"Matthee JJ, Sobral D, Best P, Khostovan AA, Oteo I, Bouwens R, Röttgering H. 2017. The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. 465(3), 3637–3655.","apa":"Matthee, J. J., Sobral, D., Best, P., Khostovan, A. A., Oteo, I., Bouwens, R., & Röttgering, H. (2017). The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2973","ieee":"J. J. Matthee et al., “The production and escape of Lyman-Continuum radiation from star-forming galaxies at z ∼ 2 and their redshift evolution,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 3. Oxford University Press, pp. 3637–3655, 2017."},"publication":"Monthly Notices of the Royal Astronomical Society","article_processing_charge":"No","day":"01","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","cosmology: observations","dark ages","reionization","first stars"],"scopus_import":"1","volume":465,"date_updated":"2022-08-19T07:53:04Z","date_created":"2022-07-12T12:12:14Z","author":[{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"full_name":"Sobral, David","first_name":"David","last_name":"Sobral"},{"last_name":"Best","first_name":"Philip","full_name":"Best, Philip"},{"full_name":"Khostovan, Ali Ahmad","last_name":"Khostovan","first_name":"Ali Ahmad"},{"full_name":"Oteo, Iván","last_name":"Oteo","first_name":"Iván"},{"full_name":"Bouwens, Rychard","last_name":"Bouwens","first_name":"Rychard"},{"full_name":"Röttgering, Huub","first_name":"Huub","last_name":"Röttgering"}],"publisher":"Oxford University Press","publication_status":"published","year":"2017","acknowledgement":"We thank the referee for the many helpful and constructive comments which have significantly improved this paper. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). PNB is grateful for support from the UK STFC via grant ST/M001229/1. IO acknowledges support from the European Research Council in the form of the Advanced Investigator Programme, 321302, COSMICISM. The authors thank Andreas Faisst, Michael Rutkowski and Andreas Sandberg for answering questions related to this work and Daniel Schaerer and Mark Dijkstra for discussions. We acknowledge the work that has been done by both the COSMOS team in assembling such large, state-of-the-art multi-wavelength data set, as this has been crucial for the results presented in this paper. We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY (Jones et al. 2001; Hunter 2007; Van Der Walt, Colbert & Varoquaux 2011) and ASTROPY (Astropy Collaboration et al. 2013) packages, the astronomical imaging tools SEXTRACTOR and SWARP (Bertin & Arnouts 1996;\r\nBertin 2010) and the TOPCAT analysis program (Taylor 2013).","extern":"1","language":[{"iso":"eng"}],"doi":"10.1093/mnras/stw2973","quality_controlled":"1","external_id":{"arxiv":["1605.08782"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1605.08782","open_access":"1"}],"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"03"},{"citation":{"ama":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 2017;471(3):2575-2586. doi:10.1093/mnras/stx1713","ista":"Stroe A, Sobral D, Matthee JJ, Calhau J, Oteo I. 2017. A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. 471(3), 2575–2586.","ieee":"A. Stroe, D. Sobral, J. J. Matthee, J. Calhau, and I. Oteo, “A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3. Oxford University Press, pp. 2575–2586, 2017.","apa":"Stroe, A., Sobral, D., Matthee, J. J., Calhau, J., & Oteo, I. (2017). A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1713","mla":"Stroe, Andra, et al. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 3, Oxford University Press, 2017, pp. 2575–86, doi:10.1093/mnras/stx1713.","short":"A. Stroe, D. Sobral, J.J. Matthee, J. Calhau, I. Oteo, Monthly Notices of the Royal Astronomical Society 471 (2017) 2575–2586.","chicago":"Stroe, Andra, David Sobral, Jorryt J Matthee, João Calhau, and Ivan Oteo. “A 1.4 Deg2 Blind Survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity Functions and Cosmic Average Line Ratios.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1713."},"publication":"Monthly Notices of the Royal Astronomical Society","page":"2575-2586","article_type":"original","date_published":"2017-11-01T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: high redshift","galaxies: luminosity function","mass function","quasars: emission lines","star formation","cosmology: observations"],"article_processing_charge":"No","day":"01","_id":"11567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 471","status":"public","title":"A 1.4 deg2 blind survey for C II], C III] and C IV at z ∼ 0.7–1.5 – II. Luminosity functions and cosmic average line ratios","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"Recently, the C III] and C IV emission lines have been observed in galaxies in the early Universe (z > 5), providing new ways to measure their redshift and study their stellar populations and active galactic nuclei (AGN). We explore the first blind C II], C III] and C IV survey (z ∼ 0.68, 1.05, 1.53, respectively) presented in Stroe et al. (2017). We derive luminosity functions (LF) and study properties of C II], C III] and C IV line emitters through comparisons to the LFs of H α and Ly α emitters, UV selected star-forming (SF) galaxies and quasars at similar redshifts. The C II] LF at z ∼ 0.68 is equally well described by a Schechter or a power-law LF, characteristic of a mixture of SF and AGN activity. The C III] LF (z ∼ 1.05) is consistent to a scaled down version of the Schechter H α and Ly α LF at their redshift, indicating a SF origin. In stark contrast, the C IV LF at z ∼ 1.53 is well fit by a power-law, quasar-like LF. We find that the brightest UV sources (MUV < −22) will universally have C III] and C IV emission. However, on average, C III] and C IV are not as abundant as H α or Ly α emitters at the same redshift, with cosmic average ratios of ∼0.02–0.06 to H α and ∼0.01–0.1 to intrinsic Ly α. We predict that the C III] and C IV lines can only be truly competitive in confirming high-redshift candidates when the hosts are intrinsically bright and the effective Ly α escape fraction is below 1 per cent. While C III] and C IV were proposed as good tracers of young, relatively low-metallicity galaxies typical of the early Universe, we find that, at least at z ∼ 1.5, C IV is exclusively hosted by AGN/quasars, especially at large line equivalent widths.","lang":"eng"}],"oa":1,"external_id":{"arxiv":["1703.10169"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.10169","open_access":"1"}],"quality_controlled":"1","doi":"10.1093/mnras/stx1713","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"11","year":"2017","publisher":"Oxford University Press","publication_status":"published","author":[{"first_name":"Andra","last_name":"Stroe","full_name":"Stroe, Andra"},{"full_name":"Sobral, David","first_name":"David","last_name":"Sobral"},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"},{"first_name":"João","last_name":"Calhau","full_name":"Calhau, João"},{"first_name":"Ivan","last_name":"Oteo","full_name":"Oteo, Ivan"}],"volume":471,"date_updated":"2022-08-19T08:02:04Z","date_created":"2022-07-12T12:54:57Z","extern":"1"},{"author":[{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"},{"full_name":"Crain, Robert A.","first_name":"Robert A.","last_name":"Crain"},{"full_name":"Schaller, Matthieu","last_name":"Schaller","first_name":"Matthieu"},{"last_name":"Bower","first_name":"Richard","full_name":"Bower, Richard"},{"first_name":"Tom","last_name":"Theuns","full_name":"Theuns, Tom"}],"volume":465,"date_updated":"2022-08-19T07:56:07Z","date_created":"2022-07-12T12:25:08Z","year":"2017","acknowledgement":"We thank the anonymous referee for their comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. JM thanks David Sobral for useful discussions and help with fitting routines and Jonas Chavez Montero and Ying Zu for providing data. We thank PRACE for the access to the Curie facility in France. We have used the DiRAC system which is a part of National E-Infrastructure at Durham University, operated by the Institute for Computational Cosmology on behalf of the STFC DiRAC HPC Facility (www.dirac.ac.uk); the equipment was funded by BIS National E-infrastructure capital grant ST/K00042X/1, STFC capital grant ST/H008519/1, STFC DiRAC Operations grant ST/K003267/1 and Durham University. The study was sponsored by the Dutch National Computing Facilities Foundation (NCF) for the use of supercomputer facilities, with financial support from the Netherlands Organisation for Scientific Research (NWO), through VICI grant 639.043.409, and the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement 278594- GasAroundGalaxies, and from the Belgian Science Policy Office ([AP P7/08 CHARM]). We have benefited greatly from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY, H5PY and RPY2 packages, and the TOPCAT analysis program (Taylor 2005).","publisher":"Oxford University Press","publication_status":"published","extern":"1","doi":"10.1093/mnras/stw2884","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08218"}],"external_id":{"arxiv":["1608.08218"]},"quality_controlled":"1","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"02","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11565","intvolume":" 465","status":"public","title":"The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation","issue":"2","abstract":[{"lang":"eng","text":"We use the hydrodynamical EAGLE simulation to study the magnitude and origin of the scatter in the stellar mass–halo mass relation for central galaxies. We separate cause and effect by correlating stellar masses in the baryonic simulation with halo properties in a matched dark matter only (DMO) simulation. The scatter in stellar mass increases with redshift and decreases with halo mass. At z = 0.1, it declines from 0.25 dex at M200, DMO ≈ 1011 M⊙ to 0.12 dex at M200, DMO ≈ 1013 M⊙, but the trend is weak above 1012 M⊙. For M200, DMO < 1012.5 M⊙ up to 0.04 dex of the scatter is due to scatter in the halo concentration. At fixed halo mass, a larger stellar mass corresponds to a more concentrated halo. This is likely because higher concentrations imply earlier formation times and hence more time for accretion and star formation, and/or because feedback is less efficient in haloes with higher binding energies. The maximum circular velocity, Vmax, DMO, and binding energy are therefore more fundamental properties than halo mass, meaning that they are more accurate predictors of stellar mass, and we provide fitting formulae for their relations with stellar mass. However, concentration alone cannot explain the total scatter in the Mstar−M200,DMO relation, and it does not explain the scatter in Mstar–Vmax, DMO. Halo spin, sphericity, triaxiality, substructure and environment are also not responsible for the remaining scatter, which thus could be due to more complex halo properties or non-linear/stochastic baryonic effects."}],"type":"journal_article","date_published":"2017-02-01T00:00:00Z","citation":{"chicago":"Matthee, Jorryt J, Joop Schaye, Robert A. Crain, Matthieu Schaller, Richard Bower, and Tom Theuns. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stw2884.","short":"J.J. Matthee, J. Schaye, R.A. Crain, M. Schaller, R. Bower, T. Theuns, Monthly Notices of the Royal Astronomical Society 465 (2017) 2381–2396.","mla":"Matthee, Jorryt J., et al. “The Origin of Scatter in the Stellar Mass–Halo Mass Relation of Central Galaxies in the EAGLE Simulation.” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2, Oxford University Press, 2017, pp. 2381–96, doi:10.1093/mnras/stw2884.","apa":"Matthee, J. J., Schaye, J., Crain, R. A., Schaller, M., Bower, R., & Theuns, T. (2017). The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stw2884","ieee":"J. J. Matthee, J. Schaye, R. A. Crain, M. Schaller, R. Bower, and T. Theuns, “The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation,” Monthly Notices of the Royal Astronomical Society, vol. 465, no. 2. Oxford University Press, pp. 2381–2396, 2017.","ista":"Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. 2017. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 465(2), 2381–2396.","ama":"Matthee JJ, Schaye J, Crain RA, Schaller M, Bower R, Theuns T. The origin of scatter in the stellar mass–halo mass relation of central galaxies in the EAGLE simulation. Monthly Notices of the Royal Astronomical Society. 2017;465(2):2381-2396. doi:10.1093/mnras/stw2884"},"publication":"Monthly Notices of the Royal Astronomical Society","page":"2381-2396","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: haloes","cosmology: theory"]},{"publication_identifier":{"issn":["0035-8711","1365-2966"]},"month":"10","doi":"10.1093/mnras/stx1569","language":[{"iso":"eng"}],"external_id":{"arxiv":["1702.04721"]},"main_file_link":[{"url":"https://arxiv.org/abs/1702.04721","open_access":"1"}],"oa":1,"quality_controlled":"1","extern":"1","author":[{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"first_name":"David","last_name":"Sobral","full_name":"Sobral, David"},{"full_name":"Best, Philip","last_name":"Best","first_name":"Philip"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"last_name":"Bian","first_name":"Fuyan","full_name":"Bian, Fuyan"},{"last_name":"Darvish","first_name":"Behnam","full_name":"Darvish, Behnam"},{"last_name":"Röttgering","first_name":"Huub","full_name":"Röttgering, Huub"},{"full_name":"Fan, Xiaohui","first_name":"Xiaohui","last_name":"Fan"}],"volume":471,"date_updated":"2022-08-19T07:15:14Z","date_created":"2022-07-12T11:01:35Z","year":"2017","publisher":"Oxford University Press","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics galaxies","active","galaxies","evolution","galaxies","high-redshift","galaxies","luminosity function","mass function","galaxies: star formation"],"date_published":"2017-10-01T00:00:00Z","citation":{"ama":"Matthee JJ, Sobral D, Best P, et al. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 2017;471(1):629-649. doi:10.1093/mnras/stx1569","ista":"Matthee JJ, Sobral D, Best P, Smail I, Bian F, Darvish B, Röttgering H, Fan X. 2017. Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. 471(1), 629–649.","ieee":"J. J. Matthee et al., “Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1. Oxford University Press, pp. 629–649, 2017.","apa":"Matthee, J. J., Sobral, D., Best, P., Smail, I., Bian, F., Darvish, B., … Fan, X. (2017). Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1569","mla":"Matthee, Jorryt J., et al. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 1, Oxford University Press, 2017, pp. 629–49, doi:10.1093/mnras/stx1569.","short":"J.J. Matthee, D. Sobral, P. Best, I. Smail, F. Bian, B. Darvish, H. Röttgering, X. Fan, Monthly Notices of the Royal Astronomical Society 471 (2017) 629–649.","chicago":"Matthee, Jorryt J, David Sobral, Philip Best, Ian Smail, Fuyan Bian, Behnam Darvish, Huub Röttgering, and Xiaohui Fan. “Boötes-HiZELS: An Optical to near-Infrared Survey of Emission-Line Galaxies at z = 0.4–4.7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1569."},"publication":"Monthly Notices of the Royal Astronomical Society","page":"629-649","article_type":"original","issue":"1","abstract":[{"lang":"eng","text":"We present a sample of ∼1000 emission-line galaxies at z = 0.4–4.7 from the ∼0.7deg2 High-z Emission-Line Survey in the Boötes field identified with a suite of six narrow-band filters at ≈0.4–2.1 μm. These galaxies have been selected on their Ly α (73), [O II] (285), H β/[O III] (387) or H α (362) emission line, and have been classified with optical to near-infrared colours. A subsample of 98 sources have reliable redshifts from multiple narrow-band (e.g. [O II]–H α) detections and/or spectroscopy. In this survey paper, we present the observations, selection and catalogues of emitters. We measure number densities of Ly α, [O II], H β/[O III] and H α and confirm strong luminosity evolution in star-forming galaxies from z ∼ 0.4 to ∼5, in agreement with previous results. To demonstrate the usefulness of dual-line emitters, we use the sample of dual [O II]–H α emitters to measure the observed [O II]/H α ratio at z = 1.47. The observed [O II]/H α ratio increases significantly from 0.40 ± 0.01 at z = 0.1 to 0.52 ± 0.05 at z = 1.47, which we attribute to either decreasing dust attenuation with redshift, or due to a bias in the (typically) fibre measurements in the local Universe that only measure the central kpc regions. At the bright end, we find that both the H α and Ly α number densities at z ≈ 2.2 deviate significantly from a Schechter form, following a power law. We show that this is driven entirely by an increasing X-ray/active galactic nucleus fraction with line luminosity, which reaches ≈100 per cent at line luminosities L ≳ 3 × 1044 erg s−1."}],"type":"journal_article","oa_version":"Preprint","_id":"11561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 471","status":"public","title":"Boötes-HiZELS: An optical to near-infrared survey of emission-line galaxies at z = 0.4–4.7"},{"language":[{"iso":"eng"}],"doi":"10.1093/mnras/stx2061","quality_controlled":"1","external_id":{"arxiv":["1706.06591"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1706.06591","open_access":"1"}],"month":"11","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"date_created":"2022-07-13T09:47:39Z","date_updated":"2022-08-19T08:05:37Z","volume":472,"author":[{"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":"Sobral","first_name":"David","full_name":"Sobral, David"},{"full_name":"Darvish, Behnam","first_name":"Behnam","last_name":"Darvish"},{"last_name":"Santos","first_name":"Sérgio","full_name":"Santos, Sérgio"},{"full_name":"Mobasher, Bahram","last_name":"Mobasher","first_name":"Bahram"},{"full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso","first_name":"Ana"},{"full_name":"Röttgering, Huub","first_name":"Huub","last_name":"Röttgering"},{"full_name":"Alegre, Lara","last_name":"Alegre","first_name":"Lara"}],"publication_status":"published","publisher":"Oxford University Press","year":"2017","acknowledgement":"We thank the referee for a constructive report that has improved the quality and clarity of this work. The authors thank Grecco Oyarzún for discussions. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organisation for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. We thank Kasper Schmidt for providing measurements. Based on observations with the W.M. Keck Observatory through programme C267D. The W.M. Keck Observatory is operated as a scientific partnership amongst the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 097.A-0943, 294.A 5018 and 098.A-0819 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 observing time (W16AN004) and 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. Based on observations made with the NASA/ESA HST, 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 programme #14699. We are grateful for the excellent data sets from the COSMOS, UltraVISTA, SXDS, UDS and CFHTLS survey teams; without these legacy surveys, this research would have been impossible. We have benefited from the public available programming language PYTHON, including the NUMPY, MATPLOTLIB, PYFITS, SCIPY and ASTROPY packages, the astronomical imaging tools SEXTRACTOR, SWARP and SCAMP and the TOPCAT analysis tool (Taylor 2013).","extern":"1","date_published":"2017-11-01T00:00:00Z","article_type":"original","page":"772-787","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"mla":"Matthee, Jorryt J., et al. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1, Oxford University Press, 2017, pp. 772–87, doi:10.1093/mnras/stx2061.","short":"J.J. Matthee, D. Sobral, B. Darvish, S. Santos, B. Mobasher, A. Paulino-Afonso, H. Röttgering, L. Alegre, Monthly Notices of the Royal Astronomical Society 472 (2017) 772–787.","chicago":"Matthee, Jorryt J, David Sobral, Behnam Darvish, Sérgio Santos, Bahram Mobasher, Ana Paulino-Afonso, Huub Röttgering, and Lara Alegre. “Spectroscopic Properties of Luminous Ly α Emitters at z ≈ 6–7 and Comparison to the Lyman-Break Population.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx2061.","ama":"Matthee JJ, Sobral D, Darvish B, et al. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 2017;472(1):772-787. doi:10.1093/mnras/stx2061","ista":"Matthee JJ, Sobral D, Darvish B, Santos S, Mobasher B, Paulino-Afonso A, Röttgering H, Alegre L. 2017. Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. 472(1), 772–787.","apa":"Matthee, J. J., Sobral, D., Darvish, B., Santos, S., Mobasher, B., Paulino-Afonso, A., … Alegre, L. (2017). Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx2061","ieee":"J. J. Matthee et al., “Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population,” Monthly Notices of the Royal Astronomical Society, vol. 472, no. 1. Oxford University Press, pp. 772–787, 2017."},"day":"01","article_processing_charge":"No","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution – galaxies: high-redshift","dark ages","reionization","first stars","cosmology: observations"],"scopus_import":"1","oa_version":"Preprint","status":"public","title":"Spectroscopic properties of luminous Ly α emitters at z ≈ 6–7 and comparison to the Lyman-break population","intvolume":" 472","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11572","abstract":[{"text":"We present spectroscopic follow-up of candidate luminous Ly α emitters (LAEs) at z = 5.7–6.6 in the SA22 field with VLT/X-SHOOTER. We confirm two new luminous LAEs at z = 5.676 (SR6) and z = 6.532 (VR7), and also present HST follow-up of both sources. These sources have luminosities LLy α ≈ 3 × 1043 erg s−1, very high rest-frame equivalent widths of EW0 ≳ 200 Å and narrow Ly α lines (200–340 km s−1). VR7 is the most UV-luminous LAE at z > 6.5, with M1500 = −22.5, even brighter in the UV than CR7. Besides Ly α, we do not detect any other rest-frame UV lines in the spectra of SR6 and VR7, and argue that rest-frame UV lines are easier to observe in bright galaxies with low Ly α equivalent widths. We confirm that Ly α line widths increase with Ly α luminosity at z = 5.7, while there are indications that Ly α lines of faint LAEs become broader at z = 6.6, potentially due to reionization. We find a large spread of up to 3 dex in UV luminosity for >L⋆ LAEs, but find that the Ly α luminosity of the brightest LAEs is strongly related to UV luminosity at z = 6.6. Under basic assumptions, we find that several LAEs at z ≈ 6–7 have Ly α escape fractions ≳ 100 per cent, indicating bursty star formation histories, alternative Ly α production mechanisms, or dust attenuating Ly α emission differently than UV emission. Finally, we present a method to compute ξion, the production efficiency of ionizing photons, and find that LAEs at z ≈ 6–7 have high values of log10(ξion/Hz erg−1) ≈ 25.51 ± 0.09 that may alleviate the need for high Lyman-Continuum escape fractions required for reionization.","lang":"eng"}],"issue":"1","type":"journal_article"},{"scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: kinematics and dynamics"],"day":"01","article_processing_charge":"No","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"chicago":"Turner, O. J., M. Cirasuolo, C. M. Harrison, R. J. McLure, J. S. Dunlop, A. M. Swinbank, H. L. Johnson, D. Sobral, Jorryt J Matthee, and R. M. Sharples. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx1366.","short":"O.J. Turner, M. Cirasuolo, C.M. Harrison, R.J. McLure, J.S. Dunlop, A.M. Swinbank, H.L. Johnson, D. Sobral, J.J. Matthee, R.M. Sharples, Monthly Notices of the Royal Astronomical Society 471 (2017) 1280–1320.","mla":"Turner, O. J., et al. “The KMOS Deep Survey (KDS) – I. Dynamical Measurements of Typical Star-Forming Galaxies at z ≃ 3.5.” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2, Oxford University Press, 2017, pp. 1280–320, doi:10.1093/mnras/stx1366.","apa":"Turner, O. J., Cirasuolo, M., Harrison, C. M., McLure, R. J., Dunlop, J. S., Swinbank, A. M., … Sharples, R. M. (2017). The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stx1366","ieee":"O. J. Turner et al., “The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5,” Monthly Notices of the Royal Astronomical Society, vol. 471, no. 2. Oxford University Press, pp. 1280–1320, 2017.","ista":"Turner OJ, Cirasuolo M, Harrison CM, McLure RJ, Dunlop JS, Swinbank AM, Johnson HL, Sobral D, Matthee JJ, Sharples RM. 2017. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 471(2), 1280–1320.","ama":"Turner OJ, Cirasuolo M, Harrison CM, et al. The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5. Monthly Notices of the Royal Astronomical Society. 2017;471(2):1280-1320. doi:10.1093/mnras/stx1366"},"article_type":"original","page":"1280-1320","date_published":"2017-10-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We present dynamical measurements from the KMOS (K-band multi-object spectrograph) Deep Survey (KDS), which comprises 77 typical star-forming galaxies at z ≃ 3.5 in the mass range 9.0 < log (M⋆/M⊙) < 10.5. These measurements constrain the internal dynamics, the intrinsic velocity dispersions (σint) and rotation velocities (VC) of galaxies in the high-redshift Universe. The mean velocity dispersion of the galaxies in our sample is σint=70.8+3.3−3.1kms−1, revealing that the increasing average σint with increasing redshift, reported for z ≲ 2, continues out to z ≃ 3.5. Only 36 ± 8 per cent of our galaxies are rotation-dominated (VC/σint > 1), with the sample average VC/σint value much smaller than at lower redshift. After carefully selecting comparable star-forming samples at multiple epochs, we find that the rotation-dominated fraction evolves with redshift with a z−0.2 dependence. The rotation-dominated KDS galaxies show no clear offset from the local rotation velocity–stellar mass (i.e. VC–M⋆) relation, although a smaller fraction of the galaxies are on the relation due to the increase in the dispersion-dominated fraction. These observations are consistent with a simple equilibrium model picture, in which random motions are boosted in high-redshift galaxies by a combination of the increasing gas fractions, accretion efficiency, specific star formation rate and stellar feedback and which may provide significant pressure support against gravity on the galactic disc scale.","lang":"eng"}],"issue":"2","_id":"11573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The KMOS Deep Survey (KDS) – I. Dynamical measurements of typical star-forming galaxies at z ≃ 3.5","intvolume":" 471","oa_version":"Preprint","month":"10","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"oa":1,"external_id":{"arxiv":["1704.06263"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.06263"}],"quality_controlled":"1","doi":"10.1093/mnras/stx1366","language":[{"iso":"eng"}],"extern":"1","year":"2017","acknowledgement":"We wish to thank the anonymous referee for their comments, which have improved the quality and clarity of this work. OJT acknowledges the financial support of the Science and Technology Facilities Council through a studentship award. MC and OJT acknowledge the KMOS team and all the personnel of the European Southern Observatory Very Large Telescope for outstanding support during the KMOS GTO observations. CMH, AMS and RMS acknowledge the Science and Technology Facilities Council through grant code ST/L00075X/1. RJM acknowledges the support of the European Research Council via the award of a Consolidator Grant (PI: McLure). JSD acknowledges the support of the European Research Council via the award of an Advanced Grant (PI J. Dunlop), and the contribution of the EC FP7 SPACE project ASTRODEEP (Ref.No: 312725). AMS acknowledges the Leverhulme Foundation. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from FCT through an FCT Investigator Starting Grant and Start-up Grant (IF/01154/2012/CP0189/CT0010). This work is based on observations taken by the CANDELS Multi-Cycle Treasury Program with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. This work is based on observations taken by the 3D HST Treasury Program (GO 12177 and 12328) with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. Based on data obtained with the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Program 185.A-0791, and made available by the VUDS team at the CESAM data centre, Laboratoire d’Astrophysique de Marseille, France. Based on observations obtained at the Very Large Telescope of the European Southern Observatory. Programme IDs: 092.A 0399(A), 093.A-0122(A,B), 094.A-0214(A,B),095.A0680(A,B),096.A-0315(A,B,C).","publication_status":"published","publisher":"Oxford University Press","author":[{"first_name":"O. J.","last_name":"Turner","full_name":"Turner, O. J."},{"full_name":"Cirasuolo, M.","last_name":"Cirasuolo","first_name":"M."},{"full_name":"Harrison, C. M.","last_name":"Harrison","first_name":"C. M."},{"first_name":"R. J.","last_name":"McLure","full_name":"McLure, R. J."},{"first_name":"J. S.","last_name":"Dunlop","full_name":"Dunlop, J. S."},{"full_name":"Swinbank, A. M.","last_name":"Swinbank","first_name":"A. M."},{"full_name":"Johnson, H. L.","last_name":"Johnson","first_name":"H. L."},{"last_name":"Sobral","first_name":"D.","full_name":"Sobral, D."},{"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":"Sharples, R. M.","last_name":"Sharples","first_name":"R. M."}],"date_updated":"2022-08-19T08:07:31Z","date_created":"2022-07-13T10:03:01Z","volume":471}]