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Sixt, Cell 179 (2019) 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047."},"publication":"Cell","date_published":"2019-09-19T00:00:00Z","type":"journal_article","issue":"1","intvolume":" 179","title":"The neural crest pitches in to remove apoptotic debris","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6877","oa_version":"None","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"month":"09","isi":1,"quality_controlled":"1","external_id":{"pmid":["31539498"],"isi":["000486618500011"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2019.08.047","publisher":"Elsevier","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2019","volume":179,"date_created":"2019-09-15T22:00:46Z","date_updated":"2024-03-28T23:30:40Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"author":[{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}]},{"day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-04T00:00:00Z","article_type":"letter_note","page":"750-752","publication":"Neuron","citation":{"ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021."},"issue":"5","type":"journal_article","oa_version":"Published Version","status":"public","title":"Memo1 tiles the radial glial cell grid","intvolume":" 103","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6830","month":"09","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2019.08.021","quality_controlled":"1","isi":1,"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"date_created":"2019-08-25T22:00:50Z","date_updated":"2024-03-28T23:30:42Z","volume":103,"author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Elsevier","year":"2019","pmid":1},{"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"article_number":"3337","date_created":"2019-07-11T12:00:32Z","date_updated":"2024-03-28T23:30:44Z","volume":20,"author":[{"first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","year":"2019","pmid":1,"month":"07","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms20133337","isi":1,"quality_controlled":"1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"oa":1,"abstract":[{"lang":"eng","text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation."}],"issue":"13","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6645","relation":"main_file","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-17T06:17:15Z","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_name":"2019_JournalMolecularScience_Adamowski.pdf","access_level":"open_access","creator":"dernst","file_size":3330291,"content_type":"application/pdf"}],"ddc":["580"],"status":"public","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","intvolume":" 20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6627","day":"07","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2019-07-07T00:00:00Z","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019)."}},{"publication":"ACM Transactions on Graphics","citation":{"ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576."},"article_type":"original","date_published":"2019-11-06T00:00:00Z","scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","_id":"7117","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","status":"public","ddc":["000"],"intvolume":" 38","file":[{"file_size":1673176,"content_type":"application/pdf","creator":"bbickel","file_name":"xcad_sup_mat_siga19.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:24:26Z","checksum":"56a2fb019adcb556d2b022f5e5acb68c","relation":"supplementary_material","file_id":"7119","title":"X-CAD Supplemental Material"},{"checksum":"5f29d76aceb5102e766cbab9b17d776e","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:24:27Z","relation":"main_file","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_id":"7120","file_size":14563618,"content_type":"application/pdf","creator":"bbickel","access_level":"open_access","description":"This is the author's version of the work.","file_name":"XCAD_authors_version.pdf"},{"date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:27:37Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","relation":"main_file","creator":"bbickel","file_size":259979129,"content_type":"video/mp4","file_name":"XCAD_video.mp4","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models."}],"issue":"6","oa":1,"external_id":{"isi":["000498397300007"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"doi":"10.1145/3355089.3356576","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["0730-0301"]},"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner"},{"full_name":"Schumacher, Christian","last_name":"Schumacher","first_name":"Christian"},{"last_name":"Knoop","first_name":"Espen","full_name":"Knoop, Espen"},{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","first_name":"Thomas"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"}],"related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}]},"date_created":"2019-11-26T14:22:09Z","date_updated":"2024-03-28T23:30:47Z","volume":38,"article_number":"157","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1},{"oa_version":"Preprint","intvolume":" 122","status":"public","title":"Transition to turbulence in particle laden flows","_id":"6189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"11","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"type":"journal_article","date_published":"2019-03-22T00:00:00Z","citation":{"ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"22","scopus_import":"1","volume":122,"date_created":"2019-03-31T21:59:12Z","date_updated":"2024-03-28T23:30:48Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","article_number":"114502","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.122.114502","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"month":"03"},{"file":[{"creator":"cigler","content_type":"application/pdf","file_size":12597663,"access_level":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","checksum":"c0085d47c58c9cbcab1b0a783480f6da","date_created":"2019-05-03T11:54:52Z","date_updated":"2021-02-11T11:17:13Z","file_id":"6373","embargo":"2020-05-02","relation":"main_file"},{"relation":"source_file","file_id":"6374","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","date_created":"2019-05-03T11:54:54Z","date_updated":"2020-07-14T12:47:28Z","access_level":"closed","embargo_to":"open_access","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","file_size":34644426,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cigler"}],"oa_version":"Published Version","_id":"6371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576","579"],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","status":"public","abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2019-05-03T00:00:00Z","citation":{"short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria."},"page":"152","day":"03","has_accepted_license":"1","article_processing_charge":"No","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"author":[{"last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"67"},{"id":"5585","status":"public","relation":"popular_science"}]},"date_created":"2019-05-03T11:55:51Z","date_updated":"2024-02-21T13:45:52Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","doi":"10.15479/AT:ISTA:6371","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"month":"05","publication_identifier":{"issn":["2663-337X"]}},{"author":[{"last_name":"Allini","first_name":"Elie Noumon","full_name":"Allini, Elie Noumon"},{"first_name":"Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"},{"full_name":"Petura, Oto","first_name":"Oto","last_name":"Petura"},{"first_name":"Florent","last_name":"Bernard","full_name":"Bernard, Florent"},{"full_name":"Laban, Marek","first_name":"Marek","last_name":"Laban"},{"full_name":"Fischer, Viktor","last_name":"Fischer","first_name":"Viktor"}],"volume":2018,"date_created":"2021-11-14T23:01:25Z","date_updated":"2021-11-15T10:48:49Z","year":"2018","publisher":"International Association for Cryptologic Research","department":[{"_id":"KrPi"}],"publication_status":"published","file_date_updated":"2021-11-15T10:27:29Z","doi":"10.13154/tches.v2018.i3.214-242","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["2569-2925"]},"month":"01","file":[{"relation":"main_file","file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5","success":1,"date_created":"2021-11-15T10:27:29Z","date_updated":"2021-11-15T10:27:29Z","access_level":"open_access","file_name":"2018_IACR_Allini.pdf","content_type":"application/pdf","file_size":955755,"creator":"cchlebak"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10286","intvolume":" 2018","status":"public","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","ddc":["000"],"issue":"3","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"type":"journal_article","date_published":"2018-01-01T00:00:00Z","citation":{"ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242."},"publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","page":"214-242","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"doi":"10.1021/acsnano.7b08044","language":[{"iso":"eng"}],"external_id":{"pmid":["29350911"]},"quality_controlled":"1","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"month":"01","author":[{"full_name":"Fisher, Patrick D. Ellis","first_name":"Patrick D. Ellis","last_name":"Fisher"},{"full_name":"Shen, Qi","last_name":"Shen","first_name":"Qi"},{"full_name":"Akpinar, Bernice","last_name":"Akpinar","first_name":"Bernice"},{"full_name":"Davis, Luke K.","first_name":"Luke K.","last_name":"Davis"},{"full_name":"Chung, Kenny Kwok Hin","last_name":"Chung","first_name":"Kenny Kwok Hin"},{"last_name":"Baddeley","first_name":"David","full_name":"Baddeley, David"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Melia, Thomas J.","last_name":"Melia","first_name":"Thomas J."},{"full_name":"Hoogenboom, Bart W.","first_name":"Bart W.","last_name":"Hoogenboom"},{"first_name":"Chenxiang","last_name":"Lin","full_name":"Lin, Chenxiang"},{"full_name":"Lusk, C. Patrick","last_name":"Lusk","first_name":"C. Patrick"}],"volume":12,"date_created":"2021-11-26T15:15:00Z","date_updated":"2021-11-26T15:57:02Z","pmid":1,"year":"2018","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","publisher":"American Chemical Society","publication_status":"published","extern":"1","date_published":"2018-01-19T00:00:00Z","citation":{"ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.7b08044","ieee":"P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044.","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518."},"publication":"ACS Nano","page":"1508-1518","article_type":"original","article_processing_charge":"No","day":"19","scopus_import":"1","keyword":["general physics and astronomy"],"oa_version":"None","_id":"10362","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 12","title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","status":"public","issue":"2","abstract":[{"text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.","lang":"eng"}],"type":"journal_article"},{"extern":"1","pmid":1,"acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","year":"2018","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Samuel I. A.","last_name":"Cohen","full_name":"Cohen, Samuel I. A."},{"full_name":"Cukalevski, Risto","last_name":"Cukalevski","first_name":"Risto"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Törnquist","first_name":"Mattias","full_name":"Törnquist, Mattias"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"full_name":"Buell, Alexander K.","first_name":"Alexander K.","last_name":"Buell"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"}],"volume":10,"date_updated":"2021-11-26T15:14:00Z","date_created":"2021-11-26T12:41:38Z","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"month":"03","external_id":{"pmid":["29581486"]},"quality_controlled":"1","doi":"10.1038/s41557-018-0023-x","language":[{"iso":"eng"}],"type":"journal_article","issue":"5","abstract":[{"text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.","lang":"eng"}],"_id":"10360","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 10","status":"public","title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","oa_version":"None","scopus_import":"1","keyword":["general chemical engineering","general chemistry"],"article_processing_charge":"No","day":"26","citation":{"mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x.","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0023-x","ieee":"S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” Nature Chemistry, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018."},"publication":"Nature Chemistry","page":"523-531","article_type":"original","date_published":"2018-03-26T00:00:00Z"},{"intvolume":" 122","status":"public","title":"Statistical mechanics of globular oligomer formation by protein molecules","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10357","oa_version":"None","type":"journal_article","issue":"49","abstract":[{"lang":"eng","text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements."}],"page":"11721-11730","article_type":"original","citation":{"short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.","chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” The Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.8b07805","ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730."},"publication":"The Journal of Physical Chemistry B","date_published":"2018-10-18T00:00:00Z","keyword":["materials chemistry"],"scopus_import":"1","article_processing_charge":"No","day":"18","publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2018","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","volume":122,"date_updated":"2021-11-26T12:40:02Z","date_created":"2021-11-26T11:55:12Z","author":[{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"}],"extern":"1","quality_controlled":"1","external_id":{"pmid":["30336667"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.jpcb.8b07805","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"month":"10"},{"extern":"1","date_created":"2021-11-26T12:15:47Z","date_updated":"2021-11-26T15:14:08Z","volume":18,"author":[{"first_name":"Tine","last_name":"Curk","full_name":"Curk, Tine"},{"full_name":"Wirnsberger, Peter","last_name":"Wirnsberger","first_name":"Peter"},{"first_name":"Jure","last_name":"Dobnikar","full_name":"Dobnikar, Jure"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"publication_status":"published","publisher":"American Chemical Society","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","year":"2018","pmid":1,"month":"04","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.8b00786","quality_controlled":"1","external_id":{"pmid":["29667410"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10147"}],"oa":1,"abstract":[{"lang":"eng","text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets."}],"issue":"9","type":"journal_article","oa_version":"Preprint","title":"Controlling cargo trafficking in multicomponent membranes","status":"public","intvolume":" 18","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10359","day":"18","article_processing_charge":"No","keyword":["mechanical engineering","condensed matter physics"],"scopus_import":"1","date_published":"2018-04-18T00:00:00Z","article_type":"original","page":"5350-5356","publication":"Nano Letters","citation":{"apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786."}},{"page":"3055-3065","article_type":"original","citation":{"chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280.","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280","ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280"},"publication":"Molecular Physics","date_published":"2018-05-24T00:00:00Z","keyword":["physical chemistry"],"scopus_import":"1","article_processing_charge":"No","day":"24","intvolume":" 116","title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10358","oa_version":"Preprint","type":"journal_article","issue":"21-22","abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"quality_controlled":"1","external_id":{"arxiv":["1803.04851"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1803.04851","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1080/00268976.2018.1474280","publication_identifier":{"eissn":["1362-3028"],"issn":["0026-8976"]},"month":"05","publisher":"Taylor & Francis","publication_status":"published","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","year":"2018","volume":116,"date_updated":"2021-11-26T12:39:58Z","date_created":"2021-11-26T12:08:02Z","author":[{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"first_name":"Lucie X.","last_name":"Liu","full_name":"Liu, Lucie X."},{"full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"last_name":"Bolhuis","first_name":"Peter G.","full_name":"Bolhuis, Peter G."},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"extern":"1"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10361","intvolume":" 69","status":"public","title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","oa_version":"None","scopus_import":"1","keyword":["physical and theoretical chemistry"],"article_processing_charge":"No","day":"28","citation":{"ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","ieee":"T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322."},"publication":"Annual Review of Physical Chemistry","page":"273-298","article_type":"original","date_published":"2018-02-28T00:00:00Z","extern":"1","pmid":1,"year":"2018","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","publisher":"Annual Reviews","publication_status":"published","author":[{"last_name":"Michaels","first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T."},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Johnny","last_name":"Habchi","full_name":"Habchi, Johnny"},{"first_name":"Sean","last_name":"Chia","full_name":"Chia, Sean"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"full_name":"Knowles, Tuomas P.J.","first_name":"Tuomas P.J.","last_name":"Knowles"}],"volume":69,"date_updated":"2021-11-26T15:58:19Z","date_created":"2021-11-26T12:52:12Z","publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"month":"02","external_id":{"pmid":["29490200"]},"quality_controlled":"1","doi":"10.1146/annurev-physchem-050317-021322","language":[{"iso":"eng"}]},{"article_number":"226801","extern":"1","publisher":"American Physical Society","publication_status":"published","year":"2018","acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","volume":121,"date_created":"2022-01-14T12:15:47Z","date_updated":"2022-01-14T13:48:35Z","author":[{"full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"H.","last_name":"Zhou","full_name":"Zhou, H."},{"first_name":"E. M.","last_name":"Spanton","full_name":"Spanton, E. M."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"11","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1805.04199","open_access":"1"}],"external_id":{"arxiv":["1805.04199"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.121.226801","type":"journal_article","issue":"22","abstract":[{"lang":"eng","text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4."}],"intvolume":" 121","title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10626","oa_version":"Preprint","keyword":["general physics and astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"28","article_type":"original","citation":{"ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018.","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801","ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801."},"publication":"Physical Review Letters","date_published":"2018-11-28T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.97.184501","quality_controlled":"1","external_id":{"arxiv":["1703.08184"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.08184","open_access":"1"}],"month":"05","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"date_created":"2022-01-14T13:48:47Z","date_updated":"2022-01-14T13:58:24Z","volume":97,"author":[{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn"},{"last_name":"Naibert","first_name":"Tyler R.","full_name":"Naibert, Tyler R."},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"publication_status":"published","publisher":"American Physical Society","acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","year":"2018","extern":"1","article_number":"184501","date_published":"2018-05-08T00:00:00Z","article_type":"original","publication":"Physical Review B","citation":{"chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.","mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501.","apa":"Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018.","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501"},"day":"08","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Imaging phase slip dynamics in micron-size superconducting rings","status":"public","intvolume":" 97","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10627","abstract":[{"lang":"eng","text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures."}],"issue":"18","type":"journal_article"},{"type":"conference","alternative_title":["EPiC Series in Computing"],"abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"_id":"10883","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","title":"Quasipolynomial set-based symbolic algorithms for parity games","ddc":["000"],"intvolume":" 57","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":720893,"file_name":"2018_EPiCs_Chatterjee.pdf","access_level":"open_access","date_created":"2022-05-17T07:51:08Z","date_updated":"2022-05-17T07:51:08Z","success":1,"checksum":"1229aa8640bd6db610c85decf2265480","file_id":"11392","relation":"main_file"}],"scopus_import":"1","day":"23","has_accepted_license":"1","article_processing_charge":"No","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","citation":{"ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k."},"page":"233-253","date_published":"2018-10-23T00:00:00Z","file_date_updated":"2022-05-17T07:51:08Z","ec_funded":1,"acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","year":"2018","publication_status":"published","publisher":"EasyChair","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvořák","first_name":"Wolfgang","full_name":"Dvořák, Wolfgang"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"date_created":"2022-03-18T12:46:32Z","date_updated":"2022-07-29T09:24:31Z","volume":57,"month":"10","publication_identifier":{"issn":["2398-7340"]},"oa":1,"external_id":{"arxiv":["1909.04983"]},"quality_controlled":"1","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia","start_date":"2018-11-17","end_date":"2018-11-21"},"doi":"10.29007/5z5k","language":[{"iso":"eng"}]},{"author":[{"full_name":"Mohammadi, Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87","first_name":"Fatemeh","last_name":"Mohammadi"},{"full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, Charles","last_name":"Wang","first_name":"Charles"},{"full_name":"Yu, Josephine","first_name":"Josephine","last_name":"Yu"}],"date_created":"2018-12-11T11:50:06Z","date_updated":"2021-01-12T06:48:13Z","oa_version":"Preprint","volume":32,"_id":"1092","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"Generalized permutohedra from probabilistic graphical models","publication_status":"published","status":"public","intvolume":" 32","publisher":"SIAM","abstract":[{"lang":"eng","text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. "}],"issue":"1","publist_id":"6284","extern":"1","type":"journal_article","doi":"10.1137/16M107894X","date_published":"2018-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"SIAM Journal on Discrete Mathematics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.01814"}],"oa":1,"citation":{"ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.","apa":"Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93.","chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X."},"quality_controlled":"1","page":"64-93","month":"01","day":"01"},{"oa":1,"external_id":{"arxiv":["1806.10843"]},"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","location":"Munich, Germany","start_date":"2017-03-30","end_date":"2017-04-01"},"doi":"10.1007/978-3-030-01602-9_9","language":[{"iso":"eng"}],"month":"10","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"author":[{"first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"}],"date_created":"2018-12-11T11:44:08Z","date_updated":"2021-01-12T06:48:16Z","volume":270,"ec_funded":1,"publist_id":"8045","citation":{"short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"page":"185 - 214","date_published":"2018-10-27T00:00:00Z","scopus_import":1,"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11","status":"public","title":"Mean-field limits of particles in interaction with quantised radiation fields","intvolume":" 270","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}]},{"extern":"1","author":[{"first_name":"Asako","last_name":"McCloskey","full_name":"McCloskey, Asako"},{"last_name":"Ibarra","first_name":"Arkaitz","full_name":"Ibarra, Arkaitz"},{"first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"volume":32,"date_created":"2022-04-07T07:45:30Z","date_updated":"2022-07-18T08:32:32Z","pmid":1,"year":"2018","publisher":"Cold Spring Harbor Laboratory","publication_status":"published","publication_identifier":{"issn":["0890-9369","1549-5477"]},"month":"09","doi":"10.1101/gad.315523.118","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/gad.315523.118","open_access":"1"}],"oa":1,"external_id":{"pmid":["30228202"]},"quality_controlled":"1","issue":"19-20","abstract":[{"lang":"eng","text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus."}],"type":"journal_article","oa_version":"Published Version","_id":"11063","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 32","status":"public","title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","article_processing_charge":"No","day":"18","scopus_import":"1","keyword":["Developmental Biology","Genetics"],"date_published":"2018-09-18T00:00:00Z","citation":{"ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.","apa":"McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118","ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.","short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118."},"publication":"Genes & Development","page":"1321-1331","article_type":"original"},{"extern":"1","article_number":"221","volume":19,"date_updated":"2022-07-18T08:32:34Z","date_created":"2022-04-07T07:45:40Z","author":[{"first_name":"Jason G.","last_name":"Fleischer","full_name":"Fleischer, Jason G."},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"last_name":"Tsai","first_name":"Hsiao H.","full_name":"Tsai, Hsiao H."},{"first_name":"Swati","last_name":"Tyagi","full_name":"Tyagi, Swati"},{"full_name":"Ibarra, Arkaitz","first_name":"Arkaitz","last_name":"Ibarra"},{"full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev","first_name":"Maxim N."},{"full_name":"Huang, Ling","last_name":"Huang","first_name":"Ling"},{"full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"},{"last_name":"Navlakha","first_name":"Saket","full_name":"Navlakha, Saket"}],"publisher":"BioMed Central","publication_status":"published","pmid":1,"year":"2018","publication_identifier":{"issn":["1474-760X"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1186/s13059-018-1599-6","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1186/s13059-018-1599-6","open_access":"1"}],"external_id":{"pmid":["30567591"]},"abstract":[{"text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 19","status":"public","title":"Predicting age from the transcriptome of human dermal fibroblasts","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11064","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2018-12-20T00:00:00Z","article_type":"original","citation":{"ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221.","short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6.","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6."},"publication":"Genome Biology"},{"intvolume":" 619","title":"Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe","status":"public","_id":"11508","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα > 22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z > 6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z < 1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z > 6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z > 5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR."}],"article_type":"original","citation":{"chicago":"Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528.","short":"J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering, Astronomy & Astrophysics 619 (2018).","mla":"Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences, 2018, doi:10.1051/0004-6361/201833528.","ieee":"J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.","apa":"Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M., & Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528","ista":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 619, A136.","ama":"Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201833528"},"publication":"Astronomy & Astrophysics","date_published":"2018-11-19T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium"],"scopus_import":"1","article_processing_charge":"No","day":"19","publisher":"EDP Sciences","publication_status":"published","acknowledgement":"JM acknowledges the award of a Huygens PhD fellowship from Leiden University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the referee for their comments that improved the paper. We also thank Christoph Behrens, Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger and Johannes Zabl for discussions. We have benefited from the public available programming language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter 2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin 2010) and ds9 and the Topcat analysis tool (Taylor 2013).","year":"2018","volume":619,"date_updated":"2022-07-19T09:32:08Z","date_created":"2022-07-06T11:14:23Z","author":[{"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":"Sobral, David","last_name":"Sobral","first_name":"David"},{"full_name":"Gronke, Max","first_name":"Max","last_name":"Gronke"},{"first_name":"Ana","last_name":"Paulino-Afonso","full_name":"Paulino-Afonso, Ana"},{"full_name":"Stefanon, Mauro","last_name":"Stefanon","first_name":"Mauro"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"}],"article_number":"A136","extern":"1","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1805.11621"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.11621"}],"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201833528","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"11"},{"article_type":"original","page":"2999-3015","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"apa":"Khostovan, A. A., Sobral, D., Mobasher, B., Best, P. N., Smail, I., Matthee, J. J., … Stott, J. P. (2018). The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty925","ieee":"A. A. Khostovan et al., “The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3. Oxford University Press, pp. 2999–3015, 2018.","ista":"Khostovan AA, Sobral D, Mobasher B, Best PN, Smail I, Matthee JJ, Darvish B, Nayyeri H, Hemmati S, Stott JP. 2018. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 478(3), 2999–3015.","ama":"Khostovan AA, Sobral D, Mobasher B, et al. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 2018;478(3):2999-3015. doi:10.1093/mnras/sty925","chicago":"Khostovan, A A, D Sobral, B Mobasher, P N Best, I Smail, Jorryt J Matthee, B Darvish, H Nayyeri, S Hemmati, and J P Stott. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty925.","short":"A.A. Khostovan, D. Sobral, B. Mobasher, P.N. Best, I. Smail, J.J. Matthee, B. Darvish, H. Nayyeri, S. Hemmati, J.P. Stott, Monthly Notices of the Royal Astronomical Society 478 (2018) 2999–3015.","mla":"Khostovan, A. A., et al. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3, Oxford University Press, 2018, pp. 2999–3015, doi:10.1093/mnras/sty925."},"date_published":"2018-08-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: haloes","galaxies: high-redshift","galaxies: star formation","cosmology: observations","large-scale structure of Universe"],"scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass","intvolume":" 478","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11549","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We investigate the clustering properties of ∼7000 H β + [O III] and [O II] narrowband-selected emitters at z ∼ 0.8–4.7 from the High-z Emission Line Survey. We find clustering lengths, r0, of 1.5–4.0 h−1 Mpc and minimum dark matter halo masses of 1010.7–12.1 M⊙ for our z = 0.8–3.2 H β + [O III] emitters and r0 ∼ 2.0–8.3 h−1 Mpc and halo masses of 1011.5–12.6 M⊙ for our z = 1.5–4.7 [O II] emitters. We find r0 to strongly increase both with increasing line luminosity and redshift. By taking into account the evolution of the characteristic line luminosity, L⋆(z), and using our model predictions of halo mass given r0, we find a strong, redshift-independent increasing trend between L/L⋆(z) and minimum halo mass. The faintest H β + [O III] emitters are found to reside in 109.5 M⊙ haloes and the brightest emitters in 1013.0 M⊙ haloes. For [O II] emitters, the faintest emitters are found in 1010.5 M⊙ haloes and the brightest emitters in 1012.6 M⊙ haloes. A redshift-independent stellar mass dependency is also observed where the halo mass increases from 1011 to 1012.5 M⊙ for stellar masses of 108.5 to 1011.5 M⊙, respectively. We investigate the interdependencies of these trends by repeating our analysis in a Lline−Mstar grid space for our most populated samples (H β + [O III] z = 0.84 and [O II] z = 1.47) and find that the line luminosity dependency is stronger than the stellar mass dependency on halo mass. For L > L⋆ emitters at all epochs, we find a relatively flat trend with halo masses of 1012.5–13 M⊙, which may be due to quenching mechanisms in massive haloes that is consistent with a transitional halo mass predicted by models.","lang":"eng"}],"issue":"3","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.01101"}],"external_id":{"arxiv":["1705.01101"]},"language":[{"iso":"eng"}],"doi":"10.1093/mnras/sty925","month":"08","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","publisher":"Oxford University Press","year":"2018","acknowledgement":"We thank the anonymous referee for their useful comments and suggestions that improved this study. AAK thanks Anahita Alavi and Irene Shivaei for useful discussion in the making of this paper. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. DS acknowledges financial support from the Netherlands Organization for Scientific Research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. PNB is grateful for support from STFC via grant STM001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Grant DUSTYGAL (321334), and a Royal Society/Wolfson Merit award. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G.","date_updated":"2022-08-19T06:53:39Z","date_created":"2022-07-08T11:48:48Z","volume":478,"author":[{"full_name":"Khostovan, A A","first_name":"A A","last_name":"Khostovan"},{"full_name":"Sobral, D","first_name":"D","last_name":"Sobral"},{"full_name":"Mobasher, B","first_name":"B","last_name":"Mobasher"},{"last_name":"Best","first_name":"P N","full_name":"Best, P N"},{"last_name":"Smail","first_name":"I","full_name":"Smail, I"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"last_name":"Darvish","first_name":"B","full_name":"Darvish, B"},{"full_name":"Nayyeri, H","last_name":"Nayyeri","first_name":"H"},{"last_name":"Hemmati","first_name":"S","full_name":"Hemmati, S"},{"full_name":"Stott, J P","first_name":"J P","last_name":"Stott"}],"extern":"1"},{"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1802.10102"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.10102"}],"language":[{"iso":"eng"}],"doi":"10.1093/mnras/sty782","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"06","publisher":"Oxford University Press","publication_status":"published","acknowledgement":"We thank the anonymous reviewer for their timely and constructive comments that greatly helped us to improve the manuscript. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot for many helpful and engaging discussions, particularly during the SnowCLAW Ly α workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton, Ali Khostovan, and Sara Perez for participating in part of the observations. We also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their assistance with the narrow-band observations which allowed to select some of the sour ces. Based on observations obtained with the William Herschel Telescope, program: W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck II telescope, program: C267D. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A-0786, 093.A-0561, 097.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005. The authors acknowledge the award of service time (SW2014b20) on the 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. The authors would also like to thank all the extremely helpful observatory staff that have greatly contributed towards our observations, particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France.","year":"2018","volume":477,"date_created":"2022-07-12T07:18:02Z","date_updated":"2022-08-19T07:01:08Z","author":[{"full_name":"Sobral, David","last_name":"Sobral","first_name":"David"},{"full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"last_name":"Darvish","first_name":"Behnam","full_name":"Darvish, Behnam"},{"full_name":"Smail, Ian","first_name":"Ian","last_name":"Smail"},{"last_name":"Best","first_name":"Philip N","full_name":"Best, Philip N"},{"first_name":"Lara","last_name":"Alegre","full_name":"Alegre, Lara"},{"full_name":"Röttgering, Huub","last_name":"Röttgering","first_name":"Huub"},{"last_name":"Mobasher","first_name":"Bahram","full_name":"Mobasher, Bahram"},{"full_name":"Paulino-Afonso, Ana","last_name":"Paulino-Afonso","first_name":"Ana"},{"full_name":"Stroe, Andra","last_name":"Stroe","first_name":"Andra"},{"last_name":"Oteo","first_name":"Iván","full_name":"Oteo, Iván"}],"extern":"1","page":"2817-2840","article_type":"original","citation":{"chicago":"Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best, Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782.","mla":"Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp. 2817–40, doi:10.1093/mnras/sty782.","short":"D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering, B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal Astronomical Society 477 (2018) 2817–2840.","ista":"Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H, Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 477(2), 2817–2840.","ieee":"D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp. 2817–2840, 2018.","apa":"Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L., … Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782","ama":"Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782"},"publication":"Monthly Notices of the Royal Astronomical Society","date_published":"2018-06-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: active","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: starburst","cosmology: observations"],"scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 477","status":"public","title":"The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN","_id":"11557","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (β=−2.0+0.3−0.1) and high Ly α escape fractions (50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11 per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11 per cent) have lower ionization parameters (logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11558","status":"public","title":"Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6","intvolume":" 476","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape."}],"issue":"4","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"apa":"Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau, J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378","ieee":"D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press, pp. 4725–4752, 2018.","ista":"Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 476(4), 4725–4752.","ama":"Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378","chicago":"Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty378.","short":"D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau, A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752.","mla":"Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press, 2018, pp. 4725–52, doi:10.1093/mnras/sty378."},"article_type":"original","page":"4725-4752","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: formation","galaxies: high-redshift","galaxies: luminosity function","mass function","galaxies: statistics"],"day":"01","article_processing_charge":"No","acknowledgement":"We thank the anonymous referee for their constructive comments that helped us improve the manuscript. DS acknowledges the hospitality of the IAC and a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA acknowledges financial support from the Science and Technology Foundation (FCT, Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014. The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke, Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett, and Tom Rose for their involvement in the early stages of this project. Based on data products from observations made with European Southern Observatory (ESO) Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819, 099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118, and 2016AN001. The 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. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France– Hawaii Telescope Legacy Survey (CFHTLS), a collaborative project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous work from previous Ly α surveys’ teams. Without these previous Ly α and the wider reach legacy surveys, this research would have been impossible. We also thank the VUDS team for making available spectroscopic redshifts from data obtained with VIMOS at the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY and SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2005). We publicly release a catalogue with all LAEs used in this paper (SC4K), so it can be freely explored by the community (see five example entries in Table A1).","year":"2018","publication_status":"published","publisher":"Oxford University Press","author":[{"full_name":"Sobral, David","first_name":"David","last_name":"Sobral"},{"full_name":"Santos, Sérgio","last_name":"Santos","first_name":"Sérgio"},{"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":"Paulino-Afonso, Ana","first_name":"Ana","last_name":"Paulino-Afonso"},{"full_name":"Ribeiro, Bruno","last_name":"Ribeiro","first_name":"Bruno"},{"last_name":"Calhau","first_name":"João","full_name":"Calhau, João"},{"full_name":"Khostovan, Ali A","last_name":"Khostovan","first_name":"Ali A"}],"date_created":"2022-07-12T10:41:08Z","date_updated":"2022-08-19T07:04:45Z","volume":476,"extern":"1","external_id":{"arxiv":["1712.04451"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.04451","open_access":"1"}],"quality_controlled":"1","doi":"10.1093/mnras/sty378","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]}},{"abstract":[{"lang":"eng","text":"We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies."}],"issue":"1","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11555","title":"Kiloparsec-scale gaseous clumps and star formation at z = 5–7","status":"public","intvolume":" 478","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: evolution","galaxies: high-redshift","galaxies: ISM","galaxies: formation"],"date_published":"2018-07-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society","citation":{"ama":"Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 2018;478(1):1170-1184. doi:10.1093/mnras/sty1088","ieee":"S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1. Oxford University Press, pp. 1170–1184, 2018.","apa":"Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara, A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1088","ista":"Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184.","short":"S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara, C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S. De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical Society 478 (2018) 1170–1184.","mla":"Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088.","chicago":"Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara, C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1088."},"article_type":"original","page":"1170-1184","extern":"1","author":[{"full_name":"Carniani, S","first_name":"S","last_name":"Carniani"},{"full_name":"Maiolino, R","first_name":"R","last_name":"Maiolino"},{"full_name":"Amorin, R","first_name":"R","last_name":"Amorin"},{"first_name":"L","last_name":"Pentericci","full_name":"Pentericci, L"},{"full_name":"Pallottini, A","last_name":"Pallottini","first_name":"A"},{"first_name":"A","last_name":"Ferrara","full_name":"Ferrara, A"},{"first_name":"C J","last_name":"Willott","full_name":"Willott, C J"},{"last_name":"Smit","first_name":"R","full_name":"Smit, R"},{"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","last_name":"Sobral","first_name":"D"},{"full_name":"Santini, P","last_name":"Santini","first_name":"P"},{"full_name":"Castellano, M","first_name":"M","last_name":"Castellano"},{"last_name":"De Barros","first_name":"S","full_name":"De Barros, S"},{"full_name":"Fontana, A","first_name":"A","last_name":"Fontana"},{"last_name":"Grazian","first_name":"A","full_name":"Grazian, A"},{"last_name":"Guaita","first_name":"L","full_name":"Guaita, L"}],"date_updated":"2022-08-19T06:58:06Z","date_created":"2022-07-11T08:05:42Z","volume":478,"year":"2018","acknowledgement":"This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S, ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S, ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S, AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/ alma-data/archive. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120.","publication_status":"published","publisher":"Oxford University Press","month":"07","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"doi":"10.1093/mnras/sty1088","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1712.03985"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.03985"}],"quality_controlled":"1"},{"date_published":"2018-09-01T00:00:00Z","publication":"Monthly Notices of the Royal Astronomical Society: Letters","citation":{"short":"J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society: Letters 479 (2018) L34–L39.","mla":"Matthee, Jorryt J., and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1, Oxford University Press, 2018, pp. L34–39, doi:10.1093/mnrasl/sly093.","chicago":"Matthee, Jorryt J, and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press, 2018. https://doi.org/10.1093/mnrasl/sly093.","ama":"Matthee JJ, Schaye J. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 2018;479(1):L34-L39. doi:10.1093/mnrasl/sly093","ieee":"J. J. Matthee and J. Schaye, “Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement,” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1. Oxford University Press, pp. L34–L39, 2018.","apa":"Matthee, J. J., & Schaye, J. (2018). Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press. https://doi.org/10.1093/mnrasl/sly093","ista":"Matthee JJ, Schaye J. 2018. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 479(1), L34–L39."},"article_type":"original","page":"L34 - L39","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: abundances","galaxies: evolution","galaxies: formation","galaxies: star formation"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11584","status":"public","title":"Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement","intvolume":" 479","abstract":[{"text":"Observations show that star-forming galaxies reside on a tight 3D plane between mass, gas-phase metallicity, and star formation rate (SFR), which can be explained by the interplay between metal-poor gas inflows, SFR and outflows. However, different metals are released on different time-scales, which may affect the slope of this relation. Here, we use central, star-forming galaxies with Mstar = 109.0–10.5 M⊙ from the EAGLE hydrodynamical simulation to examine 3D relations between mass, SFR, and chemical enrichment using absolute and relative C, N, O, and Fe abundances. We show that the scatter is smaller when gas-phase α-enhancement is used rather than metallicity. A similar plane also exists for stellar α-enhancement, implying that present-day specific SFRs are correlated with long time-scale star formation histories. Between z = 0 and 1, the α-enhancement plane is even more insensitive to redshift than the plane using metallicity. However, it evolves at z > 1 due to lagging iron yields. At fixed mass, galaxies with higher SFRs have star formation histories shifted towards late times, are more α-enhanced, and this α-enhancement increases with redshift as observed. These findings suggest that relations between physical properties inferred from observations may be affected by systematic variations in α-enhancements.","lang":"eng"}],"issue":"1","type":"journal_article","doi":"10.1093/mnrasl/sly093","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1802.06786"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.06786"}],"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["1745-3933"],"issn":["1745-3925"]},"author":[{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"last_name":"Schaye","first_name":"Joop","full_name":"Schaye, Joop"}],"date_created":"2022-07-14T12:49:47Z","date_updated":"2022-08-19T08:35:45Z","volume":479,"acknowledgement":"We thank the anonymous referee for their constructive comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Jarle Brinchmann, Rob Crain and David Sobral for discussions. We acknowledge the use of the TOPCAT software (Taylor 2013) for assisting in rapid exploration of multidimensional data sets and the use of PYTHON and its NUMPY, MATPLOTLIB, and PANDAS packages.","year":"2018","publication_status":"published","publisher":"Oxford University Press","extern":"1"},{"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.07573","open_access":"1"}],"external_id":{"arxiv":["1809.07573"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/201834289","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"month":"11","publisher":"EDP Sciences","publication_status":"published","year":"2018","volume":619,"date_updated":"2022-08-22T07:43:29Z","date_created":"2022-07-18T14:41:16Z","author":[{"last_name":"Gandolfi","first_name":"D.","full_name":"Gandolfi, D."},{"full_name":"Barragán, O.","first_name":"O.","last_name":"Barragán"},{"full_name":"Livingston, J. H.","last_name":"Livingston","first_name":"J. H."},{"full_name":"Fridlund, M.","first_name":"M.","last_name":"Fridlund"},{"first_name":"A. B.","last_name":"Justesen","full_name":"Justesen, A. B."},{"full_name":"Redfield, S.","first_name":"S.","last_name":"Redfield"},{"full_name":"Fossati, L.","first_name":"L.","last_name":"Fossati"},{"full_name":"Mathur, S.","last_name":"Mathur","first_name":"S."},{"last_name":"Grziwa","first_name":"S.","full_name":"Grziwa, S."},{"full_name":"Cabrera, J.","last_name":"Cabrera","first_name":"J."},{"full_name":"García, R. A.","first_name":"R. A.","last_name":"García"},{"full_name":"Persson, C. M.","last_name":"Persson","first_name":"C. M."},{"full_name":"Van Eylen, V.","first_name":"V.","last_name":"Van Eylen"},{"first_name":"A. P.","last_name":"Hatzes","full_name":"Hatzes, A. P."},{"full_name":"Hidalgo, D.","last_name":"Hidalgo","first_name":"D."},{"first_name":"S.","last_name":"Albrecht","full_name":"Albrecht, S."},{"first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"Cochran","first_name":"W. D.","full_name":"Cochran, W. D."},{"first_name":"Sz.","last_name":"Csizmadia","full_name":"Csizmadia, Sz."},{"full_name":"Deeg, H.","last_name":"Deeg","first_name":"H."},{"full_name":"Eigmüller, Ph.","first_name":"Ph.","last_name":"Eigmüller"},{"first_name":"M.","last_name":"Endl","full_name":"Endl, M."},{"first_name":"A.","last_name":"Erikson","full_name":"Erikson, A."},{"last_name":"Esposito","first_name":"M.","full_name":"Esposito, M."},{"last_name":"Guenther","first_name":"E.","full_name":"Guenther, E."},{"first_name":"J.","last_name":"Korth","full_name":"Korth, J."},{"full_name":"Luque, R.","first_name":"R.","last_name":"Luque"},{"full_name":"Montañes Rodríguez, P.","first_name":"P.","last_name":"Montañes Rodríguez"},{"full_name":"Nespral, D.","first_name":"D.","last_name":"Nespral"},{"first_name":"G.","last_name":"Nowak","full_name":"Nowak, G."},{"full_name":"Pätzold, M.","first_name":"M.","last_name":"Pätzold"},{"full_name":"Prieto-Arranz, J.","last_name":"Prieto-Arranz","first_name":"J."}],"article_number":"L10","extern":"1","article_type":"letter_note","citation":{"chicago":"Gandolfi, D., O. Barragán, J. H. Livingston, M. Fridlund, A. B. Justesen, S. Redfield, L. Fossati, et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201834289.","mla":"Gandolfi, D., et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics, vol. 619, L10, EDP Sciences, 2018, doi:10.1051/0004-6361/201834289.","short":"D. Gandolfi, O. Barragán, J.H. Livingston, M. Fridlund, A.B. Justesen, S. Redfield, L. Fossati, S. Mathur, S. Grziwa, J. Cabrera, R.A. García, C.M. Persson, V. Van Eylen, A.P. Hatzes, D. Hidalgo, S. Albrecht, L.A. Bugnet, W.D. Cochran, S. Csizmadia, H. Deeg, P. Eigmüller, M. Endl, A. Erikson, M. Esposito, E. Guenther, J. Korth, R. Luque, P. Montañes Rodríguez, D. Nespral, G. Nowak, M. Pätzold, J. Prieto-Arranz, Astronomy & Astrophysics 619 (2018).","ista":"Gandolfi D, Barragán O, Livingston JH, Fridlund M, Justesen AB, Redfield S, Fossati L, Mathur S, Grziwa S, Cabrera J, García RA, Persson CM, Van Eylen V, Hatzes AP, Hidalgo D, Albrecht S, Bugnet LA, Cochran WD, Csizmadia S, Deeg H, Eigmüller P, Endl M, Erikson A, Esposito M, Guenther E, Korth J, Luque R, Montañes Rodríguez P, Nespral D, Nowak G, Pätzold M, Prieto-Arranz J. 2018. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 619, L10.","apa":"Gandolfi, D., Barragán, O., Livingston, J. H., Fridlund, M., Justesen, A. B., Redfield, S., … Prieto-Arranz, J. (2018). TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834289","ieee":"D. Gandolfi et al., “TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.","ama":"Gandolfi D, Barragán O, Livingston JH, et al. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201834289"},"publication":"Astronomy & Astrophysics","date_published":"2018-11-22T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics","planetary systems / planets and satellites","detection / planets and satellites","fundamental parameters / planets and satellites","terrestrial planets / stars","fundamental parameters"],"scopus_import":"1","article_processing_charge":"No","day":"22","intvolume":" 619","title":"TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae","status":"public","_id":"11619","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We report on the confirmation and mass determination of π Men c, the first transiting planet discovered by NASA’s TESS space mission. π Men is a naked-eye (V = 5.65 mag), quiet G0 V star that was previously known to host a sub-stellar companion (π Men b) on a longperiod (Porb = 2091 days), eccentric (e = 0.64) orbit. Using TESS time-series photometry, combined with Gaia data, published UCLES at AAT Doppler measurements, and archival HARPS at ESO-3.6m radial velocities, we found that π Men c is a close-in planet with an orbital period of Porb = 6.27 days, a mass of Mc = 4.52 ± 0.81 M⊕, and a radius of Rc = 2.06 ± 0.03 R⊕. Based on the planet’s orbital period and size, π Men c is a super-Earth located at, or close to, the radius gap, while its mass and bulk density suggest it may have held on to a significant atmosphere. Because of the brightness of the host star, this system is highly suitable for a wide range of further studies to characterize the planetary atmosphere and dynamical properties. We also performed an asteroseismic analysis of the TESS data and detected a hint of power excess consistent with the seismic values expected for this star, although this result depends on the photometric aperture used to extract the light curve. This marginal detection is expected from pre-launch simulations hinting at the asteroseismic potential of the TESS mission for longer, multi-sector observations and/or for more evolved bright stars."}]},{"article_number":"A38","extern":"1","acknowledgement":"We thank the anonymous referee for the very useful comments. We would also like to thank M. Benbakoura for his help in analyzing the light curves of several binary systems included in our set of stars. L.B. and R.A.G. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges support from the National Aeronautics and Space Administration under Grant NNX15AF13G, the National Science Foundation grant AST-1411685, and the Ramon y Cajal fellowship no. RYC-2015-17697. E.C. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 664931. O.J.H and B.M.R. acknowledge the support of the UK Science and Technology Facilities Council (STFC). Funding for the Stellar Astrophysics Centre is provided by the Danish National Research Foundation (Grant DNRF106). This research has made use of NASA’s Astrophysics Data System. Data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555.","year":"2018","publisher":"EDP Sciences","publication_status":"published","author":[{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"García","first_name":"R. A.","full_name":"García, R. A."},{"full_name":"Davies, G. R.","first_name":"G. R.","last_name":"Davies"},{"last_name":"Mathur","first_name":"S.","full_name":"Mathur, S."},{"last_name":"Corsaro","first_name":"E.","full_name":"Corsaro, E."},{"full_name":"Hall, O. J.","first_name":"O. J.","last_name":"Hall"},{"last_name":"Rendle","first_name":"B. M.","full_name":"Rendle, B. M."}],"volume":620,"date_updated":"2022-08-22T07:41:07Z","date_created":"2022-07-18T14:37:39Z","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1809.05105","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1809.05105"]},"quality_controlled":"1","doi":"10.1051/0004-6361/201833106","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Asteroseismology provides global stellar parameters such as masses, radii, or surface gravities using mean global seismic parameters and effective temperature for thousands of low-mass stars (0.8 M⊙ < M < 3 M⊙). This methodology has been successfully applied to stars in which acoustic modes excited by turbulent convection are measured. Other methods such as the Flicker technique can also be used to determine stellar surface gravities, but only works for log g above 2.5 dex. In this work, we present a new metric called FliPer (Flicker in spectral power density, in opposition to the standard Flicker measurement which is computed in the time domain); it is able to extend the range for which reliable surface gravities can be obtained (0.1 < log g < 4.6 dex) without performing any seismic analysis for stars brighter than Kp < 14. FliPer takes into account the average variability of a star measured in the power density spectrum in a given range of frequencies. However, FliPer values calculated on several ranges of frequency are required to better characterize a star. Using a large set of asteroseismic targets it is possible to calibrate the behavior of surface gravity with FliPer through machine learning. This calibration made with a random forest regressor covers a wide range of surface gravities from main-sequence stars to subgiants and red giants, with very small uncertainties from 0.04 to 0.1 dex. FliPer values can be inserted in automatic global seismic pipelines to either give an estimation of the stellar surface gravity or to assess the quality of the seismic results by detecting any outliers in the obtained νmax values. FliPer also constrains the surface gravities of main-sequence dwarfs using only long-cadence data for which the Nyquist frequency is too low to measure the acoustic-mode properties."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11618","intvolume":" 620","status":"public","title":"FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants","oa_version":"Preprint","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology / methods","data analysis / stars","oscillations"],"article_processing_charge":"No","day":"01","citation":{"apa":"Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Corsaro, E., Hall, O. J., & Rendle, B. M. (2018). FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833106","ieee":"L. A. Bugnet et al., “FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants,” Astronomy & Astrophysics, vol. 620. EDP Sciences, 2018.","ista":"Bugnet LA, García RA, Davies GR, Mathur S, Corsaro E, Hall OJ, Rendle BM. 2018. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 620, A38.","ama":"Bugnet LA, García RA, Davies GR, et al. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 2018;620. doi:10.1051/0004-6361/201833106","chicago":"Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, E. Corsaro, O. J. Hall, and B. M. Rendle. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833106.","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, E. Corsaro, O.J. Hall, B.M. Rendle, Astronomy & Astrophysics 620 (2018).","mla":"Bugnet, Lisa Annabelle, et al. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics, vol. 620, A38, EDP Sciences, 2018, doi:10.1051/0004-6361/201833106."},"publication":"Astronomy & Astrophysics","article_type":"original","date_published":"2018-12-01T00:00:00Z"},{"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"month":"08","doi":"10.1093/mnras/sty1390","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1805.01860","open_access":"1"}],"external_id":{"arxiv":["1805.01860"]},"quality_controlled":"1","extern":"1","author":[{"first_name":"V","last_name":"Van Eylen","full_name":"Van Eylen, V"},{"last_name":"Dai","first_name":"F","full_name":"Dai, F"},{"last_name":"Mathur","first_name":"S","full_name":"Mathur, S"},{"full_name":"Gandolfi, D","last_name":"Gandolfi","first_name":"D"},{"full_name":"Albrecht, S","last_name":"Albrecht","first_name":"S"},{"last_name":"Fridlund","first_name":"M","full_name":"Fridlund, M"},{"full_name":"García, R A","last_name":"García","first_name":"R A"},{"first_name":"E","last_name":"Guenther","full_name":"Guenther, E"},{"first_name":"M","last_name":"Hjorth","full_name":"Hjorth, M"},{"last_name":"Justesen","first_name":"A B","full_name":"Justesen, A B"},{"full_name":"Livingston, J","first_name":"J","last_name":"Livingston"},{"full_name":"Lund, M N","first_name":"M N","last_name":"Lund"},{"first_name":"F","last_name":"Pérez Hernández","full_name":"Pérez Hernández, F"},{"full_name":"Prieto-Arranz, J","first_name":"J","last_name":"Prieto-Arranz"},{"full_name":"Regulo, C","last_name":"Regulo","first_name":"C"},{"full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000"},{"full_name":"Everett, M E","first_name":"M E","last_name":"Everett"},{"full_name":"Hirano, T","first_name":"T","last_name":"Hirano"},{"full_name":"Nespral, D","last_name":"Nespral","first_name":"D"},{"first_name":"G","last_name":"Nowak","full_name":"Nowak, G"},{"first_name":"E","last_name":"Palle","full_name":"Palle, E"},{"full_name":"Silva Aguirre, V","last_name":"Silva Aguirre","first_name":"V"},{"first_name":"T","last_name":"Trifonov","full_name":"Trifonov, T"},{"full_name":"Winn, J N","last_name":"Winn","first_name":"J N"},{"first_name":"O","last_name":"Barragán","full_name":"Barragán, O"},{"last_name":"Beck","first_name":"P G","full_name":"Beck, P G"},{"full_name":"Chaplin, W J","first_name":"W J","last_name":"Chaplin"},{"last_name":"Cochran","first_name":"W D","full_name":"Cochran, W D"},{"first_name":"S","last_name":"Csizmadia","full_name":"Csizmadia, S"},{"last_name":"Deeg","first_name":"H","full_name":"Deeg, H"},{"full_name":"Endl, M","first_name":"M","last_name":"Endl"},{"full_name":"Heeren, P","last_name":"Heeren","first_name":"P"},{"full_name":"Grziwa, S","first_name":"S","last_name":"Grziwa"},{"full_name":"Hatzes, A P","first_name":"A P","last_name":"Hatzes"},{"first_name":"D","last_name":"Hidalgo","full_name":"Hidalgo, D"},{"last_name":"Korth","first_name":"J","full_name":"Korth, J"},{"full_name":"Mathis, S","last_name":"Mathis","first_name":"S"},{"full_name":"Montañes Rodriguez, P","first_name":"P","last_name":"Montañes Rodriguez"},{"full_name":"Narita, N","first_name":"N","last_name":"Narita"},{"first_name":"M","last_name":"Patzold","full_name":"Patzold, M"},{"full_name":"Persson, C M","first_name":"C M","last_name":"Persson"},{"last_name":"Rodler","first_name":"F","full_name":"Rodler, F"},{"last_name":"Smith","first_name":"A M S","full_name":"Smith, A M S"}],"volume":478,"date_updated":"2022-08-22T07:45:38Z","date_created":"2022-07-18T14:43:17Z","acknowledgement":"We gratefully acknowledge many helpful suggestions by the anonymous referee. Based on observations made with a) the Nordic Optical Telescope, operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos; b) the ESO-3.6m telescope at La Silla Observatory under programme ID 0100.C-0808; c) the Italian Telescopio Nazionale Galileo operated on the island of La Palma by the Fundación Galileo Galilei of the Istituto Nazionale di Astrofisica. NESSI was funded by the NASA Exoplanet Exploration Program and the NASA Ames Research Center. NESSI was built at the Ames Research Center by Steve B. Howell, Nic Scott, Elliott P. Horch, and Emmett Quigley. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730890. This material reflects only the authors views and the Commission is not liable for any use that may be made of the information contained therein. DG gratefully acknowledges the financial support of the Programma Giovani Ricercatori – Rita Levi Montalcini – Rientro dei Cervelli (2012) awarded by the Italian Ministry of Education, Universities and Research (MIUR). SaM would like to acknowledge support from the Ramon y Cajal fellowship number RYC-2015-17697. AJ, MH, and SA acknowledge support by the Danish Council for Independent Research, through a DFF Sapere Aude Starting Grant nr. 4181-00487B. SzCs, APH, MP, and HR acknowledge the support of the DFG priority program SPP 1992Exploring the Diversity of Extrasolar Planets (grants HA 3279/12-1, PA 525/18-1, PA5 25/19-1 and PA525/20-1, RA 714/14-1) HD, CR, and FPH acknowledge the financial support from MINECO under grants ESP2015-65712-C5-4-R and AYA2016-76378-P. This paper has made use of the IAC Supercomputing facility HTCondor (http://research.cs.wisc.edu/htcondor/), partly financed by the Ministry of Economy and Competitiveness with FEDER funds, code IACA13-3E-2493. MF and CMP gratefully acknowledge the support of the Swedish National Space Board. RAG and StM thanks the support of the CNES PLATO grant. PGB is a postdoctoral fellow in the MINECO-programme ’Juan de la Cierva Incorporacion’ (IJCI-2015-26034). StM acknowledges support from ERC through SPIRE grant (647383) and from ISSI through the ENCELADE 2.0 team. VSA acknowledges support from VILLUM FONDEN (research grant 10118). MNL acknowledges support from the ESA-PRODEX programme. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (Grant agreement no.: DNRF106) This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This research was made with the use of NASA’s Astrophysics Data System and the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program.","year":"2018","publisher":"Oxford University Press","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics","asteroseismology","planets and satellites: composition","planets and satellites: formation","planets and satellites: fundamental parameters"],"date_published":"2018-08-01T00:00:00Z","citation":{"chicago":"Van Eylen, V, F Dai, S Mathur, D Gandolfi, S Albrecht, M Fridlund, R A García, et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1390.","mla":"Van Eylen, V., et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4, Oxford University Press, 2018, pp. 4866–80, doi:10.1093/mnras/sty1390.","short":"V. Van Eylen, F. Dai, S. Mathur, D. Gandolfi, S. Albrecht, M. Fridlund, R.A. García, E. Guenther, M. Hjorth, A.B. Justesen, J. Livingston, M.N. Lund, F. Pérez Hernández, J. Prieto-Arranz, C. Regulo, L.A. Bugnet, M.E. Everett, T. Hirano, D. Nespral, G. Nowak, E. Palle, V. Silva Aguirre, T. Trifonov, J.N. Winn, O. Barragán, P.G. Beck, W.J. Chaplin, W.D. Cochran, S. Csizmadia, H. Deeg, M. Endl, P. Heeren, S. Grziwa, A.P. Hatzes, D. Hidalgo, J. Korth, S. Mathis, P. Montañes Rodriguez, N. Narita, M. Patzold, C.M. Persson, F. Rodler, A.M.S. Smith, Monthly Notices of the Royal Astronomical Society 478 (2018) 4866–4880.","ista":"Van Eylen V, Dai F, Mathur S, Gandolfi D, Albrecht S, Fridlund M, García RA, Guenther E, Hjorth M, Justesen AB, Livingston J, Lund MN, Pérez Hernández F, Prieto-Arranz J, Regulo C, Bugnet LA, Everett ME, Hirano T, Nespral D, Nowak G, Palle E, Silva Aguirre V, Trifonov T, Winn JN, Barragán O, Beck PG, Chaplin WJ, Cochran WD, Csizmadia S, Deeg H, Endl M, Heeren P, Grziwa S, Hatzes AP, Hidalgo D, Korth J, Mathis S, Montañes Rodriguez P, Narita N, Patzold M, Persson CM, Rodler F, Smith AMS. 2018. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 478(4), 4866–4880.","apa":"Van Eylen, V., Dai, F., Mathur, S., Gandolfi, D., Albrecht, S., Fridlund, M., … Smith, A. M. S. (2018). HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1390","ieee":"V. Van Eylen et al., “HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4. Oxford University Press, pp. 4866–4880, 2018.","ama":"Van Eylen V, Dai F, Mathur S, et al. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 2018;478(4):4866-4880. doi:10.1093/mnras/sty1390"},"publication":"Monthly Notices of the Royal Astronomical Society","page":"4866-4880","article_type":"original","issue":"4","abstract":[{"text":"We report the discovery and characterization of HD 89345b (K2-234b; EPIC 248777106b), a Saturn-sized planet orbiting a slightly evolved star. HD 89345 is a bright star (V = 9.3 mag) observed by the K2 mission with 1 min time sampling. It exhibits solar-like oscillations. We conducted asteroseismology to determine the parameters of the star, finding the mass and radius to be 1.12+0.04−0.01M⊙ and 1.657+0.020−0.004R⊙, respectively. The star appears to have recently left the main sequence, based on the inferred age, 9.4+0.4−1.3Gyr, and the non-detection of mixed modes. The star hosts a ‘warm Saturn’ (P = 11.8 d, Rp = 6.86 ± 0.14 R⊕). Radial-velocity follow-up observations performed with the FIbre-fed Echelle Spectrograph, HARPS, and HARPS-N spectrographs show that the planet has a mass of 35.7 ± 3.3 M⊕. The data also show that the planet’s orbit is eccentric (e ≈ 0.2). An investigation of the rotational splitting of the oscillation frequencies of the star yields no conclusive evidence on the stellar inclination angle. We further obtained Rossiter–McLaughlin observations, which result in a broad posterior of the stellar obliquity. The planet seems to confirm to the same patterns that have been observed for other sub-Saturns regarding planet mass and multiplicity, orbital eccentricity, and stellar metallicity.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"11620","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 478","title":"HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2","status":"public"},{"type":"preprint","article_number":"1811.12140","abstract":[{"lang":"eng","text":"The recently launched NASA Transiting Exoplanet Survey Satellite (TESS) mission is going to collect lightcurves for a few hundred million of stars and we expect to increase the number of pulsating stars to analyze compared to the few thousand stars observed by the CoRoT, Kepler and K2 missions. However, most of the TESS targets have not yet been properly classified and characterized. In order to improve the analysis of the TESS data, it is crucial to determine the type of stellar pulsations in a timely manner. We propose an automatic method to classify stars attending to their pulsation properties, in particular, to identify solar-like pulsators among all TESS targets. It relies on the use of the global amount of power contained in the power spectrum (already known as the FliPer method) as a key parameter, along with\r\nthe effective temperature, to feed into a machine learning classifier. Our study, based on TESS simulated datasets, shows that we are able to classify pulsators with a 98% accuracy."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11631","year":"2018","title":"FliPer: Classifying TESS pulsating stars","status":"public","publication_status":"submitted","author":[{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"},{"last_name":"García","first_name":"R. A.","full_name":"García, R. A."},{"first_name":"G. R.","last_name":"Davies","full_name":"Davies, G. R."},{"last_name":"Mathur","first_name":"S.","full_name":"Mathur, S."},{"full_name":"Hall, O. J.","first_name":"O. J.","last_name":"Hall"},{"full_name":"Rendle, B. M.","last_name":"Rendle","first_name":"B. M."}],"oa_version":"Preprint","date_updated":"2022-08-22T08:41:55Z","date_created":"2022-07-21T07:05:23Z","keyword":["asteroseismology - methods","data analysis - stars","oscillations"],"article_processing_charge":"No","day":"29","month":"11","external_id":{"arxiv":["1811.12140"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1811.12140"}],"oa":1,"citation":{"ista":"Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv, 1811.12140.","ieee":"L. A. Bugnet, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle, “FliPer: Classifying TESS pulsating stars,” arXiv. .","apa":"Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Hall, O. J., & Rendle, B. M. (n.d.). FliPer: Classifying TESS pulsating stars. arXiv. https://doi.org/10.48550/arXiv.1811.12140","ama":"Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv. doi:10.48550/arXiv.1811.12140","chicago":"Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1811.12140.","mla":"Bugnet, Lisa Annabelle, et al. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, 1811.12140, doi:10.48550/arXiv.1811.12140.","short":"L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, O.J. Hall, B.M. Rendle, ArXiv (n.d.)."},"publication":"arXiv","doi":"10.48550/arXiv.1811.12140","date_published":"2018-11-29T00:00:00Z","language":[{"iso":"eng"}]},{"publisher":"Association for Computing Machinery","publication_status":"published","year":"2018","volume":23,"date_created":"2022-07-27T08:28:26Z","date_updated":"2022-09-09T11:32:52Z","author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Noe, Alexander","last_name":"Noe","first_name":"Alexander"},{"full_name":"Schulz, Christian","last_name":"Schulz","first_name":"Christian"},{"full_name":"Strash, Darren","first_name":"Darren","last_name":"Strash"}],"extern":"1","quality_controlled":"1","external_id":{"arxiv":["1708.06127"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.06127"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3274662","publication_identifier":{"eissn":["1084-6654"],"issn":["1084-6654"]},"month":"10","intvolume":" 23","title":"Practical minimum cut algorithms","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11657","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi’s contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm runs a factor 7.5× faster on average when using 32 threads. To further speed up computations, we also give a version of our algorithm that performs random edge contractions as preprocessing. This version achieves a lower running time and better parallel scalability at the expense of a higher error rate."}],"page":"1-22","article_type":"original","citation":{"mla":"Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics, vol. 23, Association for Computing Machinery, 2018, pp. 1–22, doi:10.1145/3274662.","short":"M.H. Henzinger, A. Noe, C. Schulz, D. Strash, ACM Journal of Experimental Algorithmics 23 (2018) 1–22.","chicago":"Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics. Association for Computing Machinery, 2018. https://doi.org/10.1145/3274662.","ama":"Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 2018;23:1-22. doi:10.1145/3274662","ista":"Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 23, 1–22.","ieee":"M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” ACM Journal of Experimental Algorithmics, vol. 23. Association for Computing Machinery, pp. 1–22, 2018.","apa":"Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. Association for Computing Machinery. https://doi.org/10.1145/3274662"},"publication":"ACM Journal of Experimental Algorithmics","date_published":"2018-10-01T00:00:00Z","keyword":["Theoretical Computer Science"],"scopus_import":"1","article_processing_charge":"No","day":"01"},{"publication_identifier":{"issn":["2167-8375"],"eissn":["2167-8383"]},"month":"05","doi":"10.1145/3232860","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.3153"}],"external_id":{"arxiv":["1310.3153"]},"oa":1,"quality_controlled":"1","extern":"1","article_number":"5","author":[{"full_name":"Dütting, Paul","last_name":"Dütting","first_name":"Paul"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Starnberger, Martin","last_name":"Starnberger","first_name":"Martin"}],"volume":6,"date_created":"2022-07-27T11:46:46Z","date_updated":"2022-09-09T12:04:42Z","year":"2018","publisher":"Association for Computing Machinery","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Theory of computation","Algorithmic game theory and mechanism design","Applied computing","Economics","Simplified mechanisms","Combinatorial auctions with item bidding","Price of anarchy"],"date_published":"2018-05-01T00:00:00Z","citation":{"ista":"Dütting P, Henzinger MH, Starnberger M. 2018. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 6(2), 5.","ieee":"P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in VCG-based combinatorial auctions,” ACM Transactions on Economics and Computation, vol. 6, no. 2. Association for Computing Machinery, 2018.","apa":"Dütting, P., Henzinger, M. H., & Starnberger, M. (2018). Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/3232860","ama":"Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 2018;6(2). doi:10.1145/3232860","chicago":"Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2018. https://doi.org/10.1145/3232860.","mla":"Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation, vol. 6, no. 2, 5, Association for Computing Machinery, 2018, doi:10.1145/3232860.","short":"P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 6 (2018)."},"publication":"ACM Transactions on Economics and Computation","article_type":"original","issue":"2","abstract":[{"lang":"eng","text":"The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions, the truthful direct-revelation mechanism that maximizes social welfare is the Vickrey-Clarke-Groves mechanism. For many valuation spaces, computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that increased expressiveness can give rise to additional equilibria of poorer efficiency."}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11667","intvolume":" 6","status":"public","title":"Valuation compressions in VCG-based combinatorial auctions"},{"type":"journal_article","issue":"2","abstract":[{"text":"We present a deterministic incremental algorithm for exactly maintaining the size of a minimum cut with O(log3 n log log2 n) amortized time per edge insertion and O(1) query time. This result partially answers an open question posed by Thorup (2007). It also stays in sharp contrast to a polynomial conditional lower bound for the fully dynamic weighted minimum cut problem. Our algorithm is obtained by combining a sparsification technique of Kawarabayashi and Thorup (2015) or its recent improvement by Henzinger, Rao, and Wang (2017), and an exact incremental algorithm of Henzinger (1997).\r\n\r\nWe also study space-efficient incremental algorithms for the minimum cut problem. Concretely, we show that there exists an O(nlog n/ε2) space Monte Carlo algorithm that can process a stream of edge insertions starting from an empty graph, and with high probability, the algorithm maintains a (1+ε)-approximation to the minimum cut. The algorithm has O((α (n) log3 n)/ε 2) amortized update time and constant query time, where α (n) stands for the inverse of Ackermann function.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11664","intvolume":" 14","title":"Incremental exact min-cut in polylogarithmic amortized update time","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"mla":"Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms, vol. 14, no. 2, 17, Association for Computing Machinery, 2018, doi:10.1145/3174803.","short":"G. Goranci, M.H. Henzinger, M. Thorup, ACM Transactions on Algorithms 14 (2018).","chicago":"Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms. Association for Computing Machinery, 2018. https://doi.org/10.1145/3174803.","ama":"Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 2018;14(2). doi:10.1145/3174803","ista":"Goranci G, Henzinger MH, Thorup M. 2018. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 14(2), 17.","ieee":"G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in polylogarithmic amortized update time,” ACM Transactions on Algorithms, vol. 14, no. 2. Association for Computing Machinery, 2018.","apa":"Goranci, G., Henzinger, M. H., & Thorup, M. (2018). Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3174803"},"publication":"ACM Transactions on Algorithms","article_type":"original","date_published":"2018-04-01T00:00:00Z","article_number":"17","extern":"1","year":"2018","acknowledgement":"We thank the two anonymous reviewers for their suggestions and comments, which improved the\r\nquality of the article.","publisher":"Association for Computing Machinery","publication_status":"published","author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Thorup","first_name":"Mikkel","full_name":"Thorup, Mikkel"}],"volume":14,"date_created":"2022-07-27T11:29:39Z","date_updated":"2022-09-09T11:38:14Z","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"month":"04","external_id":{"arxiv":["1611.06500"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1611.06500","open_access":"1"}],"quality_controlled":"1","doi":"10.1145/3174803","language":[{"iso":"eng"}]},{"issue":"08","abstract":[{"lang":"eng","text":"We develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an O ( f 2)-approximately optimal solution in O ( f · log(m + n)) amortized update time, where f is the maximum “frequency” of an element, n is the number of sets, and m is the maximum number of elements in the universe at any point in time. (2) For the dynamic b-matching problem, we maintain an O (1)-approximately optimal solution in O (log3 n) amortized update time, where n is the number of nodes in the graph."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 261","title":"Dynamic algorithms via the primal-dual method","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11757","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","page":"219-239","article_type":"original","citation":{"chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe Italiano. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation. Elsevier, 2018. https://doi.org/10.1016/j.ic.2018.02.005.","mla":"Bhattacharya, Sayan, et al. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation, vol. 261, no. 08, Elsevier, 2018, pp. 219–39, doi:10.1016/j.ic.2018.02.005.","short":"S. Bhattacharya, M.H. Henzinger, G. Italiano, Information and Computation 261 (2018) 219–239.","ista":"Bhattacharya S, Henzinger MH, Italiano G. 2018. Dynamic algorithms via the primal-dual method. Information and Computation. 261(08), 219–239.","ieee":"S. Bhattacharya, M. H. Henzinger, and G. Italiano, “Dynamic algorithms via the primal-dual method,” Information and Computation, vol. 261, no. 08. Elsevier, pp. 219–239, 2018.","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. (2018). Dynamic algorithms via the primal-dual method. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2018.02.005","ama":"Bhattacharya S, Henzinger MH, Italiano G. Dynamic algorithms via the primal-dual method. Information and Computation. 2018;261(08):219-239. doi:10.1016/j.ic.2018.02.005"},"publication":"Information and Computation","extern":"1","volume":261,"date_updated":"2023-02-10T07:27:39Z","date_created":"2022-08-08T11:20:03Z","author":[{"last_name":"Bhattacharya","first_name":"Sayan","full_name":"Bhattacharya, Sayan"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Italiano, Giuseppe","last_name":"Italiano","first_name":"Giuseppe"}],"publisher":"Elsevier","publication_status":"published","year":"2018","publication_identifier":{"issn":["0890-5401"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2018.02.005","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.ic.2018.02.005","open_access":"1"}],"oa":1},{"article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2018-08-14T00:00:00Z","citation":{"ieee":"G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and approximate schur complement on separable graphs,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112.","apa":"Goranci, G., Henzinger, M. H., & Peng, P. (2018). Dynamic effective resistances and approximate schur complement on separable graphs. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.40","ista":"Goranci G, Henzinger MH, Peng P. 2018. Dynamic effective resistances and approximate schur complement on separable graphs. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 40.","ama":"Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate schur complement on separable graphs. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.40","chicago":"Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.40.","short":"G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” 26th Annual European Symposium on Algorithms, vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.40."},"publication":"26th Annual European Symposium on Algorithms","abstract":[{"lang":"eng","text":"We consider the problem of dynamically maintaining (approximate) all-pairs effective resistances in separable graphs, which are those that admit an n^{c}-separator theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations of the all-pairs effective resistances of an n-vertex graph G undergoing edge insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable (i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its separator can be computed in O~(n) time. Our algorithm is built upon a dynamic algorithm for maintaining approximate Schur complement that approximately preserves pairwise effective resistances among a set of terminals for separable graphs, which might be of independent interest.\r\nWe complement our result by proving that for any two fixed vertices s and t, no incremental or decremental algorithm can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further show that for general graphs, no incremental or decremental algorithm can maintain the s-t effective resistance problem with worst-case update time O(n^{1-delta}) and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false."}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","_id":"11828","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","title":"Dynamic effective resistances and approximate schur complement on separable graphs","status":"public","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959770811"]},"month":"08","doi":"10.4230/LIPICS.ESA.2018.40","conference":{"name":"ESA: Annual European Symposium on Algorithms","end_date":"2018-08-22","start_date":"2018-08-20","location":"Helsinki, Finland"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1802.09111"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2018.40"}],"oa":1,"quality_controlled":"1","extern":"1","article_number":"40","author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Peng, Pan","last_name":"Peng","first_name":"Pan"}],"volume":112,"date_updated":"2023-02-16T11:08:08Z","date_created":"2022-08-12T08:26:42Z","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published"},{"scopus_import":"1","article_processing_charge":"No","day":"14","citation":{"ista":"Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 39.","ieee":"G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic facility location,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112.","apa":"Goranci, G., Henzinger, M. H., & Leniowski, D. (2018). A tree structure for dynamic facility location. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.39","ama":"Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility location. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.39","chicago":"Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure for Dynamic Facility Location.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.39.","mla":"Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” 26th Annual European Symposium on Algorithms, vol. 112, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.39.","short":"G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"publication":"26th Annual European Symposium on Algorithms","date_published":"2018-08-14T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"We study the metric facility location problem with client insertions and deletions. This setting differs from the classic dynamic facility location problem, where the set of clients remains the same, but the metric space can change over time. We show a deterministic algorithm that maintains a constant factor approximation to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion or deletion in metric spaces while answering queries about the cost in O(1) time, where kappa denotes the doubling dimension of the metric. For metric spaces with bounded doubling dimension, the update time is polylogarithmic in the parameters of the problem.","lang":"eng"}],"_id":"11827","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","title":"A tree structure for dynamic facility location","status":"public","oa_version":"Published Version","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959770811"]},"month":"08","oa":1,"main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.ESA.2018.39","open_access":"1"}],"external_id":{"arxiv":["1909.06653"]},"quality_controlled":"1","doi":"10.4230/LIPICS.ESA.2018.39","conference":{"end_date":"2018-08-22","start_date":"2018-08-20","location":"Helsinki, Finland","name":"ESA: Annual European Symposium on Algorithms"},"language":[{"iso":"eng"}],"article_number":"39","extern":"1","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"first_name":"Gramoz ","last_name":"Goranci","full_name":"Goranci, Gramoz "},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"last_name":"Leniowski","first_name":"Dariusz","full_name":"Leniowski, Dariusz"}],"volume":112,"date_updated":"2023-02-16T10:50:51Z","date_created":"2022-08-12T08:20:57Z"},{"month":"12","publication_identifier":{"eissn":["1557-735X"],"issn":["0004-5411"]},"doi":"10.1145/3218657","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1512.08148","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1512.08148"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"last_name":"Krinninger","first_name":"Sebastian","full_name":"Krinninger, Sebastian"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"related_material":{"record":[{"id":"11855","status":"public","relation":"earlier_version"}]},"date_created":"2022-08-08T12:33:17Z","date_updated":"2023-02-21T16:30:41Z","volume":65,"year":"2018","publication_status":"published","publisher":"Association for Computing Machinery","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-12-01T00:00:00Z","publication":"Journal of the ACM","citation":{"ista":"Henzinger MH, Krinninger S, Nanongkai D. 2018. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 65(6), 1–40.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” Journal of the ACM, vol. 65, no. 6. Association for Computing Machinery, pp. 1–40, 2018.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2018). Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. Association for Computing Machinery. https://doi.org/10.1145/3218657","ama":"Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 2018;65(6):1-40. doi:10.1145/3218657","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM. Association for Computing Machinery, 2018. https://doi.org/10.1145/3218657.","mla":"Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM, vol. 65, no. 6, Association for Computing Machinery, 2018, pp. 1–40, doi:10.1145/3218657.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, Journal of the ACM 65 (2018) 1–40."},"article_type":"original","page":"1-40","abstract":[{"lang":"eng","text":"In the decremental single-source shortest paths (SSSP) problem, we want to maintain the distances between a given source node s and every other node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach [16] has been the fastest known algorithm for three decades. At the cost of a (1+ϵ)-approximation factor, the running time was recently improved to n2+o(1) by Bernstein and Roditty [9]. In this article, we bring the running time down to near-linear: We give a (1+ϵ)-approximation algorithm with m1+o(1) expected total update time, thus obtaining near-linear time. Moreover, we obtain m1+o(1) log W time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn) time is the mn0.9 + o(1)-time algorithm by Henzinger et al. [18, 19], which works for directed graphs with quasi-polynomial edge weights. The expected running time bound of our algorithm holds against an oblivious adversary.\r\n\r\nIn contrast to the previous results, which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (h, ϵ)-hop set introduced by Cohen [12] in the PRAM literature. An (h, ϵ)-hop set of a graph G=(V, E) is a set F of weighted edges such that the distance between any pair of nodes in G can be (1+ϵ)-approximated by their h-hop distance (given by a path containing at most h edges) on G′=(V, E ∪ F). Our algorithm can maintain an (no(1), ϵ)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain approximate distances using this hop set, we extend the monotone Even-Shiloach tree of Henzinger et al. [20] and combine it with the bounded-hop SSSP technique of Bernstein [4, 5] and Mądry [27]. These two new tools might be of independent interest."}],"issue":"6","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11768","status":"public","title":"Decremental single-source shortest paths on undirected graphs in near-linear total update time","intvolume":" 65"},{"publication":"29th Annual ACM-SIAM Symposium on Discrete Algorithms","external_id":{"arxiv":["1711.04355"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04355"}],"oa":1,"citation":{"mla":"Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20, doi:10.1137/1.9781611975031.1.","short":"S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20.","chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon Nanongkai. “Dynamic Algorithms for Graph Coloring.” In 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 1–20. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975031.1.","ama":"Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms for graph coloring. In: 29th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2018:1-20. doi:10.1137/1.9781611975031.1","ista":"Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1–20.","apa":"Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., & Nanongkai, D. (2018). Dynamic algorithms for graph coloring. In 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1–20). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975031.1","ieee":"S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic algorithms for graph coloring,” in 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 1–20."},"quality_controlled":"1","page":"1 - 20","conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"New Orleans, LA, United States","start_date":"2018-01-07","end_date":"2018-01-10"},"date_published":"2018-01-01T00:00:00Z","doi":"10.1137/1.9781611975031.1","language":[{"iso":"eng"}],"scopus_import":"1","day":"01","month":"01","article_processing_charge":"No","publication_identifier":{"eisbn":["978-161197503-1"]},"_id":"11872","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","status":"public","title":"Dynamic algorithms for graph coloring","publisher":"Society for Industrial and Applied Mathematics","author":[{"first_name":"Sayan","last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan"},{"last_name":"Chakrabarty","first_name":"Deeparnab","full_name":"Chakrabarty, Deeparnab"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"date_updated":"2023-02-17T11:39:01Z","date_created":"2022-08-16T12:07:14Z","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We design fast dynamic algorithms for proper vertex and edge colorings in a graph undergoing edge insertions and deletions. In the static setting, there are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently maintain such colorings in the dynamic setting as well. We get the following three results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex coloring with O(log Δ) expected amortized update time. (2) We present a deterministic algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized update time. (3) We present a simple, deterministic algorithm which maintains a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the recent O(Δ)-edge coloring algorithm with worst-case update time [4]."}],"extern":"1"},{"publication_status":"published","status":"public","title":"Practical minimum cut algorithms","publisher":"Society for Industrial and Applied Mathematics","year":"2018","_id":"11882","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T14:03:39Z","date_created":"2022-08-17T07:04:57Z","oa_version":"Preprint","author":[{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Noe, Alexander","first_name":"Alexander","last_name":"Noe"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"last_name":"Strash","first_name":"Darren","full_name":"Strash, Darren"}],"type":"conference","extern":"1","abstract":[{"lang":"eng","text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi's contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm shows good scalability."}],"quality_controlled":"1","page":"48-61","publication":"20th Workshop on Algorithm Engineering and Experiments","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.06127"}],"citation":{"chicago":"Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” In 20th Workshop on Algorithm Engineering and Experiments, 48–61. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975055.5.","short":"M.H. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61.","mla":"Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61, doi:10.1137/1.9781611975055.5.","apa":"Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. In 20th Workshop on Algorithm Engineering and Experiments (pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975055.5","ieee":"M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” in 20th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2018, pp. 48–61.","ista":"Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. 20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm Engineering and Experiments, 48–61.","ama":"Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. In: 20th Workshop on Algorithm Engineering and Experiments. Society for Industrial and Applied Mathematics; 2018:48-61. doi:10.1137/1.9781611975055.5"},"external_id":{"arxiv":["1708.06127"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2018-01-07","location":"New Orleans, LA, United States","end_date":"2018-01-08","name":"ALENEX: Symposium on Algorithm Engineering and Experiments"},"doi":"10.1137/1.9781611975055.5","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","month":"01","day":"01","publication_identifier":{"eisbn":["978-1-61197-505-5"]},"article_processing_charge":"No"},{"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"05","external_id":{"arxiv":["1412.1318"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1318"}],"quality_controlled":"1","doi":"10.1137/140998925","language":[{"iso":"eng"}],"extern":"1","year":"2018","publisher":"Society for Industrial & Applied Mathematics","publication_status":"published","related_material":{"record":[{"id":"11875","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Bhattacharya, Sayan","first_name":"Sayan","last_name":"Bhattacharya"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Italiano","first_name":"Giuseppe F.","full_name":"Italiano, Giuseppe F."}],"volume":47,"date_updated":"2023-02-21T16:31:30Z","date_created":"2022-08-17T08:21:23Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2018. https://doi.org/10.1137/140998925.","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing, vol. 47, no. 3, Society for Industrial & Applied Mathematics, 2018, pp. 859–87, doi:10.1137/140998925.","short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, SIAM Journal on Computing 47 (2018) 859–887.","ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2018. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 47(3), 859–887.","apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2018). Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140998925","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” SIAM Journal on Computing, vol. 47, no. 3. Society for Industrial & Applied Mathematics, pp. 859–887, 2018.","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 2018;47(3):859-887. doi:10.1137/140998925"},"publication":"SIAM Journal on Computing","page":"859-887","article_type":"original","date_published":"2018-05-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph 𝐺=(𝑉,𝐸), with |𝑉|=𝑛 and |𝐸|=𝑚, in 𝑜(𝑚‾‾√) time per update. In particular, for minimum vertex cover, we provide deterministic data structures for maintaining a (2+𝜖) approximation in 𝑂(log𝑛/𝜖2) amortized time per update. For maximum matching, we show how to maintain a (3+𝜖) approximation in 𝑂(min(𝑛√/𝜖,𝑚1/3/𝜖2) amortized time per update and a (4+𝜖) approximation in 𝑂(𝑚1/3/𝜖2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [in 42nd ACM Symposium on Theory of Computing, Cambridge, MA, ACM, 2010, pp. 457--464]."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11890","intvolume":" 47","title":"Deterministic fully dynamic data structures for vertex cover and matching","status":"public","oa_version":"Preprint"},{"month":"07","publication_identifier":{"isbn":["9783959770705"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"conference":{"name":"SEA: Symposium on Experimental Algorithms","end_date":"2018-07-29","start_date":"2018-07-27","location":"L'Aquila, Italy"},"doi":"10.4230/LIPICS.SEA.2018.3","quality_controlled":"1","external_id":{"arxiv":["1802.07034"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.4230/LIPICS.SEA.2018.3","open_access":"1"}],"extern":"1","article_number":"3","date_updated":"2023-02-16T11:45:14Z","date_created":"2022-08-18T06:49:40Z","volume":103,"author":[{"last_name":"Biedermann","first_name":"Sonja","full_name":"Biedermann, Sonja"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"first_name":"Bernhard","last_name":"Schuster","full_name":"Schuster, Bernhard"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","publication":"17th International Symposium on Experimental Algorithms","citation":{"ama":"Biedermann S, Henzinger MH, Schulz C, Schuster B. Memetic graph clustering. In: 17th International Symposium on Experimental Algorithms. Vol 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.SEA.2018.3","ista":"Biedermann S, Henzinger MH, Schulz C, Schuster B. 2018. Memetic graph clustering. 17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental Algorithms, LIPIcs, vol. 103, 3.","apa":"Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2018). Memetic graph clustering. In 17th International Symposium on Experimental Algorithms (Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SEA.2018.3","ieee":"S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Memetic graph clustering,” in 17th International Symposium on Experimental Algorithms, L’Aquila, Italy, 2018, vol. 103.","mla":"Biedermann, Sonja, et al. “Memetic Graph Clustering.” 17th International Symposium on Experimental Algorithms, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.SEA.2018.3.","short":"S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, 17th International Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Memetic Graph Clustering.” In 17th International Symposium on Experimental Algorithms, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.SEA.2018.3."},"abstract":[{"lang":"eng","text":"It is common knowledge that there is no single best strategy for graph clustering, which justifies a plethora of existing approaches. In this paper, we present a general memetic algorithm, VieClus, to tackle the graph clustering problem. This algorithm can be adapted to optimize different objective functions. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. We instantiate our scheme with local search for modularity and show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration using a small amount of time."}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","title":"Memetic graph clustering","status":"public","intvolume":" 103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11911"},{"language":[{"iso":"eng"}],"doi":"10.1002/anie.201712568","quality_controlled":"1","external_id":{"pmid":["29377383"]},"publication_identifier":{"eissn":[" 1521-3773"],"issn":["1433-7851"]},"month":"07","volume":57,"date_updated":"2023-02-21T10:09:18Z","date_created":"2022-08-24T10:57:25Z","author":[{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"},{"last_name":"Shalom","first_name":"Menny","full_name":"Shalom, Menny"},{"full_name":"Antonietti, Markus","first_name":"Markus","last_name":"Antonietti"},{"full_name":"Seeberger, Peter H.","last_name":"Seeberger","first_name":"Peter H."},{"full_name":"Gilmore, Kerry","last_name":"Gilmore","first_name":"Kerry"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2018","extern":"1","date_published":"2018-07-26T00:00:00Z","page":"9976-9979","article_type":"letter_note","citation":{"ama":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 2018;57(31):9976-9979. doi:10.1002/anie.201712568","apa":"Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., & Gilmore, K. (2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201712568","ieee":"B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous heterogeneous photocatalysis in serial micro-batch reactors,” Angewandte Chemie International Edition, vol. 57, no. 31. Wiley, pp. 9976–9979, 2018.","ista":"Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. 2018. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 57(31), 9976–9979.","short":"B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte Chemie International Edition 57 (2018) 9976–9979.","mla":"Pieber, Bartholomäus, et al. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” Angewandte Chemie International Edition, vol. 57, no. 31, Wiley, 2018, pp. 9976–79, doi:10.1002/anie.201712568.","chicago":"Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger, and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201712568."},"publication":"Angewandte Chemie International Edition","article_processing_charge":"No","day":"26","scopus_import":"1","oa_version":"None","intvolume":" 57","title":"Continuous heterogeneous photocatalysis in serial micro-batch reactors","status":"public","_id":"11958","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"31","abstract":[{"text":"Solid reagents, leaching catalysts, and heterogeneous photocatalysts are commonly employed in batch processes but are ill-suited for continuous-flow chemistry. Heterogeneous catalysts for thermal reactions are typically used in packed-bed reactors, which cannot be penetrated by light and thus are not suitable for photocatalytic reactions involving solids. We demonstrate that serial micro-batch reactors (SMBRs) allow for the continuous utilization of solid materials together with liquids and gases in flow. This technology was utilized to develop selective and efficient fluorination reactions using a modified graphitic carbon nitride heterogeneous catalyst instead of costly homogeneous metal polypyridyl complexes. The merger of this inexpensive, recyclable catalyst and the SMBR approach enables sustainable and scalable photocatalysis.","lang":"eng"}],"type":"journal_article"},{"issue":"2","abstract":[{"lang":"eng","text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus."}],"type":"journal_article","file":[{"file_size":671125,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:13Z","date_updated":"2020-07-14T12:44:39Z","checksum":"47686d58ec21c164540f1a980ff2163f","relation":"main_file","file_id":"5266"}],"oa_version":"Published Version","pubrep_id":"712","intvolume":" 31","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","ddc":["519"],"status":"public","_id":"1215","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":1,"date_published":"2018-06-01T00:00:00Z","page":"789-826","citation":{"chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2"},"publication":"Journal of Theoretical Probability","publist_id":"6119","file_date_updated":"2020-07-14T12:44:39Z","volume":31,"date_created":"2018-12-11T11:50:45Z","date_updated":"2021-01-12T06:49:09Z","author":[{"first_name":"Franco","last_name":"Flandoli","full_name":"Flandoli, Franco"},{"full_name":"Russo, Francesco","first_name":"Francesco","last_name":"Russo"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","first_name":"Giovanni A","last_name":"Zanco","full_name":"Zanco, Giovanni A"}],"department":[{"_id":"JaMa"}],"publisher":"Springer","publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","year":"2018","month":"06","language":[{"iso":"eng"}],"doi":"10.1007/s10959-016-0724-2","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"quality_controlled":"1","page":"405 - 421","publication":"Geochimica et Cosmochimica Acta","citation":{"chicago":"Waitukaitis, Scott R, Devin Schrader, Kazuhide Nagashima, Jemma Davidson, Timothy Mccoy, Harold Conolly Jr, and Dante Lauretta. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta. Elsevier, 2018. https://doi.org/10.1016/j.gca.2017.12.014.","short":"S.R. Waitukaitis, D. Schrader, K. Nagashima, J. Davidson, T. Mccoy, H. Conolly Jr, D. Lauretta, Geochimica et Cosmochimica Acta 223 (2018) 405–421.","mla":"Waitukaitis, Scott R., et al. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta, vol. 223, Elsevier, 2018, pp. 405–21, doi:10.1016/j.gca.2017.12.014.","apa":"Waitukaitis, S. R., Schrader, D., Nagashima, K., Davidson, J., Mccoy, T., Conolly Jr, H., & Lauretta, D. (2018). The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. Elsevier. https://doi.org/10.1016/j.gca.2017.12.014","ieee":"S. R. Waitukaitis et al., “The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system,” Geochimica et Cosmochimica Acta, vol. 223. Elsevier, pp. 405–421, 2018.","ista":"Waitukaitis SR, Schrader D, Nagashima K, Davidson J, Mccoy T, Conolly Jr H, Lauretta D. 2018. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 223, 405–421.","ama":"Waitukaitis SR, Schrader D, Nagashima K, et al. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 2018;223:405-421. doi:10.1016/j.gca.2017.12.014"},"language":[{"iso":"eng"}],"doi":"10.1016/j.gca.2017.12.014","date_published":"2018-02-15T00:00:00Z","day":"15","month":"02","status":"public","title":"The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system","publication_status":"published","intvolume":" 223","publisher":"Elsevier","_id":"124","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","date_created":"2018-12-11T11:44:45Z","date_updated":"2021-01-12T06:49:19Z","oa_version":"None","volume":223,"author":[{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"},{"first_name":"Devin","last_name":"Schrader","full_name":"Schrader, Devin"},{"full_name":"Nagashima, Kazuhide","last_name":"Nagashima","first_name":"Kazuhide"},{"last_name":"Davidson","first_name":"Jemma","full_name":"Davidson, Jemma"},{"last_name":"Mccoy","first_name":"Timothy","full_name":"Mccoy, Timothy"},{"last_name":"Conolly Jr","first_name":"Harold","full_name":"Conolly Jr, Harold"},{"full_name":"Lauretta, Dante","last_name":"Lauretta","first_name":"Dante"}],"type":"journal_article","extern":"1","abstract":[{"text":"By investigating the in situ chemical and O-isotope compositions of olivine in lightly sintered dust agglomerates from the early Solar System, we constrain their origins and the retention of dust in the protoplanetary disk. The grain sizes of silicates in these agglomeratic olivine (AO) chondrules indicate that the grain sizes of chondrule precursors in the Renazzo-like carbonaceous (CR) chondrites ranged from <1 to 80 µm. We infer this grain size range to be equivalent to the size range for dust in the early Solar System. AO chondrules may contain, but are not solely composed of, recycled fragments of earlier formed chondrules. They also contain 16O-rich olivine related to amoeboid olivine aggregates and represent the best record of chondrule-precursor materials. AO chondrules contain one or more large grains, sometimes similar to FeO-poor (type I) and/or FeO-rich (type II) chondrules, while others contain a type II chondrule core. These morphologies are consistent with particle agglomeration by electrostatic charging of grains during collision, a process that may explain solid agglomeration in the protoplanetary disk in the micrometer size regime. The petrographic, isotopic, and chemical compositions of AO chondrules are consistent with chondrule formation by large-scale shocks, bow shocks, and current sheets. The petrographic, isotopic, and chemical similarities between AO chondrules in CR chondrites and chondrule-like objects from comet 81P/Wild 2 indicate that comets contain AO chondrules. We infer that these AO chondrules likely formed in the inner Solar System and migrated to the comet forming region at least 3 Ma after the formation of the first Solar System solids. Observations made in this study imply that the protoplanetary disk retained a dusty disk at least ∼3.7 Ma after the formation of the first Solar System solids, longer than half of the dusty accretion disks observed around other stars.","lang":"eng"}],"publist_id":"7930"},{"_id":"125","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"A high-speed tracking algorithm for dense granular media","status":"public","publication_status":"published","publisher":"Elsevier","intvolume":" 227","author":[{"first_name":"Mauricio","last_name":"Cerda","full_name":"Cerda, Mauricio"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"},{"last_name":"Navarro","first_name":"Cristóbal","full_name":"Navarro, Cristóbal"},{"last_name":"Silva","first_name":"Juan","full_name":"Silva, Juan"},{"full_name":"Mujica, Nicolás","last_name":"Mujica","first_name":"Nicolás"},{"full_name":"Hitschfeld, Nancy","last_name":"Hitschfeld","first_name":"Nancy"}],"date_created":"2018-12-11T11:44:45Z","date_updated":"2021-01-12T06:49:23Z","volume":227,"oa_version":"None","type":"journal_article","abstract":[{"text":"Many fields of study, including medical imaging, granular physics, colloidal physics, and active matter, require the precise identification and tracking of particle-like objects in images. While many algorithms exist to track particles in diffuse conditions, these often perform poorly when particles are densely packed together—as in, for example, solid-like systems of granular materials. Incorrect particle identification can have significant effects on the calculation of physical quantities, which makes the development of more precise and faster tracking algorithms a worthwhile endeavor. In this work, we present a new tracking algorithm to identify particles in dense systems that is both highly accurate and fast. We demonstrate the efficacy of our approach by analyzing images of dense, solid-state granular media, where we achieve an identification error of 5% in the worst evaluated cases. Going further, we propose a parallelization strategy for our algorithm using a GPU, which results in a speedup of up to 10× when compared to a sequential CPU implementation in C and up to 40× when compared to the reference MATLAB library widely used for particle tracking. Our results extend the capabilities of state-of-the-art particle tracking methods by allowing fast, high-fidelity detection in dense media at high resolutions.","lang":"eng"}],"publist_id":"7928","extern":"1","publication":"Computer Physics Communications","citation":{"ama":"Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 2018;227:8-16. doi:10.1016/j.cpc.2018.02.010","ista":"Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. 2018. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 227, 8–16.","ieee":"M. Cerda, S. R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, and N. Hitschfeld, “A high-speed tracking algorithm for dense granular media,” Computer Physics Communications, vol. 227. Elsevier, pp. 8–16, 2018.","apa":"Cerda, M., Waitukaitis, S. R., Navarro, C., Silva, J., Mujica, N., & Hitschfeld, N. (2018). A high-speed tracking algorithm for dense granular media. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.02.010","mla":"Cerda, Mauricio, et al. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications, vol. 227, Elsevier, 2018, pp. 8–16, doi:10.1016/j.cpc.2018.02.010.","short":"M. Cerda, S.R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, N. Hitschfeld, Computer Physics Communications 227 (2018) 8–16.","chicago":"Cerda, Mauricio, Scott R Waitukaitis, Cristóbal Navarro, Juan Silva, Nicolás Mujica, and Nancy Hitschfeld. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications. Elsevier, 2018. https://doi.org/10.1016/j.cpc.2018.02.010."},"quality_controlled":"1","page":"8 - 16","date_published":"2018-06-01T00:00:00Z","doi":"10.1016/j.cpc.2018.02.010","language":[{"iso":"eng"}],"day":"01","month":"06"},{"intvolume":" 121","publisher":"American Physical Society","title":"From bouncing to floating: the Leidenfrost effect with hydrogel spheres","publication_status":"published","status":"public","_id":"126","acknowledgement":"We acknowledge funding from the Netherlands Organization for Scientific Research through Grants VICI No. NWO- 680-47-609 (M. v. H. and S. W.) and VENI No. NWO-680- 47-453 (S. W.), and from the German Science Foundation through Grant No. HA8467/1-1 (K. H.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","volume":121,"oa_version":"None","date_updated":"2021-01-12T06:49:27Z","date_created":"2018-12-11T11:44:46Z","author":[{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"},{"full_name":"Harth, Kirsten","first_name":"Kirsten","last_name":"Harth"},{"full_name":"Van Hecke, Martin","last_name":"Van Hecke","first_name":"Martin"}],"type":"journal_article","article_number":"048001 ","extern":"1","issue":"4","publist_id":"7927","abstract":[{"text":"The Leidenfrost effect occurs when a liquid or stiff sublimable solid near a hot surface creates enough vapor beneath it to lift itself up and float. In contrast, vaporizable soft solids, e.g., hydrogels, have been shown to exhibit persistent bouncing - the elastic Leidenfrost effect. By carefully lowering hydrogel spheres towards a hot surface, we discover that they are also capable of floating. The bounce-to-float transition is controlled by the approach velocity and temperature, analogously to the "dynamic Leidenfrost effect." For the floating regime, we measure power-law scalings for the gap geometry, which we explain with a model that couples the vaporization rate to the spherical shape. Our results reveal that hydrogels are a promising pathway for controlling floating Leidenfrost objects through shape.","lang":"eng"}],"quality_controlled":"1","citation":{"mla":"Waitukaitis, Scott R., et al. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters, vol. 121, no. 4, 048001, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.048001.","short":"S.R. Waitukaitis, K. Harth, M. Van Hecke, Physical Review Letters 121 (2018).","chicago":"Waitukaitis, Scott R, Kirsten Harth, and Martin Van Hecke. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.048001.","ama":"Waitukaitis SR, Harth K, Van Hecke M. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 2018;121(4). doi:10.1103/PhysRevLett.121.048001","ista":"Waitukaitis SR, Harth K, Van Hecke M. 2018. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 121(4), 048001.","apa":"Waitukaitis, S. R., Harth, K., & Van Hecke, M. (2018). From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.048001","ieee":"S. R. Waitukaitis, K. Harth, and M. Van Hecke, “From bouncing to floating: the Leidenfrost effect with hydrogel spheres,” Physical Review Letters, vol. 121, no. 4. American Physical Society, 2018."},"publication":"Physical Review Letters","language":[{"iso":"eng"}],"date_published":"2018-07-25T00:00:00Z","doi":"10.1103/PhysRevLett.121.048001","day":"25","month":"07"},{"abstract":[{"lang":"eng","text":"The ideas of topology are breaking ground in origami-based metamaterials. Experiments now show that certain shapes — doughnuts included — exhibit topological bistability, and can be made to click between different topologically stable states."}],"issue":"8","publist_id":"7926","extern":"1","type":"journal_article","author":[{"first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"}],"date_created":"2018-12-11T11:44:46Z","date_updated":"2021-01-12T06:49:31Z","volume":14,"oa_version":"None","_id":"127","year":"2018","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Clicks for doughnuts","status":"public","intvolume":" 14","publisher":"Nature Publishing Group","month":"05","day":"28","doi":"10.1038/s41567-018-0160-6","date_published":"2018-05-28T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nature Physics","citation":{"short":"S.R. Waitukaitis, Nature Physics 14 (2018) 777–778.","mla":"Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 777–78, doi:10.1038/s41567-018-0160-6.","chicago":"Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0160-6.","ama":"Waitukaitis SR. Clicks for doughnuts. Nature Physics. 2018;14(8):777-778. doi:10.1038/s41567-018-0160-6","ieee":"S. R. Waitukaitis, “Clicks for doughnuts,” Nature Physics, vol. 14, no. 8. Nature Publishing Group, pp. 777–778, 2018.","apa":"Waitukaitis, S. R. (2018). Clicks for doughnuts. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0160-6","ista":"Waitukaitis SR. 2018. Clicks for doughnuts. 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Browning, in:, American Mathematical Society, 2018, pp. 89–102.","mla":"Browning, Timothy D. How Often Does the Hasse Principle Hold? Vol. 97, no. 2, American Mathematical Society, 2018, pp. 89–102, doi:10.1090/pspum/097.2/01700.","chicago":"Browning, Timothy D. “How Often Does the Hasse Principle Hold?,” 97:89–102. American Mathematical Society, 2018. https://doi.org/10.1090/pspum/097.2/01700.","ama":"Browning TD. How often does the Hasse principle hold? In: Vol 97. American Mathematical Society; 2018:89-102. doi:10.1090/pspum/097.2/01700","ieee":"T. D. Browning, “How often does the Hasse principle hold?,” presented at the Algebraic Geometry, Salt Lake City, Utah, USA, 2018, vol. 97, no. 2, pp. 89–102.","apa":"Browning, T. D. (2018). How often does the Hasse principle hold? (Vol. 97, pp. 89–102). Presented at the Algebraic Geometry, Salt Lake City, Utah, USA: American Mathematical Society. https://doi.org/10.1090/pspum/097.2/01700","ista":"Browning TD. 2018. How often does the Hasse principle hold? Algebraic Geometry, Proceedings of Symposia in Pure Mathematics, vol. 97, 89–102."},"page":"89 - 102","quality_controlled":"1","article_processing_charge":"No","day":"01","month":"01"},{"language":[{"iso":"eng"}],"doi":"10.1142/S1793042119500283","date_published":"2018-11-16T00:00:00Z","page":"547-567","article_type":"original","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04331"}],"citation":{"ama":"Browning TD, Sofos E. Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 2018;15(3):547-567. doi:10.1142/S1793042119500283","ieee":"T. D. Browning and E. Sofos, “Averages of arithmetic functions over principal ideals,” International Journal of Nuber Theory, vol. 15, no. 3. World Scientific Publishing, pp. 547–567, 2018.","apa":"Browning, T. D., & Sofos, E. (2018). Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 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The bound shows an explicit dependence on Q. It is optimal with respect to B, and is also optimal for typical forms Q.","lang":"eng"}],"intvolume":" 15","ddc":["512"],"status":"public","title":"Counting rational points on quadric surfaces","_id":"178","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","day":"07","page":"1 - 29","citation":{"short":"T.D. Browning, R. Heath-Brown, Discrete Analysis 15 (2018) 1–29.","mla":"Browning, Timothy D., and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis, vol. 15, Alliance of Diamond Open Access Journals, 2018, pp. 1–29, doi:10.19086/da.4375.","chicago":"Browning, Timothy D, and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis. Alliance of Diamond Open Access Journals, 2018. https://doi.org/10.19086/da.4375.","ama":"Browning TD, Heath-Brown R. Counting rational points on quadric surfaces. 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Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"ddc":["510"],"title":"Hanani-Tutte for approximating maps of graphs","status":"public","intvolume":" 99","_id":"185","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","date_created":"2018-12-17T12:33:52Z","date_updated":"2020-07-14T12:45:19Z","relation":"main_file","file_id":"5701","content_type":"application/pdf","file_size":718857,"creator":"dernst","access_level":"open_access","file_name":"2018_LIPIcs_Fulek.pdf"}],"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). 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Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99."},"date_published":"2018-01-01T00:00:00Z","article_number":"39","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"7735","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","date_created":"2018-12-11T11:45:04Z","date_updated":"2021-01-12T06:53:36Z","volume":99,"author":[{"last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"}],"month":"01","publication_identifier":{"isbn":["978-3-95977-066-8"]},"quality_controlled":"1","project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary"},"doi":"10.4230/LIPIcs.SoCG.2018.39"},{"date_published":"2018-06-11T00:00:00Z","page":"35:1 - 35:13","citation":{"mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","ieee":"H. Edelsbrunner, Z. Virk, and H. 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Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.35","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14"},"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","volume":99,"date_created":"2018-12-11T11:45:05Z","date_updated":"2021-01-12T06:53:48Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Virk, Ziga","first_name":"Ziga","last_name":"Virk"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2018","acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","publist_id":"7733","file_date_updated":"2020-07-14T12:45:20Z"},{"language":[{"iso":"eng"}],"doi":"10.1002/sta4.183","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0366"}],"oa":1,"external_id":{"arxiv":["1307.0366"]},"month":"04","volume":7,"date_updated":"2021-01-12T06:54:44Z","date_created":"2018-12-11T11:55:13Z","author":[{"full_name":"Raskutti, Garvesh","first_name":"Garvesh","last_name":"Raskutti"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline"}],"publisher":"Wiley","publication_status":"published","year":"2018","extern":"1","publist_id":"5061","article_number":"e183","date_published":"2018-04-17T00:00:00Z","article_type":"original","citation":{"ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183.","apa":"Raskutti, G., & Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. STAT. Wiley. https://doi.org/10.1002/sta4.183","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” STAT, vol. 7, no. 1. Wiley, 2018.","ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. STAT. 2018;7(1). doi:10.1002/sta4.183","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT. Wiley, 2018. https://doi.org/10.1002/sta4.183.","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” STAT, vol. 7, no. 1, e183, Wiley, 2018, doi:10.1002/sta4.183.","short":"G. Raskutti, C. Uhler, STAT 7 (2018)."},"publication":"STAT","article_processing_charge":"No","day":"17","oa_version":"Preprint","intvolume":" 7","title":"Learning directed acyclic graphs based on sparsest permutations","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2015","issue":"1","abstract":[{"text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size.","lang":"eng"}],"type":"journal_article"},{"issue":"4","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","date_created":"2019-02-06T07:36:24Z","date_updated":"2020-07-14T12:45:59Z","access_level":"open_access","file_name":"2018_Heliyon_DeMartino.pdf","content_type":"application/pdf","file_size":994490,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 4","title":"An introduction to the maximum entropy approach and its application to inference problems in biology","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"306","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2018-04-01T00:00:00Z","citation":{"ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596."},"publication":"Heliyon","ec_funded":1,"file_date_updated":"2020-07-14T12:45:59Z","article_number":"e00596","volume":4,"date_created":"2018-12-11T11:45:44Z","date_updated":"2021-01-12T07:40:46Z","author":[{"first_name":"Andrea","last_name":"De Martino","full_name":"De Martino, Andrea"},{"first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"}],"publisher":"Elsevier","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2018","month":"04","language":[{"iso":"eng"}],"doi":"10.1016/j.heliyon.2018.e00596","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"month":"06","day":"08","publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"article_processing_charge":"No","scopus_import":"1","doi":"10.1007/978-3-319-10575-8","date_published":"2018-06-08T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8."},"quality_controlled":"1","page":"XLVIII, 1212","abstract":[{"text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools.","lang":"eng"}],"publist_id":"3340","type":"book","place":"Cham","author":[{"last_name":"Clarke","first_name":"Edmund M.","full_name":"Clarke, Edmund M."},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"}],"edition":"1","date_created":"2018-12-11T12:02:32Z","date_updated":"2021-12-21T10:49:36Z","oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"3300","year":"2018","title":"Handbook of Model Checking","status":"public","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}]},{"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"intvolume":" 1863","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"37","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4906815,"file_name":"2018_MIMB_Zagorski.pdf","access_level":"open_access","date_created":"2020-10-13T14:20:37Z","date_updated":"2020-10-13T14:20:37Z","success":1,"checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","file_id":"8656","relation":"main_file"}],"series_title":"MIMB","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"16","page":"47 - 63","citation":{"ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63."},"publication":"Morphogen Gradients ","date_published":"2018-10-16T00:00:00Z","ec_funded":1,"publist_id":"8018","file_date_updated":"2020-10-13T14:20:37Z","department":[{"_id":"AnKi"}],"publisher":"Springer Nature","publication_status":"published","year":"2018","volume":1863,"date_created":"2018-12-11T11:44:17Z","date_updated":"2021-01-12T07:49:03Z","author":[{"first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"}],"publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"month":"10","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-8772-6_4"},{"abstract":[{"lang":"eng","text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks."}],"type":"journal_article","alternative_title":["MIMB"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"305","intvolume":" 1771","title":"Fabrication and operation of microfluidic hanging drop networks","status":"public","day":"01","scopus_import":1,"date_published":"2018-01-01T00:00:00Z","citation":{"ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202."},"publication":"Methods in Molecular Biology","page":"183 - 202","publist_id":"7574","ec_funded":1,"author":[{"full_name":"Misun, Patrick","last_name":"Misun","first_name":"Patrick"},{"last_name":"Birchler","first_name":"Axel","full_name":"Birchler, Axel"},{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Hierlemann, Andreas","last_name":"Hierlemann","first_name":"Andreas"},{"last_name":"Frey","first_name":"Olivier","full_name":"Frey, Olivier"}],"volume":1771,"date_updated":"2021-01-12T07:40:42Z","date_created":"2018-12-11T11:45:43Z","year":"2018","acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Springer","publication_status":"published","month":"01","doi":"10.1007/978-1-4939-7792-5_15","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1"},{"issue":"POPL","abstract":[{"lang":"eng","text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach."}],"type":"conference","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"325","intvolume":" 2","status":"public","title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","day":"01","date_published":"2018-01-01T00:00:00Z","citation":{"ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122."},"publist_id":"7540","article_number":"34","author":[{"full_name":"Agrawal, Sheshansh","first_name":"Sheshansh","last_name":"Agrawal"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"}],"volume":2,"date_created":"2018-12-11T11:45:50Z","date_updated":"2021-01-12T07:42:07Z","year":"2018","publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","month":"01","doi":"10.1145/3158122","conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, USA","start_date":"2018-01-07","name":"POPL: Principles of Programming Languages"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1709.04037","open_access":"1"}],"external_id":{"arxiv":["1709.04037"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1"},{"extern":"1","issue":"1","publist_id":"7435","abstract":[{"text":"The valley pseudospin in monolayer transition metal dichalcogenides (TMDs) has been proposed as a new way to manipulate information in various optoelectronic devices. This relies on a large valley polarization that remains stable over long time scales (hundreds of nanoseconds). However, time-resolved measurements report valley lifetimes of only a few picoseconds. This has been attributed to mechanisms such as phonon-mediated intervalley scattering and a precession of the valley pseudospin through electron-hole exchange. Here we use transient spin grating to directly measure the valley depolarization lifetime in monolayer MoSe2. We find a fast valley decay rate that scales linearly with the excitation density at different temperatures. This establishes the presence of strong exciton-exciton Coulomb exchange interactions enhancing the valley depolarization. Our work highlights the microscopic processes inhibiting the efficient use of the exciton valley pseudospin in monolayer TMDs. ","lang":"eng"}],"type":"journal_article","volume":18,"oa_version":"Submitted Version","date_updated":"2021-01-12T07:53:20Z","date_created":"2018-12-11T11:46:13Z","author":[{"first_name":"Fahad","last_name":"Mahmood","full_name":"Mahmood, Fahad"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"},{"full_name":"Lee, Yi","last_name":"Lee","first_name":"Yi"},{"full_name":"Kong, Jing","first_name":"Jing","last_name":"Kong"},{"full_name":"Gedik, Nuh","first_name":"Nuh","last_name":"Gedik"}],"publisher":"American Chemical Society","intvolume":" 18","title":"Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"394","year":"2018","day":"10","month":"01","language":[{"iso":"eng"}],"date_published":"2018-01-10T00:00:00Z","doi":"10.1021/acs.nanolett.7b03953","page":"223 - 228","quality_controlled":"1","external_id":{"arxiv":["1712.07925"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.07925"}],"citation":{"mla":"Mahmood, Fahad, et al. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters, vol. 18, no. 1, American Chemical Society, 2018, pp. 223–28, doi:10.1021/acs.nanolett.7b03953.","short":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, N. Gedik, Nano Letters 18 (2018) 223–228.","chicago":"Mahmood, Fahad, Zhanybek Alpichshev, Yi Lee, Jing Kong, and Nuh Gedik. “Observation of Exciton-Exciton Interaction Mediated Valley Depolarization in Monolayer MoSe2.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.7b03953.","ama":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 2018;18(1):223-228. doi:10.1021/acs.nanolett.7b03953","ista":"Mahmood F, Alpichshev Z, Lee Y, Kong J, Gedik N. 2018. Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. 18(1), 223–228.","apa":"Mahmood, F., Alpichshev, Z., Lee, Y., Kong, J., & Gedik, N. (2018). Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.7b03953","ieee":"F. Mahmood, Z. Alpichshev, Y. Lee, J. Kong, and N. Gedik, “Observation of exciton-exciton interaction mediated valley Depolarization in Monolayer MoSe2,” Nano Letters, vol. 18, no. 1. American Chemical Society, pp. 223–228, 2018."},"oa":1,"publication":"Nano Letters"},{"pmid":1,"year":"2018","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Trinh, Hoang","last_name":"Trinh","first_name":"Hoang"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"volume":1761,"date_updated":"2021-01-12T07:54:21Z","date_created":"2018-12-11T11:46:18Z","publist_id":"7421","external_id":{"pmid":["29525951"]},"quality_controlled":"1","doi":"10.1007/978-1-4939-7747-5_7","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1064-3745"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"408","intvolume":" 1761","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","status":"public","oa_version":"None","type":"book_chapter","alternative_title":["MIMB"],"abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"citation":{"short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102."},"publication":"Root Development ","page":"95 - 102","date_published":"2018-03-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"day":"11","month":"03","scopus_import":1,"series_title":"MIMB","date_published":"2018-03-11T00:00:00Z","doi":"10.1007/978-1-4939-7747-5_10","language":[{"iso":"eng"}],"citation":{"chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10"},"publication":"Root Development. Methods and Protocols","page":"131 - 143","quality_controlled":"1","publist_id":"7418","abstract":[{"text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.","lang":"eng"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"volume":1761,"oa_version":"None","date_updated":"2021-01-12T07:54:34Z","date_created":"2018-12-11T11:46:20Z","year":"2018","_id":"411","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"publisher":"Springer","editor":[{"full_name":"Ristova, Daniela","last_name":"Ristova","first_name":"Daniela"},{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"}],"intvolume":" 1761","title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","publication_status":"published","status":"public"},{"status":"public","publication_status":"published","title":"Zika-associated microcephaly: Reduce the stress and race for the treatment","publisher":"American Association for the Advancement of Science","intvolume":" 10","department":[{"_id":"GaNo"}],"_id":"456","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2018","date_created":"2018-12-11T11:46:34Z","date_updated":"2021-01-12T07:59:42Z","volume":10,"oa_version":"None","author":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"article_number":"eaar7514","type":"journal_article","abstract":[{"lang":"eng","text":"Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. "}],"issue":"423","publist_id":"7365","quality_controlled":"1","publication":"Science Translational Medicine","citation":{"chicago":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/scitranslmed.aar7514.","mla":"Novarino, Gaia. “Zika-Associated Microcephaly: Reduce the Stress and Race for the Treatment.” Science Translational Medicine, vol. 10, no. 423, eaar7514, American Association for the Advancement of Science, 2018, doi:10.1126/scitranslmed.aar7514.","short":"G. Novarino, Science Translational Medicine 10 (2018).","ista":"Novarino G. 2018. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 10(423), eaar7514.","apa":"Novarino, G. (2018). Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aar7514","ieee":"G. Novarino, “Zika-associated microcephaly: Reduce the stress and race for the treatment,” Science Translational Medicine, vol. 10, no. 423. American Association for the Advancement of Science, 2018.","ama":"Novarino G. Zika-associated microcephaly: Reduce the stress and race for the treatment. Science Translational Medicine. 2018;10(423). doi:10.1126/scitranslmed.aar7514"},"language":[{"iso":"eng"}],"date_published":"2018-01-10T00:00:00Z","doi":"10.1126/scitranslmed.aar7514","scopus_import":1,"month":"01","day":"10"},{"file_date_updated":"2020-07-14T12:46:38Z","publist_id":"8001","author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","first_name":"Barbara","last_name":"Petritsch","full_name":"Petritsch, Barbara"},{"last_name":"Porsche","first_name":"Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","full_name":"Porsche, Jana"}],"date_updated":"2021-01-12T08:01:26Z","date_created":"2018-12-11T11:44:22Z","volume":71,"year":"2018","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","month":"10","doi":"10.31263/voebm.v71i1.1993","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5702","relation":"main_file","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-17T12:40:27Z","checksum":"7ac61bade5f37db011ca435ebcf86797","file_name":"2018_VOEB_Petritsch.pdf","access_level":"open_access","creator":"dernst","file_size":509434,"content_type":"application/pdf"}],"_id":"53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["020"],"title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","intvolume":" 71","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2018-10-01T00:00:00Z","publication":"VÖB Mitteilungen","citation":{"mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206.","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018."},"page":"199 - 206"},{"abstract":[{"text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"creator":"dernst","file_size":595707,"content_type":"application/pdf","file_name":"2017_DistribComp_Alistarh.pdf","access_level":"open_access","date_created":"2019-01-22T07:25:51Z","date_updated":"2020-07-14T12:46:38Z","checksum":"69b46e537acdcac745237ddb853fcbb5","file_id":"5867","relation":"main_file"}],"oa_version":"Published Version","status":"public","title":"Communication-efficient randomized consensus","ddc":["000"],"intvolume":" 31","_id":"536","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":1,"date_published":"2018-11-01T00:00:00Z","page":"489-501","publication":"Distributed Computing","citation":{"ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501."},"file_date_updated":"2020-07-14T12:46:38Z","publist_id":"7281","date_created":"2018-12-11T11:47:01Z","date_updated":"2023-02-23T12:23:25Z","volume":31,"author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","last_name":"Aspnes","full_name":"Aspnes, James"},{"last_name":"King","first_name":"Valerie","full_name":"King, Valerie"},{"last_name":"Saia","first_name":"Jared","full_name":"Saia, Jared"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"DaAl"}],"year":"2018","month":"11","publication_identifier":{"issn":["01782770"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00446-017-0315-1","quality_controlled":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"volume":360,"date_created":"2018-12-11T11:47:09Z","date_updated":"2021-01-12T08:02:35Z","author":[{"first_name":"Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"},{"full_name":"Reuvers, Robin","last_name":"Reuvers","first_name":"Robin"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"department":[{"_id":"RoSe"}],"publisher":"Springer","publication_status":"published","year":"2018","publist_id":"7260","language":[{"iso":"eng"}],"doi":"10.1007/s00220-017-3064-x","project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1511.05953"]},"publication_identifier":{"issn":["00103616"]},"month":"05","oa_version":"Submitted Version","intvolume":" 360","status":"public","title":"The Bogoliubov free energy functional II: The dilute Limit","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"554","issue":"1","abstract":[{"lang":"eng","text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.)."}],"type":"journal_article","date_published":"2018-05-01T00:00:00Z","page":"347-403","citation":{"ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403."},"publication":"Communications in Mathematical Physics","day":"01","scopus_import":1},{"file_date_updated":"2020-07-14T12:47:09Z","publist_id":"7252","date_created":"2018-12-11T11:47:11Z","date_updated":"2021-01-12T08:03:05Z","volume":1727,"author":[{"full_name":"Dimitrov, Dimitar","last_name":"Dimitrov","first_name":"Dimitar"},{"full_name":"Guillaud, Laurent","first_name":"Laurent","last_name":"Guillaud"},{"full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"publication_status":"published","department":[{"_id":"RySh"}],"editor":[{"last_name":"Skaper","first_name":"Stephen D.","full_name":"Skaper, Stephen D."}],"publisher":"Springer","year":"2018","pmid":1,"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-7571-6_15","quality_controlled":"1","external_id":{"pmid":["29222783"]},"oa":1,"abstract":[{"text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","file":[{"access_level":"open_access","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","file_size":787407,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7046","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-11-19T07:47:43Z"}],"oa_version":"Submitted Version","status":"public","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","ddc":["570"],"intvolume":" 1727","_id":"562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2018-01-01T00:00:00Z","page":"201 - 215","publication":"Neurotrophic Factors","citation":{"chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15"}},{"month":"05","day":"19","publication_identifier":{"isbn":["978-3-319-10574-1"]},"scopus_import":1,"doi":"10.1007/978-3-319-10575-8_27","date_published":"2018-05-19T00:00:00Z","language":[{"iso":"eng"}],"publication":"Handbook of Model Checking","citation":{"chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27.","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27"},"quality_controlled":"1","page":"921 - 962","abstract":[{"text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches.","lang":"eng"}],"publist_id":"7995","type":"book_chapter","author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"edition":"1","date_updated":"2021-01-12T08:05:10Z","date_created":"2018-12-11T11:44:24Z","oa_version":"None","_id":"59","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"Graph games and reactive synthesis","status":"public","publication_status":"published","publisher":"Springer","editor":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Clarke, Edmund M.","last_name":"Clarke","first_name":"Edmund M."},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"}],"department":[{"_id":"KrCh"}]},{"abstract":[{"text":"Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.","lang":"eng"}],"publist_id":"7994","type":"book_chapter","author":[{"full_name":"Clarke, Edmund","first_name":"Edmund","last_name":"Clarke"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Veith, Helmut","first_name":"Helmut","last_name":"Veith"}],"date_updated":"2021-01-12T08:05:35Z","date_created":"2018-12-11T11:44:25Z","oa_version":"None","year":"2018","_id":"60","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Introduction to model checking","publication_status":"published","editor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"month":"05","day":"19","scopus_import":1,"series_title":"Handbook of Model Checking","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_1","language":[{"iso":"eng"}],"publication":"Handbook of Model Checking","citation":{"ama":"Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1","ieee":"E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26.","apa":"Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26.","mla":"Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1.","chicago":"Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1."},"quality_controlled":"1","page":"1 - 26"},{"author":[{"last_name":"Bondarenko","first_name":"Andriy","full_name":"Bondarenko, Andriy"},{"full_name":"Mellit, Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","last_name":"Mellit","first_name":"Anton"},{"first_name":"Andriy","last_name":"Prymak","full_name":"Prymak, Andriy"},{"full_name":"Radchenko, Danylo","last_name":"Radchenko","first_name":"Danylo"},{"full_name":"Viazovska, Maryna","first_name":"Maryna","last_name":"Viazovska"}],"date_updated":"2021-01-12T08:06:06Z","date_created":"2018-12-11T11:44:25Z","oa_version":"Preprint","year":"2018","_id":"61","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","status":"public","department":[{"_id":"TaHa"}],"publisher":"Springer","abstract":[{"lang":"eng","text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. "}],"publist_id":"7993","extern":"1","type":"book_chapter","doi":"10.1007/978-3-319-72456-0_7","date_published":"2018-05-23T00:00:00Z","language":[{"iso":"eng"}],"publication":"Contemporary Computational Mathematics","external_id":{"arxiv":["1509.06286"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06286"}],"oa":1,"citation":{"apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7."},"quality_controlled":"1","page":"131 - 134","month":"05","day":"23","article_processing_charge":"No"},{"date_updated":"2021-01-12T08:06:11Z","date_created":"2019-03-19T13:09:28Z","volume":14,"author":[{"first_name":"Ian G.","last_name":"McLachlan","full_name":"McLachlan, Ian G."},{"full_name":"Beets, Isabel","first_name":"Isabel","last_name":"Beets"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","first_name":"Mario"},{"last_name":"Heiman","first_name":"Maxwell G.","full_name":"Heiman, Maxwell G."}],"publication_status":"published","publisher":"Public Library of Science","year":"2018","pmid":1,"extern":"1","file_date_updated":"2020-07-14T12:47:19Z","article_number":"e1007435","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007435","quality_controlled":"1","external_id":{"pmid":["29879119"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","publication_identifier":{"issn":["1553-7404"]},"oa_version":"Published Version","file":[{"file_name":"2018_PLOS_McLachlan.pdf","access_level":"open_access","content_type":"application/pdf","file_size":13011506,"creator":"kschuh","relation":"main_file","file_id":"6112","date_created":"2019-03-19T13:18:01Z","date_updated":"2020-07-14T12:47:19Z","checksum":"622036b945365dbc575bea2768aa9bc8"}],"status":"public","title":"A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism","ddc":["570"],"intvolume":" 14","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6111","abstract":[{"lang":"eng","text":"Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending."}],"issue":"6","type":"journal_article","date_published":"2018-06-07T00:00:00Z","publication":"PLOS Genetics","citation":{"mla":"McLachlan, Ian G., et al. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics, vol. 14, no. 6, e1007435, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007435.","short":"I.G. McLachlan, I. Beets, M. de Bono, M.G. Heiman, PLOS Genetics 14 (2018).","chicago":"McLachlan, Ian G., Isabel Beets, Mario de Bono, and Maxwell G. Heiman. “A Neuronal MAP Kinase Constrains Growth of a Caenorhabditis Elegans Sensory Dendrite throughout the Life of the Organism.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007435.","ama":"McLachlan IG, Beets I, de Bono M, Heiman MG. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 2018;14(6). doi:10.1371/journal.pgen.1007435","ista":"McLachlan IG, Beets I, de Bono M, Heiman MG. 2018. A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. 14(6), e1007435.","apa":"McLachlan, I. G., Beets, I., de Bono, M., & Heiman, M. G. (2018). A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007435","ieee":"I. G. McLachlan, I. Beets, M. de Bono, and M. G. Heiman, “A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism,” PLOS Genetics, vol. 14, no. 6. Public Library of Science, 2018."},"day":"07","has_accepted_license":"1"},{"citation":{"mla":"Laurent, Patrick, et al. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences, vol. 115, no. 29, National Academy of Sciences, 2018, pp. E6890–99, doi:10.1073/pnas.1714610115.","short":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, M. de Bono, Proceedings of the National Academy of Sciences 115 (2018) E6890–E6899.","chicago":"Laurent, Patrick, QueeLim Ch’ng, Maëlle Jospin, Changchun Chen, Ramiro Lorenzo, and Mario de Bono. “Genetic Dissection of Neuropeptide Cell Biology at High and Low Activity in a Defined Sensory Neuron.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1714610115.","ama":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 2018;115(29):E6890-E6899. doi:10.1073/pnas.1714610115","ista":"Laurent P, Ch’ng Q, Jospin M, Chen C, Lorenzo R, de Bono M. 2018. Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. 115(29), E6890–E6899.","ieee":"P. Laurent, Q. Ch’ng, M. Jospin, C. Chen, R. Lorenzo, and M. de Bono, “Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron,” Proceedings of the National Academy of Sciences, vol. 115, no. 29. National Academy of Sciences, pp. E6890–E6899, 2018.","apa":"Laurent, P., Ch’ng, Q., Jospin, M., Chen, C., Lorenzo, R., & de Bono, M. (2018). Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1714610115"},"publication":"Proceedings of the National Academy of Sciences","page":"E6890-E6899","date_published":"2018-07-17T00:00:00Z","has_accepted_license":"1","day":"17","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6109","intvolume":" 115","status":"public","ddc":["570"],"title":"Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron","file":[{"date_created":"2019-03-19T13:01:58Z","date_updated":"2020-07-14T12:47:19Z","checksum":"5e81665377441cdd8d99ab952c534319","file_id":"6110","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":1567765,"file_name":"2018_PNAS_Laurent.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"29","abstract":[{"lang":"eng","text":"Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels."}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["29959203"]},"quality_controlled":"1","doi":"10.1073/pnas.1714610115","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"07","pmid":1,"year":"2018","publisher":"National Academy of Sciences","publication_status":"published","author":[{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"full_name":"Ch’ng, QueeLim","first_name":"QueeLim","last_name":"Ch’ng"},{"full_name":"Jospin, Maëlle","first_name":"Maëlle","last_name":"Jospin"},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"full_name":"Lorenzo, Ramiro","last_name":"Lorenzo","first_name":"Ramiro"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario"}],"volume":115,"date_created":"2019-03-19T12:41:33Z","date_updated":"2021-01-12T08:06:09Z","file_date_updated":"2020-07-14T12:47:19Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1"},{"year":"2018","_id":"6164","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D","publication_status":"published","status":"public","intvolume":" 11255","publisher":"Springer","author":[{"full_name":"Koshti, Girish","first_name":"Girish","last_name":"Koshti"},{"first_name":"Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita"},{"last_name":"Largeteau-Skapin","first_name":"Gaëlle","full_name":"Largeteau-Skapin, Gaëlle"},{"full_name":"Zrour, Rita","last_name":"Zrour","first_name":"Rita"},{"full_name":"Andres, Eric","first_name":"Eric","last_name":"Andres"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"date_created":"2019-03-21T12:16:58Z","date_updated":"2022-01-27T15:26:39Z","oa_version":"None","volume":11255,"type":"conference","place":"Cham","alternative_title":["LNCS"],"abstract":[{"text":"In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity.","lang":"eng"}],"extern":"1","publication":"19th International Workshop","citation":{"apa":"Koshti, G., Biswas, R., Largeteau-Skapin, G., Zrour, R., Andres, E., & Bhowmick, P. (2018). Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In 19th International Workshop (Vol. 11255, pp. 82–96). Cham: Springer. https://doi.org/10.1007/978-3-030-05288-1_7","ieee":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, and P. Bhowmick, “Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D,” in 19th International Workshop, Porto, Portugal, 2018, vol. 11255, pp. 82–96.","ista":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. 2018. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. 19th International Workshop. IWCIA: International Workshop on Combinatorial Image Analysis, LNCS, vol. 11255, 82–96.","ama":"Koshti G, Biswas R, Largeteau-Skapin G, Zrour R, Andres E, Bhowmick P. Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D. In: 19th International Workshop. Vol 11255. Cham: Springer; 2018:82-96. doi:10.1007/978-3-030-05288-1_7","chicago":"Koshti, Girish, Ranita Biswas, Gaëlle Largeteau-Skapin, Rita Zrour, Eric Andres, and Partha Bhowmick. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” In 19th International Workshop, 11255:82–96. Cham: Springer, 2018. https://doi.org/10.1007/978-3-030-05288-1_7.","short":"G. Koshti, R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, P. Bhowmick, in:, 19th International Workshop, Springer, Cham, 2018, pp. 82–96.","mla":"Koshti, Girish, et al. “Sphere Construction on the FCC Grid Interpreted as Layered Hexagonal Grids in 3D.” 19th International Workshop, vol. 11255, Springer, 2018, pp. 82–96, doi:10.1007/978-3-030-05288-1_7."},"quality_controlled":"1","page":"82-96","conference":{"start_date":"2018-11-22","location":"Porto, Portugal","end_date":"2018-11-24","name":"IWCIA: International Workshop on Combinatorial Image Analysis"},"date_published":"2018-11-22T00:00:00Z","doi":"10.1007/978-3-030-05288-1_7","language":[{"iso":"eng"}],"day":"22","month":"11","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-030-05288-1"],"isbn":["978-3-030-05287-4"],"eissn":["1611-3349"]},"article_processing_charge":"No"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6354","intvolume":" 8","ddc":["570"],"status":"public","title":"Platelet migration and bacterial trapping assay under flow","file":[{"access_level":"open_access","file_name":"2018_BioProtocol_Fan.pdf","content_type":"application/pdf","file_size":2928337,"creator":"dernst","relation":"main_file","file_id":"6360","checksum":"d4588377e789da7f360b553ae02c5119","date_created":"2019-04-30T08:04:33Z","date_updated":"2020-07-14T12:47:28Z"}],"oa_version":"Published Version","type":"journal_article","issue":"18","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"citation":{"ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018."},"publication":"Bio-Protocol","date_published":"2018-09-20T00:00:00Z","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"has_accepted_license":"1","day":"20","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","year":"2018","department":[{"_id":"MiSi"}],"publisher":"Bio-Protocol","publication_status":"published","author":[{"first_name":"Shuxia","last_name":"Fan","full_name":"Fan, Shuxia"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"},{"last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"}],"volume":8,"date_updated":"2021-01-12T08:07:12Z","date_created":"2019-04-29T09:40:33Z","article_number":"e3018","ec_funded":1,"file_date_updated":"2020-07-14T12:47:28Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687"}],"quality_controlled":"1","doi":"10.21769/bioprotoc.3018","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2331-8325"]},"month":"09"},{"publisher":"Springer Nature","intvolume":" 14","title":"Harnessing electro-optic correlations in an efficient mechanical converter","status":"public","publication_status":"published","_id":"6368","year":"2018","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":14,"oa_version":"Preprint","date_created":"2019-05-03T09:17:20Z","date_updated":"2021-01-12T08:07:15Z","author":[{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham"},{"last_name":"Burns","first_name":"P. S.","full_name":"Burns, P. S."},{"first_name":"M. D.","last_name":"Urmey","full_name":"Urmey, M. D."},{"last_name":"Peterson","first_name":"R. W.","full_name":"Peterson, R. W."},{"full_name":"Kampel, N. S.","first_name":"N. S.","last_name":"Kampel"},{"last_name":"Brubaker","first_name":"B. M.","full_name":"Brubaker, B. M."},{"first_name":"G.","last_name":"Smith","full_name":"Smith, G."},{"first_name":"K. W.","last_name":"Lehnert","full_name":"Lehnert, K. W."},{"first_name":"C. A.","last_name":"Regal","full_name":"Regal, C. A."}],"type":"journal_article","extern":"1","issue":"10","abstract":[{"text":"An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate.","lang":"eng"}],"page":"1038-1042","quality_controlled":"1","external_id":{"arxiv":["1712.06535"]},"citation":{"short":"A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042.","mla":"Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:10.1038/s41567-018-0210-0.","chicago":"Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0210-0.","ama":"Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 2018;14(10):1038-1042. doi:10.1038/s41567-018-0210-0","apa":"Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0210-0","ieee":"A. P. Higginbotham et al., “Harnessing electro-optic correlations in an efficient mechanical converter,” Nature Physics, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018.","ista":"Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.06535"}],"oa":1,"publication":"Nature Physics","language":[{"iso":"eng"}],"doi":"10.1038/s41567-018-0210-0","date_published":"2018-10-01T00:00:00Z","publication_identifier":{"issn":["1745-2473","1745-2481"]},"month":"10","day":"01"},{"quality_controlled":"1","publication":"Physical Review B","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.02243"}],"external_id":{"arxiv":["1802.02243"]},"oa":1,"citation":{"apa":"Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., & Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. Physical Review B. American Physical Society (APS). https://doi.org/10.1103/physrevb.97.220301","ieee":"E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” Physical Review B, vol. 97, no. 22. American Physical Society (APS), 2018.","ista":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301.","ama":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 2018;97(22). doi:10.1103/physrevb.97.220301","chicago":"Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B. American Physical Society (APS), 2018. https://doi.org/10.1103/physrevb.97.220301.","short":"E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018).","mla":"Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” Physical Review B, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:10.1103/physrevb.97.220301."},"language":[{"iso":"eng"}],"date_published":"2018-06-04T00:00:00Z","doi":"10.1103/physrevb.97.220301","month":"06","day":"04","publication_identifier":{"issn":["2469-9950","2469-9969"]},"title":"Topological phase transition measured in a dissipative metamaterial","publication_status":"published","status":"public","intvolume":" 97","publisher":"American Physical Society (APS)","_id":"6369","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","date_updated":"2021-01-12T08:07:16Z","date_created":"2019-05-03T09:29:49Z","volume":97,"oa_version":"Preprint","author":[{"first_name":"Eric I.","last_name":"Rosenthal","full_name":"Rosenthal, Eric I."},{"full_name":"Ehrlich, Nicole K.","first_name":"Nicole K.","last_name":"Ehrlich"},{"full_name":"Rudner, Mark S.","first_name":"Mark S.","last_name":"Rudner"},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"last_name":"Lehnert","first_name":"K. W.","full_name":"Lehnert, K. W."}],"article_number":"220301","type":"journal_article","extern":"1","abstract":[{"text":"We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before.","lang":"eng"}],"issue":"22"},{"citation":{"ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"Open-Access-Tage","end_date":"2018-09-26","location":"Graz, Austria","start_date":"2018-09-24"},"doi":"10.5281/zenodo.1410279","date_published":"2018-09-24T00:00:00Z","keyword":["Open Access","Publication Analysis"],"day":"24","month":"09","has_accepted_license":"1","status":"public","ddc":["020"],"title":"Open Access at IST Austria 2009-2017","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","year":"2018","_id":"6459","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2020-07-14T23:06:21Z","date_created":"2019-05-16T07:27:14Z","oa_version":"Published Version","file":[{"file_id":"6460","relation":"main_file","date_created":"2019-05-16T07:26:25Z","date_updated":"2020-07-14T12:47:30Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","file_name":"Poster_Beitrag_125_Petritsch.pdf","access_level":"open_access","creator":"dernst","file_size":1967778,"content_type":"application/pdf"}],"author":[{"full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","first_name":"Barbara"}],"type":"conference_poster","file_date_updated":"2020-07-14T12:47:30Z"},{"author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamás","full_name":"Hausel, Tamás"},{"last_name":"Mellit","first_name":"Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87","full_name":"Mellit, Anton"},{"last_name":"Pei","first_name":"Du","full_name":"Pei, Du"}],"date_updated":"2021-01-12T08:07:52Z","date_created":"2019-06-06T12:42:01Z","oa_version":"None","_id":"6525","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","title":"Mirror symmetry with branes by equivariant verlinde formulas","status":"public","department":[{"_id":"TaHa"}],"publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal."}],"type":"book_chapter","doi":"10.1093/oso/9780198802013.003.0009","date_published":"2018-01-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Geometry and Physics: Volume I","citation":{"chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009.","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","apa":"Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009"},"quality_controlled":"1","page":"189-218","day":"01","month":"01","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"scopus_import":1},{"citation":{"ieee":"S. A. Hashemi, N. Doan, M. Mondelli, and W. Gross, “Decoding Reed-Muller and polar codes by successive factor graph permutations,” in 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, Hong Kong, China, 2018, pp. 1–5.","apa":"Hashemi, S. A., Doan, N., Mondelli, M., & Gross, W. (2018). Decoding Reed-Muller and polar codes by successive factor graph permutations. In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing (pp. 1–5). Hong Kong, China: IEEE. https://doi.org/10.1109/istc.2018.8625281","ista":"Hashemi SA, Doan N, Mondelli M, Gross W. 2018. Decoding Reed-Muller and polar codes by successive factor graph permutations. 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. ISTC: Symposium on Turbo Codes & Iterative Information Processing, 1–5.","ama":"Hashemi SA, Doan N, Mondelli M, Gross W. Decoding Reed-Muller and polar codes by successive factor graph permutations. In: 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing. IEEE; 2018:1-5. doi:10.1109/istc.2018.8625281","chicago":"Hashemi, Seyyed Ali, Nghia Doan, Marco Mondelli, and Warren Gross. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” In 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, 1–5. IEEE, 2018. https://doi.org/10.1109/istc.2018.8625281.","short":"S.A. Hashemi, N. Doan, M. Mondelli, W. Gross, in:, 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5.","mla":"Hashemi, Seyyed Ali, et al. “Decoding Reed-Muller and Polar Codes by Successive Factor Graph Permutations.” 2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing, IEEE, 2018, pp. 1–5, doi:10.1109/istc.2018.8625281."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1807.03912","open_access":"1"}],"external_id":{"arxiv":["1807.03912"]},"publication":"2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing","page":"1-5","quality_controlled":"1","doi":"10.1109/istc.2018.8625281","date_published":"2018-12-01T00:00:00Z","conference":{"name":"ISTC: Symposium on Turbo Codes & Iterative Information Processing","start_date":"2018-12-03","location":"Hong Kong, China","end_date":"2018-12-07"},"language":[{"iso":"eng"}],"day":"01","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6664","year":"2018","publisher":"IEEE","publication_status":"published","status":"public","title":"Decoding Reed-Muller and polar codes by successive factor graph permutations","author":[{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Doan, Nghia","first_name":"Nghia","last_name":"Doan"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Gross, Warren ","first_name":"Warren ","last_name":"Gross"}],"oa_version":"Preprint","date_updated":"2021-01-12T08:08:29Z","date_created":"2019-07-23T09:12:43Z","type":"conference","abstract":[{"lang":"eng","text":"Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively."}],"extern":"1"},{"publication_identifier":{"eissn":["1558-0857"]},"month":"09","day":"01","language":[{"iso":"eng"}],"date_published":"2018-09-01T00:00:00Z","doi":"10.1109/tcomm.2018.2832207","page":"3749-3759","quality_controlled":"1","citation":{"ieee":"S. A. Hashemi, M. Mondelli, S. H. Hassani, C. Condo, R. L. Urbanke, and W. J. Gross, “Decoder partitioning: Towards practical list decoding of polar codes,” IEEE Transactions on Communications, vol. 66, no. 9. IEEE, pp. 3749–3759, 2018.","apa":"Hashemi, S. A., Mondelli, M., Hassani, S. H., Condo, C., Urbanke, R. L., & Gross, W. J. (2018). Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. IEEE. https://doi.org/10.1109/tcomm.2018.2832207","ista":"Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. 2018. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 66(9), 3749–3759.","ama":"Hashemi SA, Mondelli M, Hassani SH, Condo C, Urbanke RL, Gross WJ. Decoder partitioning: Towards practical list decoding of polar codes. IEEE Transactions on Communications. 2018;66(9):3749-3759. doi:10.1109/tcomm.2018.2832207","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, S. Hamed Hassani, Carlo Condo, Rudiger L. Urbanke, and Warren J. Gross. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications. IEEE, 2018. https://doi.org/10.1109/tcomm.2018.2832207.","short":"S.A. Hashemi, M. Mondelli, S.H. Hassani, C. Condo, R.L. Urbanke, W.J. Gross, IEEE Transactions on Communications 66 (2018) 3749–3759.","mla":"Hashemi, Seyyed Ali, et al. “Decoder Partitioning: Towards Practical List Decoding of Polar Codes.” IEEE Transactions on Communications, vol. 66, no. 9, IEEE, 2018, pp. 3749–59, doi:10.1109/tcomm.2018.2832207."},"publication":"IEEE Transactions on Communications","extern":"1","issue":"9","abstract":[{"lang":"eng","text":"Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel."}],"type":"journal_article","oa_version":"None","volume":66,"date_created":"2019-07-24T08:59:41Z","date_updated":"2021-01-12T08:08:31Z","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","full_name":"Mondelli, Marco"},{"full_name":"Hassani, S. Hamed","first_name":"S. Hamed","last_name":"Hassani"},{"full_name":"Condo, Carlo","first_name":"Carlo","last_name":"Condo"},{"full_name":"Urbanke, Rudiger L.","last_name":"Urbanke","first_name":"Rudiger L."},{"full_name":"Gross, Warren J.","last_name":"Gross","first_name":"Warren J."}],"publisher":"IEEE","intvolume":" 66","publication_status":"published","status":"public","title":"Decoder partitioning: Towards practical list decoding of polar codes","_id":"6674","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018"},{"publication_identifier":{"isbn":["9781538647271"]},"day":"01","month":"12","external_id":{"arxiv":["1806.11195"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.11195"}],"citation":{"chicago":"Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “On the Decoding of Polar Codes on Permuted Factor Graphs.” In 2018 IEEE Global Communications Conference . IEEE, 2018. https://doi.org/10.1109/glocom.2018.8647308.","short":"N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, in:, 2018 IEEE Global Communications Conference , IEEE, 2018.","mla":"Doan, Nghia, et al. “On the Decoding of Polar Codes on Permuted Factor Graphs.” 2018 IEEE Global Communications Conference , IEEE, 2018, doi:10.1109/glocom.2018.8647308.","ieee":"N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “On the decoding of polar codes on permuted factor graphs,” in 2018 IEEE Global Communications Conference , Abu Dhabi, United Arab Emirates, 2018.","apa":"Doan, N., Hashemi, S. A., Mondelli, M., & Gross, W. J. (2018). On the decoding of polar codes on permuted factor graphs. In 2018 IEEE Global Communications Conference . Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/glocom.2018.8647308","ista":"Doan N, Hashemi SA, Mondelli M, Gross WJ. 2018. On the decoding of polar codes on permuted factor graphs. 2018 IEEE Global Communications Conference . GLOBECOM: Global Communications Conference.","ama":"Doan N, Hashemi SA, Mondelli M, Gross WJ. On the decoding of polar codes on permuted factor graphs. In: 2018 IEEE Global Communications Conference . IEEE; 2018. doi:10.1109/glocom.2018.8647308"},"oa":1,"publication":"2018 IEEE Global Communications Conference ","quality_controlled":"1","date_published":"2018-12-01T00:00:00Z","doi":"10.1109/glocom.2018.8647308","conference":{"end_date":"2018-12-13","start_date":"2018-12-09","location":"Abu Dhabi, United Arab Emirates","name":"GLOBECOM: Global Communications Conference"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 .","lang":"eng"}],"extern":"1","year":"2018","_id":"6728","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","status":"public","publication_status":"published","title":"On the decoding of polar codes on permuted factor graphs","author":[{"full_name":"Doan, Nghia","last_name":"Doan","first_name":"Nghia"},{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"full_name":"Gross, Warren J.","first_name":"Warren J.","last_name":"Gross"}],"oa_version":"Preprint","date_created":"2019-07-30T06:43:15Z","date_updated":"2021-01-12T08:08:42Z"},{"issue":"5","abstract":[{"text":"We survey coding techniques that enable reliable transmission at rates that approach the capacity of an arbitrary discrete memoryless channel. In particular, we take the point of view of modern coding theory and discuss how recent advances in coding for symmetric channels help provide more efficient solutions for the asymmetric case. We consider, in more detail, three basic coding paradigms. The first one is Gallager's scheme that consists of concatenating a linear code with a non-linear mapping so that the input distribution can be appropriately shaped. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Furthermore, we derive a scaling law between the gap to capacity, the cardinality of the input and output alphabets, and the required size of the mapper. The second one is an integrated scheme in which the code is used both for source coding, in order to create codewords distributed according to the capacity-achieving input distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third paradigm is based on an idea of Böcherer and Mathar, and separates the two tasks of source coding and channel coding by a chaining construction that binds together several codewords. We present conditions for the source code and the channel code, and we describe how to combine any source code with any channel code that fulfill those conditions, in order to provide capacity-achieving schemes for asymmetric channels. In particular, we show that polar codes, spatially coupled codes, and homophonic codes are suitable as basic building blocks of the proposed coding strategy. Rather than focusing on the exact details of the schemes, the purpose of this tutorial is to present different coding techniques that can then be implemented with many variants. There is no absolute winner and, in order to understand the most suitable technique for a specific application scenario, we provide a detailed comparison that takes into account several performance metrics.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 64","status":"public","title":"How to achieve the capacity of asymmetric channels","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6678","day":"01","date_published":"2018-05-01T00:00:00Z","page":"3371-3393","article_type":"original","citation":{"ama":"Mondelli M, Hassani H, Urbanke R. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 2018;64(5):3371-3393. doi:10.1109/tit.2018.2789885","ista":"Mondelli M, Hassani H, Urbanke R. 2018. How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. 64(5), 3371–3393.","apa":"Mondelli, M., Hassani, H., & Urbanke, R. (2018). How to achieve the capacity of asymmetric channels. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/tit.2018.2789885","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “How to achieve the capacity of asymmetric channels,” IEEE Transactions on Information Theory, vol. 64, no. 5. IEEE, pp. 3371–3393, 2018.","mla":"Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory, vol. 64, no. 5, IEEE, 2018, pp. 3371–93, doi:10.1109/tit.2018.2789885.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Information Theory 64 (2018) 3371–3393.","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “How to Achieve the Capacity of Asymmetric Channels.” IEEE Transactions on Information Theory. IEEE, 2018. https://doi.org/10.1109/tit.2018.2789885."},"publication":"IEEE Transactions on Information Theory","extern":"1","volume":64,"date_created":"2019-07-24T12:38:49Z","date_updated":"2023-02-23T12:50:46Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6740"}]},"author":[{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"first_name":"Rudiger ","last_name":"Urbanke","full_name":"Urbanke, Rudiger "}],"publisher":"IEEE","publication_status":"published","year":"2018","publication_identifier":{"issn":["0018-9448","1557-9654"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1109/tit.2018.2789885","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.7373"}],"external_id":{"arxiv":["1406.7373"]},"oa":1},{"day":"14","scopus_import":1,"date_published":"2018-06-14T00:00:00Z","citation":{"mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8.","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8"},"publication":"Probability Theory and Related Fields","issue":"1-2","abstract":[{"lang":"eng","text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 171","status":"public","title":"Local law and Tracy–Widom limit for sparse random matrices","_id":"690","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"doi":"10.1007/s00440-017-0787-8","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"quality_controlled":"1","external_id":{"arxiv":["1605.08767"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.08767"}],"oa":1,"publist_id":"7017","ec_funded":1,"article_number":"543-616","volume":171,"date_created":"2018-12-11T11:47:56Z","date_updated":"2021-01-12T08:09:33Z","author":[{"full_name":"Lee, Jii","last_name":"Lee","first_name":"Jii"},{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"department":[{"_id":"LaEr"}],"publisher":"Springer","publication_status":"published","year":"2018"},{"month":"06","day":"16","publication_identifier":{"eissn":["2157-8117"]},"conference":{"end_date":"2018-06-22","location":"Vail, CO, United States","start_date":"2018-06-17","name":"ISIT: International Symposium on Information Theory "},"date_published":"2018-06-16T00:00:00Z","doi":"10.1109/isit.2018.8437479","language":[{"iso":"eng"}],"publication":"2018 IEEE International Symposium on Information Theory","external_id":{"arxiv":["1801.03153"]},"oa":1,"citation":{"ista":"Mondelli M, Hassani H, Urbanke R. 2018. A new coding paradigm for the primitive relay channel. 2018 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory , 351–355.","apa":"Mondelli, M., Hassani, H., & Urbanke, R. (2018). A new coding paradigm for the primitive relay channel. In 2018 IEEE International Symposium on Information Theory (pp. 351–355). Vail, CO, United States: IEEE. https://doi.org/10.1109/isit.2018.8437479","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” in 2018 IEEE International Symposium on Information Theory, Vail, CO, United States, 2018, pp. 351–355.","ama":"Mondelli M, Hassani H, Urbanke R. A new coding paradigm for the primitive relay channel. In: 2018 IEEE International Symposium on Information Theory. IEEE; 2018:351-355. doi:10.1109/isit.2018.8437479","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” In 2018 IEEE International Symposium on Information Theory, 351–55. IEEE, 2018. https://doi.org/10.1109/isit.2018.8437479.","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–55, doi:10.1109/isit.2018.8437479.","short":"M. Mondelli, H. Hassani, R. Urbanke, in:, 2018 IEEE International Symposium on Information Theory, IEEE, 2018, pp. 351–355."},"main_file_link":[{"url":"https://arxiv.org/abs/1801.03153","open_access":"1"}],"quality_controlled":"1","page":"351-355","abstract":[{"lang":"eng","text":"We present a coding paradigm that provides a new achievable rate for the primitive relay channel by combining compress-and-forward and decode-and-forward with a chaining construction. In the primitive relay channel model, the source broadcasts a message to the relay and to the destination; and the relay facilitates this communication by sending an additional message to the destination through a separate channel. Two well-known coding approaches for this setting are decode-and-forward and compress-and-forward: in the former, the relay decodes the message and sends some of the information to the destination; in the latter, the relay does not attempt to decode, but it sends a compressed description of the received sequence to the destination via Wyner-Ziv coding. In our scheme, we transmit over pairs of blocks and we use compress-and-forward for the first block and decode-and-forward for the second. In particular, in the first block, the relay does not attempt to decode and it sends only a part of the compressed description of the received sequence; in the second block, the relay decodes the message and sends this information plus the remaining part of the compressed sequence relative to the first block. As a result, we strictly outperform both compress-and- forward and decode-and-forward. Furthermore, this paradigm can be implemented with a low-complexity polar coding scheme that has the typical attractive features of polar codes, i.e., quasi-linear encoding/decoding complexity and super-polynomial decay of the error probability. Throughout the paper we consider as a running example the special case of the erasure relay channel and we compare the rates achievable by our proposed scheme with the existing upper and lower bounds."}],"extern":"1","type":"conference","author":[{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"first_name":"Hamed","last_name":"Hassani","full_name":"Hassani, Hamed"},{"last_name":"Urbanke","first_name":"Rudiger","full_name":"Urbanke, Rudiger"}],"related_material":{"record":[{"id":"7007","status":"public","relation":"later_version"}]},"date_updated":"2023-02-23T12:56:49Z","date_created":"2019-07-24T09:10:38Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6675","year":"2018","publication_status":"published","status":"public","title":"A new coding paradigm for the primitive relay channel","publisher":"IEEE"},{"doi":"10.1109/TPAMI.2017.2730884","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1508.07902","open_access":"1"}],"external_id":{"arxiv":["1508.07902"]},"quality_controlled":"1","publication_identifier":{"issn":["01628828"]},"month":"07","author":[{"full_name":"Shekhovtsov, Alexander","first_name":"Alexander","last_name":"Shekhovtsov"},{"last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"volume":40,"date_created":"2018-12-11T11:48:01Z","date_updated":"2021-01-12T08:11:32Z","year":"2018","department":[{"_id":"VlKo"}],"publisher":"IEEE","publication_status":"published","publist_id":"6992","date_published":"2018-07-01T00:00:00Z","citation":{"chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884"},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"1668-1682","day":"01","scopus_import":1,"oa_version":"Preprint","_id":"703","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 40","title":"Maximum persistency via iterative relaxed inference with graphical models","status":"public","issue":"7","abstract":[{"lang":"eng","text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision."}],"type":"journal_article"},{"_id":"7063","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","ddc":["530"],"status":"public","title":"Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity","file":[{"date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-20T14:00:27Z","checksum":"5c6180c7d19da599dd50a067eb2efd50","relation":"main_file","file_id":"7090","file_size":1563353,"content_type":"application/pdf","creator":"dernst","file_name":"2018_IUCrJ_Martino.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"The high-pressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Pt-only corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a near-flat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a long-range crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to long-range ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focused-ion-beam micro-fabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed."}],"citation":{"ista":"Martino E, Arakcheeva A, Autès G, Pisoni A, Bachmann MD, Modic KA, Helm T, Yazyev OV, Moll PJW, Forró L, Katrych S. 2018. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 5(4), 470–477.","ieee":"E. Martino et al., “Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity,” IUCrJ, vol. 5, no. 4. International Union of Crystallography (IUCr), pp. 470–477, 2018.","apa":"Martino, E., Arakcheeva, A., Autès, G., Pisoni, A., Bachmann, M. D., Modic, K. A., … Katrych, S. (2018). Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. International Union of Crystallography (IUCr). https://doi.org/10.1107/s2052252518007303","ama":"Martino E, Arakcheeva A, Autès G, et al. Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity. IUCrJ. 2018;5(4):470-477. doi:10.1107/s2052252518007303","chicago":"Martino, Edoardo, Alla Arakcheeva, Gabriel Autès, Andrea Pisoni, Maja D. Bachmann, Kimberly A Modic, Toni Helm, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ. International Union of Crystallography (IUCr), 2018. https://doi.org/10.1107/s2052252518007303.","mla":"Martino, Edoardo, et al. “Sr2Pt8−xAs: A Layered Incommensurately Modulated Metal with Saturated Resistivity.” IUCrJ, vol. 5, no. 4, International Union of Crystallography (IUCr), 2018, pp. 470–77, doi:10.1107/s2052252518007303.","short":"E. Martino, A. Arakcheeva, G. Autès, A. Pisoni, M.D. Bachmann, K.A. Modic, T. Helm, O.V. Yazyev, P.J.W. Moll, L. Forró, S. Katrych, IUCrJ 5 (2018) 470–477."},"publication":"IUCrJ","page":"470-477","article_type":"original","date_published":"2018-07-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2018","publisher":"International Union of Crystallography (IUCr)","publication_status":"published","author":[{"last_name":"Martino","first_name":"Edoardo","full_name":"Martino, Edoardo"},{"full_name":"Arakcheeva, Alla","last_name":"Arakcheeva","first_name":"Alla"},{"last_name":"Autès","first_name":"Gabriel","full_name":"Autès, Gabriel"},{"first_name":"Andrea","last_name":"Pisoni","full_name":"Pisoni, Andrea"},{"last_name":"Bachmann","first_name":"Maja D.","full_name":"Bachmann, Maja D."},{"last_name":"Modic","first_name":"Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"},{"first_name":"Toni","last_name":"Helm","full_name":"Helm, Toni"},{"full_name":"Yazyev, Oleg V.","first_name":"Oleg V.","last_name":"Yazyev"},{"last_name":"Moll","first_name":"Philip J. W.","full_name":"Moll, Philip J. W."},{"last_name":"Forró","first_name":"László","full_name":"Forró, László"},{"last_name":"Katrych","first_name":"Sergiy","full_name":"Katrych, Sergiy"}],"volume":5,"date_updated":"2021-01-12T08:11:38Z","date_created":"2019-11-19T13:11:15Z","file_date_updated":"2020-07-14T12:47:48Z","extern":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1107/s2052252518007303","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2052-2525"]},"month":"07"},{"issue":"1","abstract":[{"text":"Weyl fermions are a recently discovered ingredient for correlated states of electronic matter. A key difficulty has been that real materials also contain non-Weyl quasiparticles, and disentangling the experimental signatures has proven challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal TaAs far into its quantum limit, where only the purely chiral 0th Landau levels of the Weyl fermions are occupied. We find the electrical resistivity to be nearly independent of magnetic field up to 50 T: unusual for conventional metals but consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a two-order-of-magnitude increase in resistivity, indicating that a gap opens in the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation below 2 K, suggesting a mesoscopically textured state of matter. These results point the way to inducing new correlated states of matter in the quantum limit of Weyl semimetals.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2018_NatureComm_Ramshaw.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1794797,"file_id":"7089","relation":"main_file","date_created":"2019-11-20T13:55:44Z","date_updated":"2020-07-14T12:47:48Z","checksum":"9c53f9a1f06a4d83d5fe879d2478b7d7"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7062","intvolume":" 9","status":"public","ddc":["530"],"title":"Quantum limit transport and destruction of the Weyl nodes in TaAs","has_accepted_license":"1","article_processing_charge":"No","day":"07","date_published":"2018-06-07T00:00:00Z","citation":{"chicago":"Ramshaw, B. J., Kimberly A Modic, Arkady Shekhter, Yi Zhang, Eun-Ah Kim, Philip J. W. Moll, Maja D. Bachmann, et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04542-9.","mla":"Ramshaw, B. J., et al. “Quantum Limit Transport and Destruction of the Weyl Nodes in TaAs.” Nature Communications, vol. 9, no. 1, 2217, Springer Nature, 2018, doi:10.1038/s41467-018-04542-9.","short":"B.J. Ramshaw, K.A. Modic, A. Shekhter, Y. Zhang, E.-A. Kim, P.J.W. Moll, M.D. Bachmann, M.K. Chan, J.B. Betts, F. Balakirev, A. Migliori, N.J. Ghimire, E.D. Bauer, F. Ronning, R.D. McDonald, Nature Communications 9 (2018).","ista":"Ramshaw BJ, Modic KA, Shekhter A, Zhang Y, Kim E-A, Moll PJW, Bachmann MD, Chan MK, Betts JB, Balakirev F, Migliori A, Ghimire NJ, Bauer ED, Ronning F, McDonald RD. 2018. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 9(1), 2217.","ieee":"B. J. Ramshaw et al., “Quantum limit transport and destruction of the Weyl nodes in TaAs,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","apa":"Ramshaw, B. J., Modic, K. A., Shekhter, A., Zhang, Y., Kim, E.-A., Moll, P. J. W., … McDonald, R. D. (2018). Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04542-9","ama":"Ramshaw BJ, Modic KA, Shekhter A, et al. Quantum limit transport and destruction of the Weyl nodes in TaAs. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04542-9"},"publication":"Nature Communications","article_type":"original","file_date_updated":"2020-07-14T12:47:48Z","extern":"1","article_number":"2217","author":[{"first_name":"B. J.","last_name":"Ramshaw","full_name":"Ramshaw, B. J."},{"first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A"},{"last_name":"Shekhter","first_name":"Arkady","full_name":"Shekhter, Arkady"},{"full_name":"Zhang, Yi","first_name":"Yi","last_name":"Zhang"},{"last_name":"Kim","first_name":"Eun-Ah","full_name":"Kim, Eun-Ah"},{"first_name":"Philip J. W.","last_name":"Moll","full_name":"Moll, Philip J. W."},{"full_name":"Bachmann, Maja D.","last_name":"Bachmann","first_name":"Maja D."},{"first_name":"M. K.","last_name":"Chan","full_name":"Chan, M. K."},{"full_name":"Betts, J. B.","first_name":"J. B.","last_name":"Betts"},{"full_name":"Balakirev, F.","first_name":"F.","last_name":"Balakirev"},{"full_name":"Migliori, A.","last_name":"Migliori","first_name":"A."},{"last_name":"Ghimire","first_name":"N. J.","full_name":"Ghimire, N. J."},{"last_name":"Bauer","first_name":"E. D.","full_name":"Bauer, E. D."},{"first_name":"F.","last_name":"Ronning","full_name":"Ronning, F."},{"first_name":"R. D.","last_name":"McDonald","full_name":"McDonald, R. D."}],"volume":9,"date_updated":"2021-01-12T08:11:38Z","date_created":"2019-11-19T13:10:33Z","year":"2018","publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"month":"06","doi":"10.1038/s41467-018-04542-9","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1"},{"has_accepted_license":"1","article_processing_charge":"No","day":"28","date_published":"2018-09-28T00:00:00Z","page":"3975","article_type":"original","citation":{"chicago":"Modic, Kimberly A, Maja D. Bachmann, B. J. Ramshaw, F. Arnold, K. R. Shirer, Amelia Estry, J. B. Betts, et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-06412-w.","mla":"Modic, Kimberly A., et al. “Resonant Torsion Magnetometry in Anisotropic Quantum Materials.” Nature Communications, vol. 9, no. 1, Springer Nature, 2018, p. 3975, doi:10.1038/s41467-018-06412-w.","short":"K.A. Modic, M.D. Bachmann, B.J. Ramshaw, F. Arnold, K.R. Shirer, A. Estry, J.B. Betts, N.J. Ghimire, E.D. Bauer, M. Schmidt, M. Baenitz, E. Svanidze, R.D. McDonald, A. Shekhter, P.J.W. Moll, Nature Communications 9 (2018) 3975.","ista":"Modic KA, Bachmann MD, Ramshaw BJ, Arnold F, Shirer KR, Estry A, Betts JB, Ghimire NJ, Bauer ED, Schmidt M, Baenitz M, Svanidze E, McDonald RD, Shekhter A, Moll PJW. 2018. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 9(1), 3975.","apa":"Modic, K. A., Bachmann, M. D., Ramshaw, B. J., Arnold, F., Shirer, K. R., Estry, A., … Moll, P. J. W. (2018). Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-06412-w","ieee":"K. A. Modic et al., “Resonant torsion magnetometry in anisotropic quantum materials,” Nature Communications, vol. 9, no. 1. Springer Nature, p. 3975, 2018.","ama":"Modic KA, Bachmann MD, Ramshaw BJ, et al. Resonant torsion magnetometry in anisotropic quantum materials. Nature Communications. 2018;9(1):3975. doi:10.1038/s41467-018-06412-w"},"publication":"Nature Communications","issue":"1","abstract":[{"text":"Unusual behavior in quantum materials commonly arises from their effective low-dimensional physics, reflecting the underlying anisotropy in the spin and charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2, the second derivative of the free energy F with respect to the magnetic field orientation θ in the crystal. We show that the magnetotropic coefficient can be quantitatively determined from a shift in the resonant frequency of a commercially available atomic force microscopy cantilever under magnetic field. This detection method enables part per 100 million sensitivity and the ability to measure magnetic anisotropy in nanogram-scale samples, as demonstrated on the Weyl semimetal NbP. Measurement of the magnetotropic coefficient in the spin-liquid candidate RuCl3 highlights its sensitivity to anisotropic phase transitions and allows a quantitative comparison to other thermodynamic coefficients via the Ehrenfest relations.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7088","checksum":"46a313c816e66899d4dad2cf3583e5b0","date_updated":"2020-07-14T12:47:48Z","date_created":"2019-11-20T12:48:58Z","access_level":"open_access","file_name":"2018_NatureComm_Modic.pdf","content_type":"application/pdf","file_size":1257681,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 9","title":"Resonant torsion magnetometry in anisotropic quantum materials","ddc":["530"],"status":"public","_id":"7059","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2041-1723"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-06412-w","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"extern":"1","file_date_updated":"2020-07-14T12:47:48Z","volume":9,"date_created":"2019-11-19T13:02:20Z","date_updated":"2021-01-12T08:11:37Z","author":[{"first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A"},{"full_name":"Bachmann, Maja D.","last_name":"Bachmann","first_name":"Maja D."},{"full_name":"Ramshaw, B. J.","first_name":"B. J.","last_name":"Ramshaw"},{"first_name":"F.","last_name":"Arnold","full_name":"Arnold, F."},{"last_name":"Shirer","first_name":"K. R.","full_name":"Shirer, K. R."},{"first_name":"Amelia","last_name":"Estry","full_name":"Estry, Amelia"},{"first_name":"J. B.","last_name":"Betts","full_name":"Betts, J. B."},{"full_name":"Ghimire, Nirmal J.","last_name":"Ghimire","first_name":"Nirmal J."},{"first_name":"E. D.","last_name":"Bauer","full_name":"Bauer, E. D."},{"first_name":"Marcus","last_name":"Schmidt","full_name":"Schmidt, Marcus"},{"full_name":"Baenitz, Michael","last_name":"Baenitz","first_name":"Michael"},{"full_name":"Svanidze, E.","first_name":"E.","last_name":"Svanidze"},{"last_name":"McDonald","first_name":"Ross D.","full_name":"McDonald, Ross D."},{"first_name":"Arkady","last_name":"Shekhter","full_name":"Shekhter, Arkady"},{"last_name":"Moll","first_name":"Philip J. W.","full_name":"Moll, Philip J. W."}],"publisher":"Springer Nature","publication_status":"published","year":"2018"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7058","status":"public","title":"Chiral spin order in some purported Kitaev spin-liquid compounds","intvolume":" 98","abstract":[{"text":"We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3 and RuCl3, which have been discussed as possible realizations of the Kitaev model. The analysis of the reported discontinuity in torque, as an external magnetic field is rotated across the c axis in both crystals, suggests that they have a translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the ground state and persisting over a very wide range of magnetic field and temperature. An extraordinary |B|B2 dependence of the torque for small fields, beside the usual B2 part, is predicted by the chiral spin order. Data for small fields are available for γ−Li2IrO3 and are found to be consistent with the prediction upon further analysis. Other experiments such as inelastic scattering and thermal Hall effect and several questions raised by the discovery of chiral spin order, including its topological consequences, are discussed.","lang":"eng"}],"issue":"20","type":"journal_article","date_published":"2018-11-05T00:00:00Z","publication":"Physical Review B","citation":{"ista":"Modic KA, Ramshaw BJ, Shekhter A, Varma CM. 2018. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 98(20), 205110.","ieee":"K. A. Modic, B. J. Ramshaw, A. Shekhter, and C. M. Varma, “Chiral spin order in some purported Kitaev spin-liquid compounds,” Physical Review B, vol. 98, no. 20. APS, 2018.","apa":"Modic, K. A., Ramshaw, B. J., Shekhter, A., & Varma, C. M. (2018). Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. APS. https://doi.org/10.1103/physrevb.98.205110","ama":"Modic KA, Ramshaw BJ, Shekhter A, Varma CM. Chiral spin order in some purported Kitaev spin-liquid compounds. Physical Review B. 2018;98(20). doi:10.1103/physrevb.98.205110","chicago":"Modic, Kimberly A, B. J. Ramshaw, A. Shekhter, and C. M. Varma. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B. APS, 2018. https://doi.org/10.1103/physrevb.98.205110.","mla":"Modic, Kimberly A., et al. “Chiral Spin Order in Some Purported Kitaev Spin-Liquid Compounds.” Physical Review B, vol. 98, no. 20, 205110, APS, 2018, doi:10.1103/physrevb.98.205110.","short":"K.A. Modic, B.J. Ramshaw, A. Shekhter, C.M. Varma, Physical Review B 98 (2018)."},"article_type":"original","day":"05","article_processing_charge":"No","author":[{"full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","first_name":"Kimberly A"},{"last_name":"Ramshaw","first_name":"B. J.","full_name":"Ramshaw, B. J."},{"first_name":"A.","last_name":"Shekhter","full_name":"Shekhter, A."},{"full_name":"Varma, C. M.","first_name":"C. M.","last_name":"Varma"}],"date_created":"2019-11-19T13:01:31Z","date_updated":"2021-01-12T08:11:36Z","volume":98,"year":"2018","publication_status":"published","publisher":"APS","extern":"1","article_number":"205110 ","doi":"10.1103/physrevb.98.205110","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.06637"}],"external_id":{"arxiv":["1807.06637"]},"oa":1,"quality_controlled":"1","month":"11","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"abstract":[{"lang":"eng","text":"The anomalous metallic state in the high-temperature superconducting cuprates is masked by superconductivity near a quantum critical point. Applying high magnetic fields to suppress superconductivity has enabled detailed studies of the normal state, yet the direct effect of strong magnetic fields on the metallic state is poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4 cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that the metallic state exposed by suppressing superconductivity is characterized by magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude of the linear-in-field resistivity mirrors the magnitude and doping evolution of the well-known linear-in-temperature resistivity that has been associated with quantum criticality in high-temperature superconductors."}],"issue":"6401","extern":"1","type":"journal_article","author":[{"full_name":"Giraldo-Gallo, P.","first_name":"P.","last_name":"Giraldo-Gallo"},{"full_name":"Galvis, J. A.","first_name":"J. A.","last_name":"Galvis"},{"last_name":"Stegen","first_name":"Z.","full_name":"Stegen, Z."},{"first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A"},{"last_name":"Balakirev","first_name":"F. F.","full_name":"Balakirev, F. F."},{"last_name":"Betts","first_name":"J. B.","full_name":"Betts, J. B."},{"last_name":"Lian","first_name":"X.","full_name":"Lian, X."},{"full_name":"Moir, C.","first_name":"C.","last_name":"Moir"},{"first_name":"S. C.","last_name":"Riggs","full_name":"Riggs, S. C."},{"full_name":"Wu, J.","last_name":"Wu","first_name":"J."},{"last_name":"Bollinger","first_name":"A. T.","full_name":"Bollinger, A. T."},{"first_name":"X.","last_name":"He","full_name":"He, X."},{"last_name":"Božović","first_name":"I.","full_name":"Božović, I."},{"last_name":"Ramshaw","first_name":"B. J.","full_name":"Ramshaw, B. J."},{"full_name":"McDonald, R. D.","last_name":"McDonald","first_name":"R. D."},{"first_name":"G. S.","last_name":"Boebinger","full_name":"Boebinger, G. S."},{"first_name":"A.","last_name":"Shekhter","full_name":"Shekhter, A."}],"date_created":"2019-11-19T13:03:16Z","date_updated":"2021-01-12T08:11:37Z","volume":361,"oa_version":"None","year":"2018","_id":"7060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Scale-invariant magnetoresistance in a cuprate superconductor","status":"public","publication_status":"published","intvolume":" 361","publisher":"AAAS","month":"08","day":"03","article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"date_published":"2018-08-03T00:00:00Z","doi":"10.1126/science.aan3178","language":[{"iso":"eng"}],"publication":"Science","citation":{"ista":"Giraldo-Gallo P, Galvis JA, Stegen Z, Modic KA, Balakirev FF, Betts JB, Lian X, Moir C, Riggs SC, Wu J, Bollinger AT, He X, Božović I, Ramshaw BJ, McDonald RD, Boebinger GS, Shekhter A. 2018. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 361(6401), 479–481.","apa":"Giraldo-Gallo, P., Galvis, J. A., Stegen, Z., Modic, K. A., Balakirev, F. F., Betts, J. B., … Shekhter, A. (2018). Scale-invariant magnetoresistance in a cuprate superconductor. Science. AAAS. https://doi.org/10.1126/science.aan3178","ieee":"P. Giraldo-Gallo et al., “Scale-invariant magnetoresistance in a cuprate superconductor,” Science, vol. 361, no. 6401. AAAS, pp. 479–481, 2018.","ama":"Giraldo-Gallo P, Galvis JA, Stegen Z, et al. Scale-invariant magnetoresistance in a cuprate superconductor. Science. 2018;361(6401):479-481. doi:10.1126/science.aan3178","chicago":"Giraldo-Gallo, P., J. A. Galvis, Z. Stegen, Kimberly A Modic, F. F. Balakirev, J. B. Betts, X. Lian, et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science. AAAS, 2018. https://doi.org/10.1126/science.aan3178.","mla":"Giraldo-Gallo, P., et al. “Scale-Invariant Magnetoresistance in a Cuprate Superconductor.” Science, vol. 361, no. 6401, AAAS, 2018, pp. 479–81, doi:10.1126/science.aan3178.","short":"P. Giraldo-Gallo, J.A. Galvis, Z. Stegen, K.A. Modic, F.F. Balakirev, J.B. Betts, X. Lian, C. Moir, S.C. Riggs, J. Wu, A.T. Bollinger, X. He, I. Božović, B.J. Ramshaw, R.D. McDonald, G.S. Boebinger, A. Shekhter, Science 361 (2018) 479–481."},"quality_controlled":"1","article_type":"original","page":"479-481"},{"file":[{"creator":"dernst","file_size":1603204,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_OpenProceedings_Grubic.pdf","checksum":"ec979b56abc71016d6e6adfdadbb4afe","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-26T14:23:04Z","file_id":"7118","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7116","status":"public","ddc":["000"],"title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","abstract":[{"text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.","lang":"eng"}],"type":"conference","date_published":"2018-03-26T00:00:00Z","citation":{"ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14."},"publication":"Proceedings of the 21st International Conference on Extending Database Technology","page":"145-156","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":1,"author":[{"first_name":"Demjan","last_name":"Grubic","full_name":"Grubic, Demjan"},{"first_name":"Leo","last_name":"Tam","full_name":"Tam, Leo"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"}],"date_updated":"2023-02-23T12:59:17Z","date_created":"2019-11-26T14:19:11Z","year":"2018","department":[{"_id":"DaAl"}],"publisher":"OpenProceedings","publication_status":"published","file_date_updated":"2020-07-14T12:47:49Z","doi":"10.5441/002/EDBT.2018.14","conference":{"name":"EDBT: Conference on Extending Database Technology","start_date":"2018-03-26","location":"Vienna, Austria","end_date":"2018-03-29"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","publication_identifier":{"issn":["2367-2005"],"isbn":["9783893180783"]},"month":"03"},{"issue":"10","abstract":[{"lang":"eng","text":"In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are taken as generative models of samples, they generate samples with broad empirical distributions and with a high value of the relevance, defined as the entropy of the empirical frequencies. These results are derived for different statistical models (Dirichlet model, independent and pairwise dependent spin models, and restricted Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition point where the symmetry between the sampled outcomes is spontaneously broken. The order parameter controlling the phase transition is the coding cost of the samples. The phase transition is a manifestation of the optimality of MDL codes, and it arises because codes that achieve a higher compression do not exist. These results suggest a clear interpretation of the widespread occurrence of statistical criticality as a characterization of samples which are maximally informative on the underlying generative process."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"d642b7b661e1d5066b62e6ea9986b917","date_created":"2019-11-26T22:23:08Z","date_updated":"2020-07-14T12:47:50Z","file_id":"7127","relation":"main_file","creator":"rcubero","file_size":1366813,"content_type":"application/pdf","access_level":"open_access","file_name":"entropy-20-00755-v2.pdf"}],"intvolume":" 20","title":"Minimum description length codes are critical","status":"public","ddc":["519"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7126","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["Minimum Description Length","normalized maximum likelihood","statistical criticality","phase transitions","large deviations"],"date_published":"2018-10-01T00:00:00Z","article_type":"original","citation":{"ista":"Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are critical. Entropy. 20(10), 755.","apa":"Cubero, R. J., Marsili, M., & Roudi, Y. (2018). Minimum description length codes are critical. Entropy. MDPI. https://doi.org/10.3390/e20100755","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes are critical,” Entropy, vol. 20, no. 10. MDPI, 2018.","ama":"Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical. Entropy. 2018;20(10). doi:10.3390/e20100755","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description Length Codes Are Critical.” Entropy. MDPI, 2018. https://doi.org/10.3390/e20100755.","mla":"Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” Entropy, vol. 20, no. 10, 755, MDPI, 2018, doi:10.3390/e20100755.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018)."},"publication":"Entropy","extern":"1","file_date_updated":"2020-07-14T12:47:50Z","article_number":"755","volume":20,"date_created":"2019-11-26T22:18:05Z","date_updated":"2021-01-12T08:11:56Z","author":[{"first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J"},{"full_name":"Marsili, Matteo","last_name":"Marsili","first_name":"Matteo"},{"last_name":"Roudi","first_name":"Yasser","full_name":"Roudi, Yasser"}],"publisher":"MDPI","publication_status":"published","year":"2018","publication_identifier":{"issn":["1099-4300"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.3390/e20100755","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"page":"5529-5533","article_type":"original","citation":{"mla":"Mahne, Nika, et al. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition, vol. 57, no. 19, Wiley, 2018, pp. 5529–33, doi:10.1002/anie.201802277.","short":"N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie International Edition 57 (2018) 5529–5533.","chicago":"Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander Freunberger. “Electrochemical Oxidation of Lithium Carbonate Generates Singlet Oxygen.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201802277.","ama":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 2018;57(19):5529-5533. doi:10.1002/anie.201802277","ista":"Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. 57(19), 5529–5533.","ieee":"N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Electrochemical oxidation of Lithium Carbonate generates singlet oxygen,” Angewandte Chemie International Edition, vol. 57, no. 19. Wiley, pp. 5529–5533, 2018.","apa":"Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018). Electrochemical oxidation of Lithium Carbonate generates singlet oxygen. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201802277"},"publication":"Angewandte Chemie International Edition","date_published":"2018-03-15T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"15","intvolume":" 57","ddc":["540"],"status":"public","title":"Electrochemical oxidation of Lithium Carbonate generates singlet oxygen","_id":"7277","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"7357","checksum":"45868d0adc2d13a506bb9a59eb4f409c","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-01-22T16:28:31Z","access_level":"open_access","file_name":"2018_AngewChemie_Mahne.pdf","file_size":657963,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"19","abstract":[{"lang":"eng","text":"Solid alkali metal carbonates are universal passivation layer components of intercalation battery materials and common side products in metal‐O2 batteries, and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs. Li/Li+. However, O2 evolution, as would be expected according to the decomposition reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted for, which was previously ascribed to unidentified parasitic reactions. Here, we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3 in an aprotic electrolyte and therefore does not evolve as O2. These results have substantial implications for the long‐term cyclability of batteries: they underpin the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and help explain the interfacial reactivity of transition‐metal cathodes with residual Li2CO3."}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"doi":"10.1002/anie.201802277","publication_identifier":{"issn":["1433-7851"]},"month":"03","publisher":"Wiley","publication_status":"published","year":"2018","volume":57,"date_updated":"2021-01-12T08:12:42Z","date_created":"2020-01-15T07:20:09Z","author":[{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"full_name":"Renfrew, Sara E.","first_name":"Sara E.","last_name":"Renfrew"},{"first_name":"Bryan D.","last_name":"McCloskey","full_name":"McCloskey, Bryan D."},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"}],"extern":"1","file_date_updated":"2020-07-14T12:47:55Z"},{"publication_identifier":{"issn":["2574-0970"]},"article_processing_charge":"No","day":"28","month":"09","language":[{"iso":"eng"}],"date_published":"2018-09-28T00:00:00Z","doi":"10.1021/acsanm.8b01036","page":"4863-4874","quality_controlled":"1","article_type":"original","citation":{"mla":"Costanzo, Tommaso, et al. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials, vol. 1, no. 9, ACS, 2018, pp. 4863–74, doi:10.1021/acsanm.8b01036.","short":"T. Costanzo, J. McCracken, A. Rotaru, G. Caruntu, ACS Applied Nano Materials 1 (2018) 4863–4874.","chicago":"Costanzo, Tommaso, John McCracken, Aurelian Rotaru, and Gabriel Caruntu. “Quasi-Monodisperse Transition-Metal-Doped BaTiO3 (M = Cr, Mn, Fe, Co) Colloidal Nanocrystals with Multiferroic Properties.” ACS Applied Nano Materials. ACS, 2018. https://doi.org/10.1021/acsanm.8b01036.","ama":"Costanzo T, McCracken J, Rotaru A, Caruntu G. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 2018;1(9):4863-4874. doi:10.1021/acsanm.8b01036","ista":"Costanzo T, McCracken J, Rotaru A, Caruntu G. 2018. Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. 1(9), 4863–4874.","apa":"Costanzo, T., McCracken, J., Rotaru, A., & Caruntu, G. (2018). Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties. ACS Applied Nano Materials. ACS. https://doi.org/10.1021/acsanm.8b01036","ieee":"T. Costanzo, J. McCracken, A. Rotaru, and G. Caruntu, “Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties,” ACS Applied Nano Materials, vol. 1, no. 9. ACS, pp. 4863–4874, 2018."},"publication":"ACS Applied Nano Materials","extern":"1","issue":"9","abstract":[{"text":"The recent demand of multifunctional materials and devices for advanced applications in energy conversion and data storage resulted into a revival of multiferroics, that is, materials characterized by the coexistence of ferromagnetism and ferroelectricity. Despite intense efforts made in the past decade, single-phase room temperature multiferroics are yet to be discovered/fabricated. Nanostructured ferroic materials could potentially exhibit multiferroism since a high fraction of their atoms/ions are superficial, thereby altering significantly the properties of the bulk phase. Alternately, a magnetic order can be induced into ferroelectric materials upon aliovalent doping with magnetic ions. Here, we report on the synthesis of aggregate-free single-phase transition-metal-doped BaTiO3 quasi-monodisperse cuboidal nanocrystals (NC) which exhibit multiferroic properties at room temperature and can be suitable for applications in data storage. The proposed synthetic route allows the inclusion of a high concentration of magnetic ions such as Mn+ (M = Cr, Mn, Fe, Co) up to a nominal concentration of 4% without the formation of any secondary phase. The size of the nanocrystals was controlled in a wide range from ∼15 up to ∼70 nm by varying the reaction time from 48 to 144 h. The presence of unpaired electrons and their magnetic ordering have been probed by electron paramagnetic resonance spectroscopy (EPR), and a vibrating sample magnetometer (VSM). Likewise, an acentric structure, associated with the existence of a dielectric polarization, was observed by lattice dynamics analysis and piezoresponse force microscopy (PFM). These results show that high-quality titanium-containing perovskite nanocrystals which display multiferroic properties at room temperature can be fabricated via soft solution-based synthetic routes, and the properties of these materials can be modulated by changing the size of the nanocrystals and the concentration of the dopant thereby opening the door to the design and study of single-phase multiferroic materials.","lang":"eng"}],"type":"journal_article","volume":1,"oa_version":"None","date_created":"2020-01-13T21:58:27Z","date_updated":"2023-02-23T13:02:57Z","author":[{"full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815"},{"full_name":"McCracken, John","last_name":"McCracken","first_name":"John"},{"full_name":"Rotaru, Aurelian","last_name":"Rotaru","first_name":"Aurelian"},{"last_name":"Caruntu","first_name":"Gabriel","full_name":"Caruntu, Gabriel"}],"intvolume":" 1","publisher":"ACS","publication_status":"published","title":"Quasi-monodisperse transition-metal-doped BaTiO3 (M = Cr, Mn, Fe, Co) colloidal nanocrystals with multiferroic properties","status":"public","_id":"7271","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018"},{"article_type":"letter_note","page":"170-176","publication":"ACS Energy Letters","citation":{"chicago":"Schafzahl, Bettina, Eléonore Mourad, Lukas Schafzahl, Yann K. Petit, Anjana R. Raju, Musthafa Ottakam Thotiyl, Martin Wilkening, Christian Slugovc, and Stefan Alexander Freunberger. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters. ACS, 2018. https://doi.org/10.1021/acsenergylett.7b01111.","short":"B. Schafzahl, E. Mourad, L. Schafzahl, Y.K. Petit, A.R. Raju, M.O. Thotiyl, M. Wilkening, C. Slugovc, S.A. Freunberger, ACS Energy Letters 3 (2018) 170–176.","mla":"Schafzahl, Bettina, et al. “Quantifying Total Superoxide, Peroxide, and Carbonaceous Compounds in Metal–O2 Batteries and the Solid Electrolyte Interphase.” ACS Energy Letters, vol. 3, no. 1, ACS, 2018, pp. 170–76, doi:10.1021/acsenergylett.7b01111.","apa":"Schafzahl, B., Mourad, E., Schafzahl, L., Petit, Y. K., Raju, A. R., Thotiyl, M. O., … Freunberger, S. A. (2018). Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. ACS. https://doi.org/10.1021/acsenergylett.7b01111","ieee":"B. Schafzahl et al., “Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase,” ACS Energy Letters, vol. 3, no. 1. ACS, pp. 170–176, 2018.","ista":"Schafzahl B, Mourad E, Schafzahl L, Petit YK, Raju AR, Thotiyl MO, Wilkening M, Slugovc C, Freunberger SA. 2018. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 3(1), 170–176.","ama":"Schafzahl B, Mourad E, Schafzahl L, et al. Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase. ACS Energy Letters. 2018;3(1):170-176. doi:10.1021/acsenergylett.7b01111"},"date_published":"2018-01-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase","ddc":["540","543","546","547"],"intvolume":" 3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7287","file":[{"content_type":"application/pdf","file_size":1892355,"creator":"sfreunbe","access_level":"open_access","file_name":"O2 TIOC_fin_incl_SI.pdf","checksum":"461ccf575ba077af90314fe72d20521e","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-06-29T14:19:36Z","relation":"main_file","file_id":"8049"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Passivation layers on electrode materials are ubiquitous in nonaqueous battery chemistries and strongly govern performance and lifetime. They comprise breakdown products of the electrolyte including carbonate, alkyl carbonates, alkoxides, carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar products and is tied to the deviation of the O2 balance from the ideal stoichiometry during formation/decomposition of alkaline peroxides or superoxides. Accurate and integral quantification of carbonaceous species and peroxides or superoxides in battery electrodes remains, however, elusive. We present a refined procedure to quantify them accurately and sensitively by pointing out and rectifying pitfalls of previous procedures. Carbonaceous compounds are differentiated into inorganic and organic ones. We combine mass and UV–vis spectrometry to quantify evolved O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid treatment and Fenton’s reaction. The capabilities of the method are exemplified by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2 cathodes."}],"issue":"1","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acsenergylett.7b01111","month":"01","publication_identifier":{"issn":["2380-8195","2380-8195"]},"publication_status":"published","publisher":"ACS","year":"2018","date_created":"2020-01-15T12:13:52Z","date_updated":"2021-01-12T08:12:46Z","volume":3,"author":[{"last_name":"Schafzahl","first_name":"Bettina","full_name":"Schafzahl, Bettina"},{"full_name":"Mourad, Eléonore","last_name":"Mourad","first_name":"Eléonore"},{"first_name":"Lukas","last_name":"Schafzahl","full_name":"Schafzahl, Lukas"},{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"first_name":"Anjana R.","last_name":"Raju","full_name":"Raju, Anjana R."},{"first_name":"Musthafa Ottakam","last_name":"Thotiyl","full_name":"Thotiyl, Musthafa Ottakam"},{"full_name":"Wilkening, Martin","first_name":"Martin","last_name":"Wilkening"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"extern":"1","file_date_updated":"2020-07-14T12:47:55Z"},{"date_created":"2020-01-15T12:13:25Z","date_updated":"2021-01-12T08:12:46Z","volume":12,"author":[{"full_name":"Burian, Max","first_name":"Max","last_name":"Burian"},{"last_name":"Rigodanza","first_name":"Francesco","full_name":"Rigodanza, Francesco"},{"full_name":"Demitri, Nicola","last_name":"Demitri","first_name":"Nicola"},{"first_name":"Luka","last_name":"D̵ord̵ević","full_name":"D̵ord̵ević, Luka"},{"full_name":"Marchesan, Silvia","last_name":"Marchesan","first_name":"Silvia"},{"last_name":"Steinhartova","first_name":"Tereza","full_name":"Steinhartova, Tereza"},{"last_name":"Letofsky-Papst","first_name":"Ilse","full_name":"Letofsky-Papst, Ilse"},{"last_name":"Khalakhan","first_name":"Ivan","full_name":"Khalakhan, Ivan"},{"full_name":"Mourad, Eléonore","last_name":"Mourad","first_name":"Eléonore"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"last_name":"Amenitsch","first_name":"Heinz","full_name":"Amenitsch, Heinz"},{"full_name":"Prato, Maurizio","first_name":"Maurizio","last_name":"Prato"},{"full_name":"Syrgiannis, Zois","last_name":"Syrgiannis","first_name":"Zois"}],"publication_status":"published","publisher":"ACS","year":"2018","extern":"1","file_date_updated":"2020-07-14T12:47:55Z","language":[{"iso":"eng"}],"doi":"10.1021/acsnano.8b01689","quality_controlled":"1","oa":1,"month":"06","publication_identifier":{"issn":["1936-0851"]},"oa_version":"Submitted Version","file":[{"creator":"sfreunbe","file_size":1333353,"content_type":"application/pdf","access_level":"open_access","file_name":"Manuscript 20092017_subm.pdf","checksum":"050f7f0ba5d845c5c71779ef14ad5ef3","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-06-29T14:56:40Z","file_id":"8052","relation":"main_file"}],"ddc":["540","541"],"title":"Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels","status":"public","intvolume":" 12","_id":"7285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Hydrogelation, the self-assembly of molecules into soft, water-loaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for long-range conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its long-range conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbon-like structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels."}],"issue":"6","type":"journal_article","date_published":"2018-06-05T00:00:00Z","article_type":"original","page":"5800-5806","publication":"ACS Nano","citation":{"short":"M. Burian, F. Rigodanza, N. Demitri, L. D̵ord̵ević, S. Marchesan, T. Steinhartova, I. Letofsky-Papst, I. Khalakhan, E. Mourad, S.A. Freunberger, H. Amenitsch, M. Prato, Z. Syrgiannis, ACS Nano 12 (2018) 5800–5806.","mla":"Burian, Max, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano, vol. 12, no. 6, ACS, 2018, pp. 5800–06, doi:10.1021/acsnano.8b01689.","chicago":"Burian, Max, Francesco Rigodanza, Nicola Demitri, Luka D̵ord̵ević, Silvia Marchesan, Tereza Steinhartova, Ilse Letofsky-Papst, et al. “Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.” ACS Nano. ACS, 2018. https://doi.org/10.1021/acsnano.8b01689.","ama":"Burian M, Rigodanza F, Demitri N, et al. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 2018;12(6):5800-5806. doi:10.1021/acsnano.8b01689","apa":"Burian, M., Rigodanza, F., Demitri, N., D̵ord̵ević, L., Marchesan, S., Steinhartova, T., … Syrgiannis, Z. (2018). Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. ACS. https://doi.org/10.1021/acsnano.8b01689","ieee":"M. Burian et al., “Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels,” ACS Nano, vol. 12, no. 6. ACS, pp. 5800–5806, 2018.","ista":"Burian M, Rigodanza F, Demitri N, D̵ord̵ević L, Marchesan S, Steinhartova T, Letofsky-Papst I, Khalakhan I, Mourad E, Freunberger SA, Amenitsch H, Prato M, Syrgiannis Z. 2018. Inter-backbone charge transfer as prerequisite for long-range conductivity in perylene bisimide hydrogels. ACS Nano. 12(6), 5800–5806."},"day":"05","article_processing_charge":"No","has_accepted_license":"1"},{"day":"03","month":"05","article_processing_charge":"No","publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"date_published":"2018-05-03T00:00:00Z","doi":"10.1021/acs.chemmater.8b00750","language":[{"iso":"eng"}],"publication":"Chemistry of Materials","citation":{"ista":"Schafzahl L, Ehmann H, Kriechbaum M, Sattelkow J, Ganner T, Plank H, Wilkening M, Freunberger SA. 2018. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 30(10), 3338–3345.","ieee":"L. Schafzahl et al., “Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties,” Chemistry of Materials, vol. 30, no. 10. ACS, pp. 3338–3345, 2018.","apa":"Schafzahl, L., Ehmann, H., Kriechbaum, M., Sattelkow, J., Ganner, T., Plank, H., … Freunberger, S. A. (2018). Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.8b00750","ama":"Schafzahl L, Ehmann H, Kriechbaum M, et al. Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties. Chemistry of Materials. 2018;30(10):3338-3345. doi:10.1021/acs.chemmater.8b00750","chicago":"Schafzahl, Lukas, Heike Ehmann, Manfred Kriechbaum, Jürgen Sattelkow, Thomas Ganner, Harald Plank, Martin Wilkening, and Stefan Alexander Freunberger. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials. ACS, 2018. https://doi.org/10.1021/acs.chemmater.8b00750.","mla":"Schafzahl, Lukas, et al. “Long-Chain Li and Na Alkyl Carbonates as Solid Electrolyte Interphase Components: Structure, Ion Transport, and Mechanical Properties.” Chemistry of Materials, vol. 30, no. 10, ACS, 2018, pp. 3338–45, doi:10.1021/acs.chemmater.8b00750.","short":"L. Schafzahl, H. Ehmann, M. Kriechbaum, J. Sattelkow, T. Ganner, H. Plank, M. Wilkening, S.A. Freunberger, Chemistry of Materials 30 (2018) 3338–3345."},"quality_controlled":"1","article_type":"original","page":"3338-3345","abstract":[{"lang":"eng","text":"The solid electrolyte interphase (SEI) in Li and Na ion batteries forms when highly reducing or oxidizing electrode materials come into contact with a liquid organic electrolyte. Its ability to form a mechanically robust, ion-conducting, and electron-insulating layer critically determines performance, cycle life, and safety. Li or Na alkyl carbonates (LiAC and NaAC, respectively) are lead SEI components in state-of-the-art carbonate based electrolytes, and our fundamental understanding of their charge transport and mechanical properties may hold the key to designing electrolytes forming an improved SEI. We synthesized a homologous series of LiACs and NaACs from methyl to octyl analogues and characterized them with respect to structure, ionic conductivity, and stiffness. The compounds assume layered structures except for the lithium methyl carbonate. Room-temperature conductivities were found to be ∼10–9 S cm–1 for lithium methyl carbonate, <10–12 S cm–1 for the other LiACs, and <10–12 S cm–1 for the NaACs with ion transport mostly attributed to grain boundaries. While LiACs show stiffnesses of ∼1 GPa, NaACs become significantly softer with increasing chain lengths. These findings will help to more precisely interpret the complex results from charge transport and mechanical characterization of real SEIs and can give a rationale for influencing the SEI’s mechanical properties via the electrolyte."}],"issue":"10","extern":"1","type":"journal_article","author":[{"last_name":"Schafzahl","first_name":"Lukas","full_name":"Schafzahl, Lukas"},{"full_name":"Ehmann, Heike","first_name":"Heike","last_name":"Ehmann"},{"first_name":"Manfred","last_name":"Kriechbaum","full_name":"Kriechbaum, Manfred"},{"full_name":"Sattelkow, Jürgen","last_name":"Sattelkow","first_name":"Jürgen"},{"full_name":"Ganner, Thomas","last_name":"Ganner","first_name":"Thomas"},{"full_name":"Plank, Harald","first_name":"Harald","last_name":"Plank"},{"last_name":"Wilkening","first_name":"Martin","full_name":"Wilkening, Martin"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"date_updated":"2021-01-12T08:12:46Z","date_created":"2020-01-15T12:13:37Z","volume":30,"oa_version":"None","_id":"7286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","title":"Long-chain Li and Na alkyl carbonates as solid electrolyte interphase components: Structure, ion transport, and mechanical properties","status":"public","publication_status":"published","publisher":"ACS","intvolume":" 30"},{"file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2020-01-30T09:16:05Z","date_updated":"2021-01-12T08:13:26Z","volume":124,"year":"2018","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","month":"12","publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"conference":{"name":"ITCS: Innovations in theoretical Computer Science Conference","start_date":"2019-01-10","location":"San Diego, CA, United States","end_date":"2019-01-12"},"doi":"10.4230/LIPICS.ITCS.2019.59","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/194"}],"oa":1,"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"abstract":[{"text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"checksum":"5cebb7f7849a3beda898f697d755dd96","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T08:17:52Z","file_id":"7443","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":822884,"access_level":"open_access","file_name":"2018_LIPIcs_Pietrzak.pdf"}],"_id":"7407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Proofs of catalytic space","status":"public","intvolume":" 124","day":"31","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2018-12-31T00:00:00Z","publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","citation":{"ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59."},"page":"59:1-59:25"},{"day":"10","month":"08","article_processing_charge":"No","publication_identifier":{"issn":["0021-8979","1089-7550"]},"date_published":"2018-08-10T00:00:00Z","doi":"10.1063/1.5038726","language":[{"iso":"eng"}],"publication":"Journal of Applied Physics","citation":{"ieee":"D. Viehland et al., “Tutorial: Product properties in multiferroic nanocomposites,” Journal of Applied Physics, vol. 124, no. 6. AIP, 2018.","apa":"Viehland, D., Li, J. F., Yang, Y., Costanzo, T., Yourdkhani, A., Caruntu, G., … Srinivasan, G. (2018). Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. AIP. https://doi.org/10.1063/1.5038726","ista":"Viehland D, Li JF, Yang Y, Costanzo T, Yourdkhani A, Caruntu G, Zhou P, Zhang T, Li T, Gupta A, Popov M, Srinivasan G. 2018. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 124(6), 061101.","ama":"Viehland D, Li JF, Yang Y, et al. Tutorial: Product properties in multiferroic nanocomposites. Journal of Applied Physics. 2018;124(6). doi:10.1063/1.5038726","chicago":"Viehland, Dwight, Jie Fang Li, Yaodong Yang, Tommaso Costanzo, Amin Yourdkhani, Gabriel Caruntu, Peng Zhou, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics. AIP, 2018. https://doi.org/10.1063/1.5038726.","short":"D. Viehland, J.F. Li, Y. Yang, T. Costanzo, A. Yourdkhani, G. Caruntu, P. Zhou, T. Zhang, T. Li, A. Gupta, M. Popov, G. Srinivasan, Journal of Applied Physics 124 (2018).","mla":"Viehland, Dwight, et al. “Tutorial: Product Properties in Multiferroic Nanocomposites.” Journal of Applied Physics, vol. 124, no. 6, 061101, AIP, 2018, doi:10.1063/1.5038726."},"quality_controlled":"1","article_type":"original","abstract":[{"text":"The coupling between magnetic and electric subsystems in composites of ferromagnetic and ferroelectric phases is a product property that is facilitated by mechanical strain that arises due to magnetostriction and the piezoelectric effect in the constituent phases. Such multiferroic composites are of immense interests for studies on the physics of electromagnetic coupling and for use in a variety of applications. Here, we focus on magneto-electric (ME) coupling in nanocomposites. Particular emphasis is on core-shell particles and coaxial fibers, thin film heterostructures, and planar structures with a variety of mechanical connectivity. A brief review of models that predict strong ME effects in nanostructures is followed by synthesis and characterization. Core-shell particulate composites can be prepared by hydrothermal processes and chemical or deoxyribonucleic acid-assisted assembly. Electrospinning techniques have been utilized to prepare defect free core-shell nanofibers. Core-shell particles and fibers can be assembled into superstructures with the aid of magnetic and electric fields and characterized for possible use in advanced technologies. Chemical-vapor deposition techniques have been shown to be effective for the preparation of heterostructures of ferrites and ferroelectrics. Exotic planar multiferroic structures with potential for enhancing ME coupling strengths are also considered. Scanning probe microscopy techniques are ideal for probing the nature of direct- and converse-ME coupling in individual nanostructures. Magnetoelectric characterization of assemblies of nanocomposites can be done by ME voltage coefficient, magnetic field induced polarization, and magneto-dielectric effects. We conclude with a brief discussion on possible avenues for strengthening the product properties in the nanocomposites.","lang":"eng"}],"issue":"6","extern":"1","article_number":"061101","type":"journal_article","author":[{"first_name":"Dwight","last_name":"Viehland","full_name":"Viehland, Dwight"},{"first_name":"Jie Fang","last_name":"Li","full_name":"Li, Jie Fang"},{"last_name":"Yang","first_name":"Yaodong","full_name":"Yang, Yaodong"},{"full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815"},{"first_name":"Amin","last_name":"Yourdkhani","full_name":"Yourdkhani, Amin"},{"last_name":"Caruntu","first_name":"Gabriel","full_name":"Caruntu, Gabriel"},{"full_name":"Zhou, Peng","first_name":"Peng","last_name":"Zhou"},{"full_name":"Zhang, Tianjin","first_name":"Tianjin","last_name":"Zhang"},{"first_name":"Tianqian","last_name":"Li","full_name":"Li, Tianqian"},{"first_name":"Arunava","last_name":"Gupta","full_name":"Gupta, Arunava"},{"last_name":"Popov","first_name":"Maksym","full_name":"Popov, Maksym"},{"full_name":"Srinivasan, Gopalan","first_name":"Gopalan","last_name":"Srinivasan"}],"date_updated":"2023-02-23T13:08:29Z","date_created":"2020-02-05T14:18:22Z","oa_version":"None","volume":124,"_id":"7458","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publication_status":"published","title":"Tutorial: Product properties in multiferroic nanocomposites","status":"public","publisher":"AIP","intvolume":" 124"},{"oa_version":"Published Version","_id":"7717","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","title":"Genotype effects contribute to variation in longitudinal methylome patterns in older people","status":"public","issue":"1","abstract":[{"lang":"eng","text":"Background: DNA methylation levels change along with age, but few studies have examined the variation in the rate of such changes between individuals.\r\nMethods: We performed a longitudinal analysis to quantify the variation in the rate of change of DNA methylation between individuals using whole blood DNA methylation array profiles collected at 2–4 time points (N = 2894) in 954 individuals (67–90 years).\r\nResults: After stringent quality control, we identified 1507 DNA methylation CpG sites (rsCpGs) with statistically significant variation in the rate of change (random slope) of DNA methylation among individuals in a mixed linear model analysis. Genes in the vicinity of these rsCpGs were found to be enriched in Homeobox transcription factors and the Wnt signalling pathway, both of which are related to ageing processes. Furthermore, we investigated the SNP effect on the random slope. We found that 4 out of 1507 rsCpGs had one significant (P < 5 × 10−8/1507) SNP effect and 343 rsCpGs had at least one SNP effect (436 SNP-probe pairs) reaching genome-wide significance (P < 5 × 10−8). Ninety-five percent of the significant (P < 5 × 10−8) SNPs are on different chromosomes from their corresponding probes.\r\nConclusions: We identified CpG sites that have variability in the rate of change of DNA methylation between individuals, and our results suggest a genetic basis of this variation. Genes around these CpG sites have been reported to be involved in the ageing process."}],"type":"journal_article","date_published":"2018-10-22T00:00:00Z","citation":{"ista":"Zhang Q, Marioni RE, Robinson MR, Higham J, Sproul D, Wray NR, Deary IJ, McRae AF, Visscher PM. 2018. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 10(1), 75.","apa":"Zhang, Q., Marioni, R. E., Robinson, M. R., Higham, J., Sproul, D., Wray, N. R., … Visscher, P. M. (2018). Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-018-0585-7","ieee":"Q. Zhang et al., “Genotype effects contribute to variation in longitudinal methylome patterns in older people,” Genome Medicine, vol. 10, no. 1. Springer Nature, 2018.","ama":"Zhang Q, Marioni RE, Robinson MR, et al. Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine. 2018;10(1). doi:10.1186/s13073-018-0585-7","chicago":"Zhang, Qian, Riccardo E Marioni, Matthew Richard Robinson, Jon Higham, Duncan Sproul, Naomi R Wray, Ian J Deary, Allan F McRae, and Peter M Visscher. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine. Springer Nature, 2018. https://doi.org/10.1186/s13073-018-0585-7.","mla":"Zhang, Qian, et al. “Genotype Effects Contribute to Variation in Longitudinal Methylome Patterns in Older People.” Genome Medicine, vol. 10, no. 1, 75, Springer Nature, 2018, doi:10.1186/s13073-018-0585-7.","short":"Q. Zhang, R.E. Marioni, M.R. Robinson, J. Higham, D. Sproul, N.R. Wray, I.J. Deary, A.F. McRae, P.M. Visscher, Genome Medicine 10 (2018)."},"publication":"Genome Medicine","article_type":"original","article_processing_charge":"No","day":"22","author":[{"full_name":"Zhang, Qian","first_name":"Qian","last_name":"Zhang"},{"full_name":"Marioni, Riccardo E","last_name":"Marioni","first_name":"Riccardo E"},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"last_name":"Higham","first_name":"Jon","full_name":"Higham, Jon"},{"full_name":"Sproul, Duncan","first_name":"Duncan","last_name":"Sproul"},{"first_name":"Naomi R","last_name":"Wray","full_name":"Wray, Naomi R"},{"first_name":"Ian J","last_name":"Deary","full_name":"Deary, Ian J"},{"last_name":"McRae","first_name":"Allan F","full_name":"McRae, Allan F"},{"first_name":"Peter M","last_name":"Visscher","full_name":"Visscher, Peter M"}],"volume":10,"date_created":"2020-04-30T10:42:50Z","date_updated":"2021-01-12T08:15:04Z","year":"2018","publisher":"Springer Nature","publication_status":"published","extern":"1","article_number":"75","doi":"10.1186/s13073-018-0585-7","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13073-018-0585-7"}],"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1756-994X"]},"month":"10"},{"_id":"7718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 361","title":"Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia","status":"public","oa_version":"None","type":"journal_article","issue":"6401","abstract":[{"lang":"eng","text":"Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores."}],"citation":{"mla":"Tucci, Serena, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science, vol. 361, no. 6401, American Association for the Advancement of Science, 2018, pp. 511–16, doi:10.1126/science.aar8486.","short":"S. Tucci, S.H. Vohr, R.C. McCoy, B. Vernot, M.R. Robinson, C. Barbieri, B.J. Nelson, W. Fu, G.A. Purnomo, H. Sudoyo, E.E. Eichler, G. Barbujani, P.M. Visscher, J.M. Akey, R.E. Green, Science 361 (2018) 511–516.","chicago":"Tucci, Serena, Samuel H. Vohr, Rajiv C. McCoy, Benjamin Vernot, Matthew Richard Robinson, Chiara Barbieri, Brad J. Nelson, et al. “Evolutionary History and Adaptation of a Human Pygmy Population of Flores Island, Indonesia.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aar8486.","ama":"Tucci S, Vohr SH, McCoy RC, et al. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 2018;361(6401):511-516. doi:10.1126/science.aar8486","ista":"Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 361(6401), 511–516.","ieee":"S. Tucci et al., “Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia,” Science, vol. 361, no. 6401. American Association for the Advancement of Science, pp. 511–516, 2018.","apa":"Tucci, S., Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., … Green, R. E. (2018). Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aar8486"},"publication":"Science","page":"511-516","article_type":"original","date_published":"2018-08-03T00:00:00Z","article_processing_charge":"No","day":"03","pmid":1,"year":"2018","publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"full_name":"Tucci, Serena","last_name":"Tucci","first_name":"Serena"},{"full_name":"Vohr, Samuel H.","last_name":"Vohr","first_name":"Samuel H."},{"first_name":"Rajiv C.","last_name":"McCoy","full_name":"McCoy, Rajiv C."},{"last_name":"Vernot","first_name":"Benjamin","full_name":"Vernot, Benjamin"},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"full_name":"Barbieri, Chiara","last_name":"Barbieri","first_name":"Chiara"},{"full_name":"Nelson, Brad J.","last_name":"Nelson","first_name":"Brad J."},{"last_name":"Fu","first_name":"Wenqing","full_name":"Fu, Wenqing"},{"first_name":"Gludhug A.","last_name":"Purnomo","full_name":"Purnomo, Gludhug A."},{"full_name":"Sudoyo, Herawati","last_name":"Sudoyo","first_name":"Herawati"},{"full_name":"Eichler, Evan E.","first_name":"Evan E.","last_name":"Eichler"},{"first_name":"Guido","last_name":"Barbujani","full_name":"Barbujani, Guido"},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"full_name":"Akey, Joshua M.","first_name":"Joshua M.","last_name":"Akey"},{"last_name":"Green","first_name":"Richard E.","full_name":"Green, Richard E."}],"volume":361,"date_updated":"2021-01-12T08:15:04Z","date_created":"2020-04-30T10:43:24Z","extern":"1","external_id":{"pmid":["30072539"]},"quality_controlled":"1","doi":"10.1126/science.aar8486","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-8075","1095-9203"]},"month":"08"}]