[{"abstract":[{"text":"Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis.","lang":"eng"}],"_id":"9097","acknowledgement":"RP acknowledges the Department of Science and Technology, India for the support through the DST-INSPIRE Faculty Award (DST/INSPIRE/04/2015/001939). This work was supported by the Engineering and Physical Sciences Research Council (EPSRC), United Kingdom (Grant numbers EP/J018295/1, EP/J018392/1, EP/N014391/1). The contribution of RP was also supported by the later Grant. This work was generously supported by the Welcome Trust Institutional Strategic Support Award (204909/Z/16/Z) too. The contribution of MG was supported by the EPSRC via EP/N014391/1 and a Wellcome Trust Institutional Strategic Support Award (WT105618MA). The contribution of YA was generously supported by the Wellcome Trust Institutional Strategic Support Award (WT105618MA).","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":11,"ddc":["570"],"file_date_updated":"2021-02-09T07:33:23Z","date_created":"2021-02-07T23:01:12Z","month":"01","language":[{"iso":"eng"}],"author":[{"first_name":"Rakesh","full_name":"Pandey, Rakesh","last_name":"Pandey"},{"last_name":"Al-Nuaimi","full_name":"Al-Nuaimi, Yusur","first_name":"Yusur"},{"first_name":"Rajiv Kumar","full_name":"Mishra, Rajiv Kumar","last_name":"Mishra","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Spurgeon","first_name":"Sarah K.","full_name":"Spurgeon, Sarah K."},{"full_name":"Goodfellow, Marc","first_name":"Marc","last_name":"Goodfellow"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"Scientific Reports","citation":{"apa":"Pandey, R., Al-Nuaimi, Y., Mishra, R. K., Spurgeon, S. K., &#38; Goodfellow, M. (2021). Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-80507-7\">https://doi.org/10.1038/s41598-020-80507-7</a>","ama":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. <i>Scientific Reports</i>. 2021;11. doi:<a href=\"https://doi.org/10.1038/s41598-020-80507-7\">10.1038/s41598-020-80507-7</a>","chicago":"Pandey, Rakesh, Yusur Al-Nuaimi, Rajiv Kumar Mishra, Sarah K. Spurgeon, and Marc Goodfellow. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-020-80507-7\">https://doi.org/10.1038/s41598-020-80507-7</a>.","mla":"Pandey, Rakesh, et al. “Role of Subnetworks Mediated by TNF α, IL-23/IL-17 and IL-15 in a Network Involved in the Pathogenesis of Psoriasis.” <i>Scientific Reports</i>, vol. 11, 2204, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-020-80507-7\">10.1038/s41598-020-80507-7</a>.","short":"R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific Reports 11 (2021).","ieee":"R. Pandey, Y. Al-Nuaimi, R. K. Mishra, S. K. Spurgeon, and M. Goodfellow, “Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis,” <i>Scientific Reports</i>, vol. 11. Springer Nature, 2021.","ista":"Pandey R, Al-Nuaimi Y, Mishra RK, Spurgeon SK, Goodfellow M. 2021. Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis. Scientific Reports. 11, 2204."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","file":[{"date_updated":"2021-02-09T07:33:23Z","relation":"main_file","access_level":"open_access","file_size":2885056,"checksum":"e8a68df48750712671f5c47b0228e531","file_name":"2021_ScientificReports_Pandey.pdf","success":1,"date_created":"2021-02-09T07:33:23Z","file_id":"9106","content_type":"application/pdf","creator":"dernst"}],"department":[{"_id":"PeJo"}],"date_published":"2021-01-26T00:00:00Z","article_type":"original","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1038/s41598-020-80507-7","article_number":"2204","title":"Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis","has_accepted_license":"1","publication_identifier":{"eissn":["20452322"]},"year":"2021","license":"https://creativecommons.org/licenses/by/4.0/","oa":1,"status":"public","intvolume":"        11","date_updated":"2022-08-19T07:22:23Z"},{"citation":{"ieee":"G. Ivanov, “On the volume of projections of the cross-polytope,” <i>Discrete Mathematics</i>, vol. 344, no. 5. Elsevier, 2021.","short":"G. Ivanov, Discrete Mathematics 344 (2021).","mla":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>, vol. 344, no. 5, 112312, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>.","ista":"Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete Mathematics. 344(5), 112312.","apa":"Ivanov, G. (2021). On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>","ama":"Ivanov G. On the volume of projections of the cross-polytope. <i>Discrete Mathematics</i>. 2021;344(5). doi:<a href=\"https://doi.org/10.1016/j.disc.2021.112312\">10.1016/j.disc.2021.112312</a>","chicago":"Ivanov, Grigory. “On the Volume of Projections of the Cross-Polytope.” <i>Discrete Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.disc.2021.112312\">https://doi.org/10.1016/j.disc.2021.112312</a>."},"publication_status":"published","arxiv":1,"quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"UlWa"}],"date_published":"2021-05-01T00:00:00Z","article_type":"original","isi":1,"day":"01","doi":"10.1016/j.disc.2021.112312","article_number":"112312","publication_identifier":{"issn":["0012365X"]},"title":"On the volume of projections of the cross-polytope","issue":"5","year":"2021","external_id":{"arxiv":["1808.09165"],"isi":["000633365200001"]},"oa":1,"status":"public","intvolume":"       344","date_updated":"2023-08-07T13:40:37Z","abstract":[{"lang":"eng","text":"We study properties of the volume of projections of the n-dimensional\r\ncross-polytope $\\crosp^n = \\{ x \\in \\R^n \\mid |x_1| + \\dots + |x_n| \\leqslant 1\\}.$ We prove that the projection of $\\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.\r\nWe obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\\crosp^n$ onto a k-dimensional subspace for any n>k⩾2."}],"_id":"9098","acknowledgement":"Research was supported by the Russian Foundation for Basic Research, project 18-01-00036A (Theorems 1.5 and 5.3) and by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926 (Theorems 1.2 and 7.3).","publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/1808.09165","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":344,"date_created":"2021-02-07T23:01:12Z","month":"05","language":[{"iso":"eng"}],"author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"Discrete Mathematics"},{"arxiv":1,"quality_controlled":"1","publication_status":"published","citation":{"ieee":"T. K. Srivastava, “Lifting automorphisms on Abelian varieties as derived autoequivalences,” <i>Archiv der Mathematik</i>, vol. 116, no. 5. Springer Nature, pp. 515–527, 2021.","short":"T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.","mla":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>, vol. 116, no. 5, Springer Nature, 2021, pp. 515–27, doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>.","ista":"Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 116(5), 515–527.","ama":"Srivastava TK. Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv der Mathematik</i>. 2021;116(5):515-527. doi:<a href=\"https://doi.org/10.1007/s00013-020-01564-y\">10.1007/s00013-020-01564-y</a>","apa":"Srivastava, T. K. (2021). Lifting automorphisms on Abelian varieties as derived autoequivalences. <i>Archiv Der Mathematik</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>","chicago":"Srivastava, Tanya K. “Lifting Automorphisms on Abelian Varieties as Derived Autoequivalences.” <i>Archiv Der Mathematik</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00013-020-01564-y\">https://doi.org/10.1007/s00013-020-01564-y</a>."},"date_published":"2021-05-01T00:00:00Z","article_type":"original","oa_version":"Preprint","department":[{"_id":"TaHa"}],"year":"2021","isi":1,"doi":"10.1007/s00013-020-01564-y","day":"01","title":"Lifting automorphisms on Abelian varieties as derived autoequivalences","issue":"5","publication_identifier":{"eissn":["14208938"],"issn":["0003889X"]},"status":"public","intvolume":"       116","date_updated":"2023-08-07T13:42:38Z","external_id":{"isi":["000612580200001"],"arxiv":["2001.07762"]},"oa":1,"_id":"9099","acknowledgement":"I would like to thank Piotr Achinger, Daniel Huybrechts, Katrina Honigs, Marcin Lara, and Maciek Zdanowicz for the mathematical discussions, Tamas Hausel for hosting me in his research group at IST Austria, and the referees for their valuable suggestions. This research has received funding from the European Union’s Horizon 2020 research and innovation programme under Marie Sklodowska-Curie Grant Agreement No. 754411.","abstract":[{"lang":"eng","text":"We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations."}],"ec_funded":1,"publisher":"Springer Nature","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/2001.07762","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-02-07T23:01:13Z","page":"515-527","volume":116,"scopus_import":"1","article_processing_charge":"No","publication":"Archiv der Mathematik","month":"05","author":[{"first_name":"Tanya K","full_name":"Srivastava, Tanya K","last_name":"Srivastava","id":"4D046628-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"date_created":"2021-02-07T23:01:13Z","page":"4-15","file_date_updated":"2021-02-09T09:04:02Z","ddc":["570"],"volume":34,"scopus_import":"1","publication":"Journal of Evolutionary Biology","article_processing_charge":"No","type":"journal_article","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean"}],"language":[{"iso":"eng"}],"month":"01","acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","_id":"9100","abstract":[{"text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.","lang":"eng"}],"publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","doi":"10.1111/jeb.13756","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"18","isi":1,"publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"title":"Speciation in marine environments: Diving under the surface","issue":"1","has_accepted_license":"1","intvolume":"        34","status":"public","date_updated":"2023-08-07T13:42:08Z","external_id":{"isi":["000608367500001"]},"oa":1,"quality_controlled":"1","citation":{"ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>.","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>.","ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. 2021;34(1):4-15. doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>","apa":"Faria, R., Johannesson, K., &#38; Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>"},"publication_status":"published","article_type":"original","date_published":"2021-01-18T00:00:00Z","oa_version":"Published Version","file":[{"date_updated":"2021-02-09T09:04:02Z","file_name":"2021_JourEvolBiology_Faria.pdf","access_level":"open_access","relation":"main_file","file_size":561340,"checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","file_id":"9108","content_type":"application/pdf","date_created":"2021-02-09T09:04:02Z","success":1,"creator":"dernst"}],"department":[{"_id":"NiBa"}]},{"type":"journal_article","month":"07","author":[{"last_name":"Reber","full_name":"Reber, Stephan A.","first_name":"Stephan A."},{"first_name":"Jinook","full_name":"Oh, Jinook","last_name":"Oh","orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E"},{"full_name":"Janisch, Judith","first_name":"Judith","last_name":"Janisch"},{"first_name":"Colin","full_name":"Stevenson, Colin","last_name":"Stevenson"},{"last_name":"Foggett","full_name":"Foggett, Shaun","first_name":"Shaun"},{"full_name":"Wilkinson, Anna","first_name":"Anna","last_name":"Wilkinson"}],"language":[{"iso":"eng"}],"scopus_import":"1","publication":"Animal Cognition","article_processing_charge":"No","file_date_updated":"2021-02-09T07:40:14Z","volume":24,"ddc":["590"],"date_created":"2021-02-07T23:01:13Z","page":"753-764","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians."}],"acknowledgement":"We thank Jamie Gilks and Terry Miles for their support at Crocodiles of the World. We are grateful to the Department of Cognitive Biology, University of Vienna for provision of working space and hardware. Finally, we would like to thank Cliodhna Quigley, Rachael Harrison and Urs A. Reber for discussion. Open Access funding provided by Lund University. This project was funded by the Marietta Blau grant (BMFWF) to S. A. R.","_id":"9101","external_id":{"isi":["000608382100001"]},"oa":1,"intvolume":"        24","status":"public","date_updated":"2023-08-07T13:41:08Z","doi":"10.1007/s10071-020-01461-5","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","isi":1,"issue":"4","title":"Early life differences in behavioral predispositions in two Alligatoridae species","has_accepted_license":"1","publication_identifier":{"eissn":["14359456"],"issn":["14359448"]},"year":"2021","oa_version":"Published Version","file":[{"file_name":"2021_AnimalCognition_Reber.pdf","relation":"main_file","access_level":"open_access","file_size":1117991,"checksum":"d9dfa0d1de6d684692b041d936dd858e","date_updated":"2021-02-09T07:40:14Z","creator":"dernst","file_id":"9107","content_type":"application/pdf","date_created":"2021-02-09T07:40:14Z","success":1}],"department":[{"_id":"SyCr"}],"article_type":"original","date_published":"2021-07-01T00:00:00Z","citation":{"ama":"Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. Early life differences in behavioral predispositions in two Alligatoridae species. <i>Animal Cognition</i>. 2021;24(4):753-764. doi:<a href=\"https://doi.org/10.1007/s10071-020-01461-5\">10.1007/s10071-020-01461-5</a>","apa":"Reber, S. A., Oh, J., Janisch, J., Stevenson, C., Foggett, S., &#38; Wilkinson, A. (2021). Early life differences in behavioral predispositions in two Alligatoridae species. <i>Animal Cognition</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10071-020-01461-5\">https://doi.org/10.1007/s10071-020-01461-5</a>","chicago":"Reber, Stephan A., Jinook Oh, Judith Janisch, Colin Stevenson, Shaun Foggett, and Anna Wilkinson. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” <i>Animal Cognition</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s10071-020-01461-5\">https://doi.org/10.1007/s10071-020-01461-5</a>.","short":"S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal Cognition 24 (2021) 753–764.","mla":"Reber, Stephan A., et al. “Early Life Differences in Behavioral Predispositions in Two Alligatoridae Species.” <i>Animal Cognition</i>, vol. 24, no. 4, Springer Nature, 2021, pp. 753–64, doi:<a href=\"https://doi.org/10.1007/s10071-020-01461-5\">10.1007/s10071-020-01461-5</a>.","ieee":"S. A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, and A. Wilkinson, “Early life differences in behavioral predispositions in two Alligatoridae species,” <i>Animal Cognition</i>, vol. 24, no. 4. Springer Nature, pp. 753–764, 2021.","ista":"Reber SA, Oh J, Janisch J, Stevenson C, Foggett S, Wilkinson A. 2021. Early life differences in behavioral predispositions in two Alligatoridae species. Animal Cognition. 24(4), 753–764."},"publication_status":"published","quality_controlled":"1"},{"page":"99-140","date_created":"2021-02-11T14:41:02Z","volume":5,"ddc":["510"],"file_date_updated":"2021-02-11T14:43:59Z","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Applied and Computational Topology","scopus_import":"1","month":"03","language":[{"iso":"eng"}],"author":[{"last_name":"Brown","full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425"},{"full_name":"Bobrowski, Omer","first_name":"Omer","last_name":"Bobrowski"},{"last_name":"Munch","first_name":"Elizabeth","full_name":"Munch, Elizabeth"},{"full_name":"Wang, Bei","first_name":"Bei","last_name":"Wang"}],"type":"journal_article","_id":"9111","acknowledgement":"AB was supported in part by the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Sklodowska-Curie GrantAgreement No. 754411 and NSF IIS-1513616. OB was supported in part by the Israel Science Foundation, Grant 1965/19. BW was supported in part by NSF IIS-1513616 and DBI-1661375. EM was supported in part by NSF CMMI-1800466, DMS-1800446, and CCF-1907591.We would like to thank the Institute for Mathematics and its Applications for hosting a workshop titled Bridging Statistics and Sheaves in May 2018, where this work was conceived.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria).","abstract":[{"lang":"eng","text":"We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data."}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"year":"2021","issue":"1","title":"Probabilistic convergence and stability of random mapper graphs","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"has_accepted_license":"1","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1007/s41468-020-00063-x","date_updated":"2023-09-05T15:37:56Z","status":"public","intvolume":"         5","oa":1,"external_id":{"arxiv":["1909.03488"]},"arxiv":1,"quality_controlled":"1","citation":{"mla":"Brown, Adam, et al. “Probabilistic Convergence and Stability of Random Mapper Graphs.” <i>Journal of Applied and Computational Topology</i>, vol. 5, no. 1, Springer Nature, 2021, pp. 99–140, doi:<a href=\"https://doi.org/10.1007/s41468-020-00063-x\">10.1007/s41468-020-00063-x</a>.","short":"A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational Topology 5 (2021) 99–140.","ieee":"A. Brown, O. Bobrowski, E. Munch, and B. Wang, “Probabilistic convergence and stability of random mapper graphs,” <i>Journal of Applied and Computational Topology</i>, vol. 5, no. 1. Springer Nature, pp. 99–140, 2021.","ista":"Brown A, Bobrowski O, Munch E, Wang B. 2021. Probabilistic convergence and stability of random mapper graphs. Journal of Applied and Computational Topology. 5(1), 99–140.","ama":"Brown A, Bobrowski O, Munch E, Wang B. Probabilistic convergence and stability of random mapper graphs. <i>Journal of Applied and Computational Topology</i>. 2021;5(1):99-140. doi:<a href=\"https://doi.org/10.1007/s41468-020-00063-x\">10.1007/s41468-020-00063-x</a>","apa":"Brown, A., Bobrowski, O., Munch, E., &#38; Wang, B. (2021). Probabilistic convergence and stability of random mapper graphs. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-020-00063-x\">https://doi.org/10.1007/s41468-020-00063-x</a>","chicago":"Brown, Adam, Omer Bobrowski, Elizabeth Munch, and Bei Wang. “Probabilistic Convergence and Stability of Random Mapper Graphs.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s41468-020-00063-x\">https://doi.org/10.1007/s41468-020-00063-x</a>."},"publication_status":"published","date_published":"2021-03-01T00:00:00Z","article_type":"original","department":[{"_id":"HeEd"}],"oa_version":"Published Version","file":[{"date_updated":"2021-02-11T14:43:59Z","file_name":"2020_JourApplCompTopology_Brown.pdf","relation":"main_file","access_level":"open_access","file_size":2090265,"checksum":"3f02e9d47c428484733da0f588a3c069","file_id":"9112","content_type":"application/pdf","success":1,"date_created":"2021-02-11T14:43:59Z","creator":"dernst"}]},{"date_updated":"2023-08-07T13:43:19Z","status":"public","intvolume":"         9","external_id":{"isi":["000625460400010"]},"year":"2021","publication_identifier":{"eissn":["2168-0485"]},"title":"Ambient condition alcohol reforming to hydrogen with electricity output","issue":"8","isi":1,"day":"11","doi":"10.1021/acssuschemeng.0c07547","date_published":"2021-02-11T00:00:00Z","article_type":"original","department":[{"_id":"StFr"}],"oa_version":"None","quality_controlled":"1","publication_status":"published","citation":{"ista":"Manzoor Bhat ZM, Thimmappa R, Dargily NC, Raafik A, Kottaichamy AR, Devendrachari MC, Itagi M,  Makri Nimbegondi Kotresh H, Freunberger SA, Ottakam Thotiyl M. 2021. Ambient condition alcohol reforming to hydrogen with electricity output. ACS Sustainable Chemistry and Engineering. 9(8), 3104–3111.","short":"Z.M. Manzoor Bhat, R. Thimmappa, N.C. Dargily, A. Raafik, A.R. Kottaichamy, M.C. Devendrachari, M. Itagi, H.  Makri Nimbegondi Kotresh, S.A. Freunberger, M. Ottakam Thotiyl, ACS Sustainable Chemistry and Engineering 9 (2021) 3104–3111.","mla":"Manzoor Bhat, Zahid Manzoor, et al. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” <i>ACS Sustainable Chemistry and Engineering</i>, vol. 9, no. 8, American Chemical Society, 2021, pp. 3104–11, doi:<a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">10.1021/acssuschemeng.0c07547</a>.","ieee":"Z. M. Manzoor Bhat <i>et al.</i>, “Ambient condition alcohol reforming to hydrogen with electricity output,” <i>ACS Sustainable Chemistry and Engineering</i>, vol. 9, no. 8. American Chemical Society, pp. 3104–3111, 2021.","chicago":"Manzoor Bhat, Zahid Manzoor, Ravikumar Thimmappa, Neethu Christudas  Dargily, Abdul  Raafik, Alagar Raja  Kottaichamy, Mruthyunjayachari Chattanahalli  Devendrachari, Mahesh Itagi, Harish  Makri Nimbegondi Kotresh, Stefan Alexander Freunberger, and Musthafa  Ottakam Thotiyl. “Ambient Condition Alcohol Reforming to Hydrogen with Electricity Output.” <i>ACS Sustainable Chemistry and Engineering</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">https://doi.org/10.1021/acssuschemeng.0c07547</a>.","apa":"Manzoor Bhat, Z. M., Thimmappa, R., Dargily, N. C., Raafik, A., Kottaichamy, A. R., Devendrachari, M. C., … Ottakam Thotiyl, M. (2021). Ambient condition alcohol reforming to hydrogen with electricity output. <i>ACS Sustainable Chemistry and Engineering</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">https://doi.org/10.1021/acssuschemeng.0c07547</a>","ama":"Manzoor Bhat ZM, Thimmappa R, Dargily NC, et al. Ambient condition alcohol reforming to hydrogen with electricity output. <i>ACS Sustainable Chemistry and Engineering</i>. 2021;9(8):3104-3111. doi:<a href=\"https://doi.org/10.1021/acssuschemeng.0c07547\">10.1021/acssuschemeng.0c07547</a>"},"article_processing_charge":"No","publication":"ACS Sustainable Chemistry and Engineering","scopus_import":"1","month":"02","author":[{"full_name":"Manzoor Bhat, Zahid Manzoor","first_name":"Zahid Manzoor","last_name":"Manzoor Bhat"},{"last_name":"Thimmappa","full_name":"Thimmappa, Ravikumar","first_name":"Ravikumar"},{"full_name":"Dargily, Neethu Christudas ","first_name":"Neethu Christudas ","last_name":"Dargily"},{"full_name":"Raafik, Abdul ","first_name":"Abdul ","last_name":"Raafik"},{"full_name":"Kottaichamy, Alagar Raja ","first_name":"Alagar Raja ","last_name":"Kottaichamy"},{"last_name":"Devendrachari","first_name":"Mruthyunjayachari Chattanahalli ","full_name":"Devendrachari, Mruthyunjayachari Chattanahalli "},{"first_name":"Mahesh","full_name":"Itagi, Mahesh","last_name":"Itagi"},{"full_name":" Makri Nimbegondi Kotresh, Harish","first_name":"Harish","last_name":" Makri Nimbegondi Kotresh"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Ottakam Thotiyl","first_name":"Musthafa ","full_name":"Ottakam Thotiyl, Musthafa "}],"language":[{"iso":"eng"}],"type":"journal_article","page":"3104-3111","date_created":"2021-02-12T09:20:18Z","volume":9,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","_id":"9113","acknowledgement":"M.O.T. acknowledges DST/TMD/HFC/2 K18/58, DST-SERB, MHRD fast track, and DST Nanomission forfinancialassistance. Z.M.B. acknowledges CSIR-SRF fellowship fromMHRD, India. S.A.F. acknowledges support from IST Austria.","abstract":[{"text":"“Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions.","lang":"eng"}]},{"acknowledgement":"M.C. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. ICN2\r\nacknowledges funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 − ESTEEM3. M.V.K. acknowledges the support by the European Research Council under the Horizon 2020 Framework Program (ERC Consolidator Grant SCALEHALO\r\nGrant Agreement No. 819740) and by FET-OPEN project no. 862656 (DROP-IT).","_id":"9118","abstract":[{"text":"Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors.","lang":"eng"}],"ec_funded":1,"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-02-14T23:01:14Z","page":"581-587","related_material":{"record":[{"status":"public","id":"12885","relation":"dissertation_contains"}]},"file_date_updated":"2021-02-17T07:36:52Z","ddc":["540"],"volume":6,"scopus_import":"1","publication":"ACS Energy Letters","article_processing_charge":"Yes (via OA deal)","type":"journal_article","author":[{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"},{"last_name":"Genc","full_name":"Genc, Aziz","first_name":"Aziz"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","first_name":"Yu","full_name":"Liu, Yu"},{"first_name":"Tobias","full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee"},{"last_name":"Dirin","first_name":"Dmitry N.","full_name":"Dirin, Dmitry N."},{"full_name":"Akkerman, Quinten A.","first_name":"Quinten A.","last_name":"Akkerman"},{"first_name":"Maksym V.","full_name":"Kovalenko, Maksym V.","last_name":"Kovalenko"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"01","quality_controlled":"1","publication_status":"published","citation":{"ieee":"M. Calcabrini <i>et al.</i>, “Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites,” <i>ACS Energy Letters</i>, vol. 6, no. 2. American Chemical Society, pp. 581–587, 2021.","mla":"Calcabrini, Mariano, et al. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor Nanocomposites.” <i>ACS Energy Letters</i>, vol. 6, no. 2, American Chemical Society, 2021, pp. 581–87, doi:<a href=\"https://doi.org/10.1021/acsenergylett.0c02448\">10.1021/acsenergylett.0c02448</a>.","short":"M. Calcabrini, A. Genc, Y. Liu, T. Kleinhanns, S. Lee, D.N. Dirin, Q.A. Akkerman, M.V. Kovalenko, J. Arbiol, M. Ibáñez, ACS Energy Letters 6 (2021) 581–587.","ista":"Calcabrini M, Genc A, Liu Y, Kleinhanns T, Lee S, Dirin DN, Akkerman QA, Kovalenko MV, Arbiol J, Ibáñez M. 2021. Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. ACS Energy Letters. 6(2), 581–587.","ama":"Calcabrini M, Genc A, Liu Y, et al. Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. <i>ACS Energy Letters</i>. 2021;6(2):581-587. doi:<a href=\"https://doi.org/10.1021/acsenergylett.0c02448\">10.1021/acsenergylett.0c02448</a>","apa":"Calcabrini, M., Genc, A., Liu, Y., Kleinhanns, T., Lee, S., Dirin, D. N., … Ibáñez, M. (2021). Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites. <i>ACS Energy Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsenergylett.0c02448\">https://doi.org/10.1021/acsenergylett.0c02448</a>","chicago":"Calcabrini, Mariano, Aziz Genc, Yu Liu, Tobias Kleinhanns, Seungho Lee, Dmitry N. Dirin, Quinten A. Akkerman, Maksym V. Kovalenko, Jordi Arbiol, and Maria Ibáñez. “Exploiting the Lability of Metal Halide Perovskites for Doping Semiconductor Nanocomposites.” <i>ACS Energy Letters</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsenergylett.0c02448\">https://doi.org/10.1021/acsenergylett.0c02448</a>."},"article_type":"original","date_published":"2021-01-20T00:00:00Z","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"9155","date_created":"2021-02-17T07:36:52Z","success":1,"file_name":"2021_ACSEnergyLetters_Calcabrini.pdf","file_size":5071201,"checksum":"6fa7374bf8b95fdfe6e6c595322a6689","access_level":"open_access","relation":"main_file","date_updated":"2021-02-17T07:36:52Z"}],"department":[{"_id":"MaIb"}],"year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1021/acsenergylett.0c02448","day":"20","isi":1,"title":"Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites","issue":"2","publication_identifier":{"eissn":["2380-8195"]},"has_accepted_license":"1","intvolume":"         6","status":"public","date_updated":"2023-08-07T13:46:00Z","external_id":{"isi":["000619803400036"]},"oa":1},{"oa_version":"Preprint","department":[{"_id":"NiBa"}],"date_published":"2021-01-15T00:00:00Z","article_type":"original","citation":{"ieee":"C. Fraisse <i>et al.</i>, “DILS: Demographic inferences with linked selection by using ABC,” <i>Molecular Ecology Resources</i>, vol. 21. Wiley, pp. 2629–2644, 2021.","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>, vol. 21, Wiley, 2021, pp. 2629–44, doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. 2021;21:2629-2644. doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>","chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>."},"publication_status":"published","quality_controlled":"1","external_id":{"isi":["000614183100001"]},"oa":1,"status":"public","intvolume":"        21","date_updated":"2023-08-07T13:45:18Z","isi":1,"day":"15","doi":"10.1111/1755-0998.13323","publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"title":"DILS: Demographic inferences with linked selection by using ABC","year":"2021","publisher":"Wiley","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.","lang":"eng"}],"_id":"9119","author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Popovic","first_name":"Iva","full_name":"Popovic, Iva"},{"full_name":"Mazoyer, Clément","first_name":"Clément","last_name":"Mazoyer"},{"first_name":"Bruno","full_name":"Spataro, Bruno","last_name":"Spataro"},{"first_name":"Stéphane","full_name":"Delmotte, Stéphane","last_name":"Delmotte"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"last_name":"Loire","full_name":"Loire, Étienne","first_name":"Étienne"},{"first_name":"Alexis","full_name":"Simon, Alexis","last_name":"Simon"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"last_name":"Duret","first_name":"Laurent","full_name":"Duret, Laurent"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"},{"first_name":"Xavier","full_name":"Vekemans, Xavier","last_name":"Vekemans"},{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"}],"language":[{"iso":"eng"}],"month":"01","type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"Molecular Ecology Resources","volume":21,"date_created":"2021-02-14T23:01:14Z","page":"2629-2644"},{"abstract":[{"lang":"eng","text":"We show that the energy gap for the BCS gap equation is\r\nΞ=μ(8e−2+o(1))exp(π2μ−−√a)\r\nin the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states."}],"_id":"9121","acknowledgement":"Most of this work was done as part of the author’s master’s thesis. The author would like to thank Jan Philip Solovej for his supervision of this process.\r\nOpen Access funding provided by Institute of Science and Technology (IST Austria)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"volume":111,"ddc":["510"],"file_date_updated":"2021-02-15T09:31:07Z","date_created":"2021-02-15T09:27:14Z","month":"02","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","publication":"Letters in Mathematical Physics","publication_status":"published","citation":{"ama":"Lauritsen AB. The BCS energy gap at low density. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01358-5\">10.1007/s11005-021-01358-5</a>","apa":"Lauritsen, A. B. (2021). The BCS energy gap at low density. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01358-5\">https://doi.org/10.1007/s11005-021-01358-5</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01358-5\">https://doi.org/10.1007/s11005-021-01358-5</a>.","ieee":"A. B. Lauritsen, “The BCS energy gap at low density,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","mla":"Lauritsen, Asbjørn Bækgaard. “The BCS Energy Gap at Low Density.” <i>Letters in Mathematical Physics</i>, vol. 111, 20, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01358-5\">10.1007/s11005-021-01358-5</a>.","short":"A.B. Lauritsen, Letters in Mathematical Physics 111 (2021).","ista":"Lauritsen AB. 2021. The BCS energy gap at low density. Letters in Mathematical Physics. 111, 20."},"quality_controlled":"1","department":[{"_id":"GradSch"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"eaf1b3ff5026f120f0929a5c417dc842","file_size":329332,"file_name":"2021_LettersMathPhysics_Lauritsen.pdf","date_updated":"2021-02-15T09:31:07Z","creator":"dernst","success":1,"date_created":"2021-02-15T09:31:07Z","file_id":"9122","content_type":"application/pdf"}],"oa_version":"Published Version","date_published":"2021-02-12T00:00:00Z","article_type":"original","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"title":"The BCS energy gap at low density","has_accepted_license":"1","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"20","doi":"10.1007/s11005-021-01358-5","day":"12","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"year":"2021","oa":1,"external_id":{"isi":["000617531900001"]},"date_updated":"2023-09-05T15:17:16Z","status":"public","intvolume":"       111"},{"article_type":"original","date_published":"2021-01-05T00:00:00Z","oa_version":"Published Version","file":[{"creator":"dernst","success":1,"date_created":"2021-02-19T14:04:40Z","file_id":"9172","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":1693609,"checksum":"64e2aae4837790db26e1dd1986c69c07","file_name":"2021_JourStatMech_deNicola.pdf","date_updated":"2021-02-19T14:04:40Z"}],"department":[{"_id":"MaSe"}],"quality_controlled":"1","citation":{"ama":"De Nicola S. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2021;2021(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">10.1088/1742-5468/abc7c7</a>","apa":"De Nicola, S. (2021). Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">https://doi.org/10.1088/1742-5468/abc7c7</a>","chicago":"De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">https://doi.org/10.1088/1742-5468/abc7c7</a>.","ieee":"S. De Nicola, “Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2021, no. 1. IOP Publishing, 2021.","short":"S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021 (2021).","mla":"De Nicola, Stefano. “Disentanglement Approach to Quantum Spin Ground States: Field Theory and Stochastic Simulation.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2021, no. 1, 013101, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1742-5468/abc7c7\">10.1088/1742-5468/abc7c7</a>.","ista":"De Nicola S. 2021. Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation. Journal of Statistical Mechanics: Theory and Experiment. 2021(1), 013101."},"publication_status":"published","intvolume":"      2021","status":"public","date_updated":"2023-08-07T13:46:28Z","external_id":{"isi":["000605080300001"]},"oa":1,"year":"2021","article_number":"013101","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"05","doi":"10.1088/1742-5468/abc7c7","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability","Statistical and Nonlinear Physics"],"isi":1,"title":"Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation","has_accepted_license":"1","publication_identifier":{"issn":["1742-5468"]},"issue":"1","ec_funded":1,"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publisher":"IOP Publishing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"S D N would like to thank M J Bhaseen, J Chalker, B Doyon, V Gritsev, A Lamacraft,\r\nA Michailidis and M Serbyn for helpful feedback and stimulating conversations. S D N\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and\r\nfrom the European Union’s Horizon 2020 research and innovation program under the\r\nMarie Sk\blodowska-Curie Grant Agreement No. 754411. S D N also acknowledges funding\r\nfrom the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to Non-\r\nEquilibrium Systems (CANES) under Grant EP/L015854/1. S D N is grateful to IST\r\nAustria for providing open access funding.","_id":"9158","abstract":[{"text":"While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.","lang":"eng"}],"publication":"Journal of Statistical Mechanics: Theory and Experiment","article_processing_charge":"No","type":"journal_article","month":"01","author":[{"last_name":"De Nicola","full_name":"De Nicola, Stefano","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671"}],"language":[{"iso":"eng"}],"date_created":"2021-02-17T17:48:46Z","file_date_updated":"2021-02-19T14:04:40Z","ddc":["530"],"volume":2021},{"quality_controlled":"1","publication_status":"published","citation":{"chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021."},"article_type":"original","date_published":"2021-02-01T00:00:00Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"year":"2021","article_number":"iyaa025","day":"01","doi":"10.1093/genetics/iyaa025","isi":1,"issue":"2","publication_identifier":{"issn":["1943-2631"]},"title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","intvolume":"       217","status":"public","date_updated":"2023-08-07T13:47:01Z","external_id":{"isi":["000637218100005"]},"oa":1,"acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","_id":"9168","abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02463"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"publisher":"Genetics Society of America","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-02-18T14:41:30Z","volume":217,"publication":"Genetics","article_processing_charge":"No","type":"journal_article","month":"02","author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}]},{"date_published":"2021-03-01T00:00:00Z","article_type":"original","department":[{"_id":"TaHa"}],"oa_version":"Preprint","arxiv":1,"quality_controlled":"1","citation":{"chicago":"Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” <i>Bulletin Des Sciences Mathematiques</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">https://doi.org/10.1016/j.bulsci.2021.102957</a>.","apa":"Srivastava, T. K. (2021). Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. <i>Bulletin Des Sciences Mathematiques</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">https://doi.org/10.1016/j.bulsci.2021.102957</a>","ama":"Srivastava TK. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. <i>Bulletin des Sciences Mathematiques</i>. 2021;167(03). doi:<a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">10.1016/j.bulsci.2021.102957</a>","ista":"Srivastava TK. 2021. Pathologies of the Hilbert scheme of points of a supersingular Enriques surface. Bulletin des Sciences Mathematiques. 167(03), 102957.","mla":"Srivastava, Tanya K. “Pathologies of the Hilbert Scheme of Points of a Supersingular Enriques Surface.” <i>Bulletin Des Sciences Mathematiques</i>, vol. 167, no. 03, 102957, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.bulsci.2021.102957\">10.1016/j.bulsci.2021.102957</a>.","short":"T.K. Srivastava, Bulletin Des Sciences Mathematiques 167 (2021).","ieee":"T. K. Srivastava, “Pathologies of the Hilbert scheme of points of a supersingular Enriques surface,” <i>Bulletin des Sciences Mathematiques</i>, vol. 167, no. 03. Elsevier, 2021."},"publication_status":"published","date_updated":"2023-08-07T13:47:48Z","status":"public","intvolume":"       167","oa":1,"external_id":{"arxiv":["2010.08976"],"isi":["000623881600009"]},"year":"2021","issue":"03","publication_identifier":{"issn":["0007-4497"]},"title":"Pathologies of the Hilbert scheme of points of a supersingular Enriques surface","isi":1,"doi":"10.1016/j.bulsci.2021.102957","article_number":"102957","day":"01","ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"main_file_link":[{"url":"https://arxiv.org/abs/2010.08976","open_access":"1"}],"_id":"9173","acknowledgement":"I would like to thank M. Zdanwociz for various mathematical discussions which lead to this article, Tamas Hausel for hosting me in his research group at IST Austria and the anonymous referee for their helpful suggestions and comments. This research has received funding from the European Union's Horizon 2020 Marie Sklodowska-Curie Actions Grant No. 754411 and Institue of Science and Technology Austria IST-PLUS Grant No. 754411.","abstract":[{"lang":"eng","text":"We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem."}],"article_processing_charge":"No","publication":"Bulletin des Sciences Mathematiques","scopus_import":"1","author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","last_name":"Srivastava","full_name":"Srivastava, Tanya K","first_name":"Tanya K"}],"language":[{"iso":"eng"}],"month":"03","type":"journal_article","date_created":"2021-02-21T23:01:20Z","volume":167},{"article_type":"original","date_published":"2021-05-01T00:00:00Z","oa_version":"Published Version","file":[{"file_name":"2021_NCI_Pauler.pdf","relation":"main_file","access_level":"open_access","checksum":"c6d7a40089cd29e289f9b22e75768304","file_size":7083499,"date_updated":"2021-08-11T12:30:38Z","creator":"kschuh","file_id":"9883","content_type":"application/pdf","date_created":"2021-08-11T12:30:38Z","success":1}],"department":[{"_id":"SiHi"}],"quality_controlled":"1","citation":{"ama":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. 2021;145(5). doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>","apa":"Pauler, F., Hudson, Q., Laukoter, S., &#38; Hippenmeyer, S. (2021). Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. <i>Neurochemistry International</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>","chicago":"Pauler, Florian, Quanah Hudson, Susanne Laukoter, and Simon Hippenmeyer. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">https://doi.org/10.1016/j.neuint.2021.104986</a>.","ieee":"F. Pauler, Q. Hudson, S. Laukoter, and S. Hippenmeyer, “Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond,” <i>Neurochemistry International</i>, vol. 145, no. 5. Elsevier, 2021.","mla":"Pauler, Florian, et al. “Inducible Uniparental Chromosome Disomy to Probe Genomic Imprinting at Single-Cell Level in Brain and Beyond.” <i>Neurochemistry International</i>, vol. 145, no. 5, 104986, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.neuint.2021.104986\">10.1016/j.neuint.2021.104986</a>.","short":"F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International 145 (2021).","ista":"Pauler F, Hudson Q, Laukoter S, Hippenmeyer S. 2021. Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond. Neurochemistry International. 145(5), 104986."},"publication_status":"published","intvolume":"       145","status":"public","date_updated":"2023-08-07T13:48:26Z","external_id":{"pmid":["33600873"],"isi":["000635575000005"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.1016/j.neuint.2021.104986","article_number":"104986","keyword":["Cell Biology","Cellular and Molecular Neuroscience"],"day":"01","isi":1,"issue":"5","has_accepted_license":"1","title":"Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond","publication_identifier":{"issn":["0197-0186"]},"ec_funded":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"},{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Melissa Stouffer for critically reading the manuscript. This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung n[f + b] life science call grant (C13-002) to S.H. and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","_id":"9188","pmid":1,"abstract":[{"lang":"eng","text":"Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues."}],"scopus_import":"1","publication":"Neurochemistry International","article_processing_charge":"Yes (via OA deal)","type":"journal_article","author":[{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"},{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"language":[{"iso":"eng"}],"month":"05","date_created":"2021-02-23T12:31:43Z","file_date_updated":"2021-08-11T12:30:38Z","volume":145,"ddc":["570"]},{"department":[{"_id":"JiFr"}],"file":[{"file_size":8437528,"checksum":"a812418fede076741c9c4dc07f317068","relation":"main_file","access_level":"open_access","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","date_updated":"2023-11-02T17:02:11Z","creator":"amally","success":1,"date_created":"2023-11-02T17:02:11Z","content_type":"application/pdf","file_id":"14481"}],"oa_version":"Submitted Version","date_published":"2021-06-01T00:00:00Z","article_type":"original","publication_status":"published","citation":{"apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. Wiley. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. <i>Plant, Cell &#38; Environment</i>. 2021;44(6):1846-1857. doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/pce.14029\">https://doi.org/10.1111/pce.14029</a>.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell &#38; Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:<a href=\"https://doi.org/10.1111/pce.14029\">10.1111/pce.14029</a>.","ieee":"Y. Zhao <i>et al.</i>, “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” <i>Plant, Cell &#38; Environment</i>, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell &#38; Environment. 44(6), 1846–1857."},"quality_controlled":"1","oa":1,"external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"date_updated":"2023-11-07T08:18:36Z","status":"public","intvolume":"        44","issue":"6","publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"has_accepted_license":"1","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","isi":1,"doi":"10.1111/pce.14029","day":"01","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","abstract":[{"lang":"eng","text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses."}],"pmid":1,"_id":"9189","month":"06","author":[{"full_name":"Zhao, Y","first_name":"Y","last_name":"Zhao"},{"last_name":"Wu","first_name":"L","full_name":"Wu, L"},{"first_name":"Q","full_name":"Fu, Q","last_name":"Fu"},{"last_name":"Wang","full_name":"Wang, D","first_name":"D"},{"first_name":"J","full_name":"Li, J","last_name":"Li"},{"last_name":"Yao","full_name":"Yao, B","first_name":"B"},{"full_name":"Yu, S","first_name":"S","last_name":"Yu"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"last_name":"Qian","first_name":"J","full_name":"Qian, J"},{"first_name":"X","full_name":"Zhou, X","last_name":"Zhou"},{"last_name":"Han","full_name":"Han, L","first_name":"L"},{"last_name":"Zhao","full_name":"Zhao, S","first_name":"S"},{"first_name":"C","full_name":"Ma, C","last_name":"Ma"},{"full_name":"Zhang, Y","first_name":"Y","last_name":"Zhang"},{"last_name":"Luo","first_name":"C","full_name":"Luo, C"},{"last_name":"Dong","first_name":"Q","full_name":"Dong, Q"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"full_name":"Zhang, L","first_name":"L","last_name":"Zhang"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"first_name":"Y","full_name":"Li, Y","last_name":"Li"},{"first_name":"H","full_name":"Luo, H","last_name":"Luo"},{"full_name":"Li, K","first_name":"K","last_name":"Li"},{"full_name":"Yang, J","first_name":"J","last_name":"Yang"},{"full_name":"Luo, Q","first_name":"Q","last_name":"Luo"},{"full_name":"Li, L","first_name":"L","last_name":"Li"},{"last_name":"Peng","full_name":"Peng, S","first_name":"S"},{"first_name":"H","full_name":"Huang, H","last_name":"Huang"},{"full_name":"Zuo, Z","first_name":"Z","last_name":"Zuo"},{"full_name":"Liu, C","first_name":"C","last_name":"Liu"},{"full_name":"Wang, L","first_name":"L","last_name":"Wang"},{"last_name":"Li","first_name":"C","full_name":"Li, C"},{"last_name":"He","first_name":"X","full_name":"He, X"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y","full_name":"Du, Y","last_name":"Du"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication":"Plant, Cell & Environment","scopus_import":"1","volume":44,"ddc":["580"],"file_date_updated":"2023-11-02T17:02:11Z","page":"1846-1857","date_created":"2021-02-24T10:07:21Z"},{"type":"research_data","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","full_name":"Arathoon, Louise S","first_name":"Louise S","last_name":"Arathoon"},{"last_name":"Baskett","full_name":"Baskett, Carina","first_name":"Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup","full_name":"Pickup, Melinda","first_name":"Melinda"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"oa":1,"month":"02","date_updated":"2024-02-21T12:41:09Z","article_processing_charge":"No","status":"public","file_date_updated":"2021-02-24T17:45:13Z","related_material":{"record":[{"relation":"used_in_publication","id":"11411","status":"public"},{"relation":"later_version","id":"11321","status":"public"},{"relation":"earlier_version","id":"8254","status":"public"}]},"has_accepted_license":"1","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"26","doi":"10.15479/AT:ISTA:9192","date_created":"2021-02-24T17:49:21Z","year":"2021","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2021-02-24T17:45:13Z","success":1,"content_type":"application/x-zip-compressed","file_id":"9193","creator":"larathoo","date_updated":"2021-02-24T17:45:13Z","file_size":5934452,"checksum":"f85537815809a8a4b7da9d01163f88c0","access_level":"open_access","relation":"main_file","file_name":"Data_Code.zip"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","date_published":"2021-02-26T00:00:00Z","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document."}],"contributor":[{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Louise S","last_name":"Arathoon"},{"first_name":"Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"last_name":"Field","first_name":"David","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","contributor_type":"project_leader","first_name":"Nicholas H","last_name":"Barton"}],"citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021."},"_id":"9192"},{"date_updated":"2023-08-07T13:49:33Z","status":"public","oa":1,"external_id":{"isi":["000932821700028"],"arxiv":["2102.12734"]},"year":"2021","publication_identifier":{"isbn":["9781450383394"]},"has_accepted_license":"1","title":"Synthesis of hybrid automata with affine dynamics from time-series data","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1145/3447928.3456704","day":"01","keyword":["hybrid automaton","membership","system identification"],"date_published":"2021-05-01T00:00:00Z","department":[{"_id":"ToHe"}],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_id":"9424","date_created":"2021-05-25T13:53:22Z","success":1,"creator":"kschuh","date_updated":"2021-05-25T13:53:22Z","file_name":"2021_HSCC_Soto.pdf","file_size":1474786,"checksum":"4c1202c1abf71384c3ee6fea88c2f80e","access_level":"open_access","relation":"main_file"}],"arxiv":1,"quality_controlled":"1","citation":{"ieee":"M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata with affine dynamics from time-series data,” in <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Nashville, TN, United States, 2021, p. 2102.12734.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734.","mla":"Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, Association for Computing Machinery, 2021, p. 2102.12734, doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>.","ista":"Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. HSCC: International Conference on Hybrid Systems Computation and Control, 2102.12734.","apa":"Garcia Soto, M., Henzinger, T. A., &#38; Schilling, C. (2021). Synthesis of hybrid automata with affine dynamics from time-series data. In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i> (p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>","ama":"Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with affine dynamics from time-series data. In: <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>. Association for Computing Machinery; 2021:2102.12734. doi:<a href=\"https://doi.org/10.1145/3447928.3456704\">10.1145/3447928.3456704</a>","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” In <i>HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control</i>, 2102.12734. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3447928.3456704\">https://doi.org/10.1145/3447928.3456704</a>."},"publication_status":"published","article_processing_charge":"No","publication":"HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control","scopus_import":"1","author":[{"last_name":"Garcia Soto","full_name":"Garcia Soto, Miriam","first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2936-5719"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"}],"conference":{"start_date":"2021-05-19","end_date":"2021-05-21","location":"Nashville, TN, United States","name":"HSCC: International Conference on Hybrid Systems Computation and Control"},"language":[{"iso":"eng"}],"month":"05","type":"conference","page":"2102.12734","date_created":"2021-02-26T16:30:39Z","ddc":["000"],"file_date_updated":"2021-05-25T13:53:22Z","ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","project":[{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"_id":"9200","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","abstract":[{"text":"Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.","lang":"eng"}]},{"quality_controlled":"1","publication_status":"published","citation":{"ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>","apa":"Kampjut, D., Steiner, J., &#38; Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>","chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021).","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>, vol. 24, no. 3, 102139, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>.","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021.","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139."},"date_published":"2021-03-19T00:00:00Z","article_type":"original","department":[{"_id":"LeSa"}],"file":[{"creator":"dernst","success":1,"date_created":"2021-03-03T07:38:14Z","file_id":"9219","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":7431411,"checksum":"50585447386fe5842f07ab9b3a66e7e9","file_name":"2021_iScience_Kampjut.pdf","date_updated":"2021-03-03T07:38:14Z"}],"oa_version":"Published Version","year":"2021","has_accepted_license":"1","publication_identifier":{"eissn":["25890042"]},"title":"Cryo-EM grid optimization for membrane proteins","issue":"3","isi":1,"doi":"10.1016/j.isci.2021.102139","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_number":"102139","day":"19","date_updated":"2023-08-07T13:54:06Z","status":"public","intvolume":"        24","oa":1,"external_id":{"pmid":["33665558"],"isi":["000631646000012"]},"pmid":1,"_id":"9205","acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","abstract":[{"text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"date_created":"2021-02-28T23:01:24Z","volume":24,"ddc":["570"],"file_date_updated":"2021-03-03T07:38:14Z","article_processing_charge":"No","publication":"iScience","scopus_import":"1","month":"03","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen","full_name":"Kampjut, Domen"},{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner","full_name":"Steiner, Julia","first_name":"Julia"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"language":[{"iso":"eng"}],"type":"journal_article"},{"citation":{"mla":"Cadavid, Doris, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>, vol. 14, no. 4, 853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>.","short":"D. Cadavid, K. Wei, Y. Liu, Y. Zhang, M. Li, A. Genç, T. Berestok, M. Ibáñez, A. Shavel, G.S. Nolas, A. Cabot, Materials 14 (2021).","ieee":"D. Cadavid <i>et al.</i>, “Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks,” <i>Materials</i>, vol. 14, no. 4. MDPI, 2021.","ista":"Cadavid D, Wei K, Liu Y, Zhang Y, Li M, Genç A, Berestok T, Ibáñez M, Shavel A, Nolas GS, Cabot A. 2021. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. Materials. 14(4), 853.","apa":"Cadavid, D., Wei, K., Liu, Y., Zhang, Y., Li, M., Genç, A., … Cabot, A. (2021). Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>","ama":"Cadavid D, Wei K, Liu Y, et al. Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks. <i>Materials</i>. 2021;14(4). doi:<a href=\"https://doi.org/10.3390/ma14040853\">10.3390/ma14040853</a>","chicago":"Cadavid, Doris, Kaya Wei, Yu Liu, Yu Zhang, Mengyao Li, Aziz Genç, Taisiia Berestok, et al. “Synthesis, Bottom up Assembly and Thermoelectric Properties of Sb-Doped PbS Nanocrystal Building Blocks.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14040853\">https://doi.org/10.3390/ma14040853</a>."},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_id":"9218","date_created":"2021-03-03T07:32:01Z","success":1,"creator":"dernst","date_updated":"2021-03-03T07:32:01Z","file_name":"2021_Materials_Cadavid.pdf","file_size":2722517,"checksum":"76d6c7f97b810ce504ab151c9bf3524e","relation":"main_file","access_level":"open_access"}],"department":[{"_id":"MaIb"}],"article_type":"original","date_published":"2021-02-10T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.3390/ma14040853","day":"10","article_number":"853","isi":1,"title":"Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks","publication_identifier":{"eissn":["1996-1944"]},"has_accepted_license":"1","issue":"4","year":"2021","external_id":{"isi":["000624094100001"]},"oa":1,"intvolume":"        14","status":"public","date_updated":"2023-08-07T13:50:03Z","abstract":[{"text":"The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. ","lang":"eng"}],"acknowledgement":"This work was supported by European Regional Development Funds and the Framework 7\r\nprogram under project UNION (FP7-NMP 310250). GSN acknowledges support from the US National Science Foundation under grant No. DMR-1748188. DC acknowledges support from COLCIENCIAS under project 120480863414. ","_id":"9206","publisher":"MDPI","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-03-03T07:32:01Z","volume":14,"ddc":["540"],"date_created":"2021-02-28T23:01:24Z","type":"journal_article","language":[{"iso":"eng"}],"month":"02","author":[{"last_name":"Cadavid","first_name":"Doris","full_name":"Cadavid, Doris"},{"first_name":"Kaya","full_name":"Wei, Kaya","last_name":"Wei"},{"first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"last_name":"Genç","first_name":"Aziz","full_name":"Genç, Aziz"},{"first_name":"Taisiia","full_name":"Berestok, Taisiia","last_name":"Berestok"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"first_name":"George S.","full_name":"Nolas, George S.","last_name":"Nolas"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"scopus_import":"1","publication":"Materials","article_processing_charge":"No"},{"quality_controlled":"1","citation":{"ieee":"L. Klotz, A. M. Pavlenko, and J. E. Wesfreid, “Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow,” <i>Journal of Fluid Mechanics</i>, vol. 912. Cambridge University Press, 2021.","mla":"Klotz, Lukasz, et al. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>, vol. 912, A24, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>.","short":"L. Klotz, A.M. Pavlenko, J.E. Wesfreid, Journal of Fluid Mechanics 912 (2021).","ista":"Klotz L, Pavlenko AM, Wesfreid JE. 2021. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. Journal of Fluid Mechanics. 912, A24.","apa":"Klotz, L., Pavlenko, A. M., &#38; Wesfreid, J. E. (2021). Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>","ama":"Klotz L, Pavlenko AM, Wesfreid JE. Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow. <i>Journal of Fluid Mechanics</i>. 2021;912. doi:<a href=\"https://doi.org/10.1017/jfm.2020.1089\">10.1017/jfm.2020.1089</a>","chicago":"Klotz, Lukasz, A. M. Pavlenko, and J. E. Wesfreid. “Experimental Measurements in Plane Couette-Poiseuille Flow: Dynamics of the Large- and Small-Scale Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/jfm.2020.1089\">https://doi.org/10.1017/jfm.2020.1089</a>."},"publication_status":"published","date_published":"2021-02-15T00:00:00Z","article_type":"original","file":[{"success":1,"date_created":"2021-03-03T09:49:34Z","file_id":"9220","content_type":"application/pdf","creator":"dernst","date_updated":"2021-03-03T09:49:34Z","access_level":"open_access","relation":"main_file","file_size":4124471,"checksum":"b8020d6338667673e34fde0608913dd2","file_name":"2021_JourFluidMechanics_Klotz.pdf"}],"oa_version":"Published Version","department":[{"_id":"BjHo"}],"year":"2021","isi":1,"day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_number":"A24","doi":"10.1017/jfm.2020.1089","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"has_accepted_license":"1","title":"Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow","status":"public","intvolume":"       912","date_updated":"2023-08-07T13:55:40Z","external_id":{"isi":["000618034400001"]},"oa":1,"_id":"9207","acknowledgement":"We thank Y. Duguet, S. Gomé, G. Lemoult, T. Liu, B. Semin and L.S. Tuckerman for\r\nfruitful discussions. \r\nThis work was supported by a grant, TRANSFLOW, provided by the Agence Nationale de\r\nla Recherche (ANR). A.M.P. was partially supported by the French Embassy in Russia (I.I. Mechnikov scholarship) and by the Russian Science Foundation (project no. 18-79-00189). L.K. was partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","abstract":[{"lang":"eng","text":"In this paper we experimentally study the transitional range of Reynolds numbers in\r\nplane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures\r\ntriggered by a strong impulsive jet and the large-scale flow generated around these\r\nstructures. We present a detailed investigation of the large-scale flow and show how\r\nits amplitude depends on Reynolds number and amplitude perturbation. In addition,\r\nwe characterize the initial dynamics of the localized turbulent spot, which includes the\r\ncoupling between the small and large scales, as well as the dependence of the advection\r\nspeed on the large-scale flow generated around the spot. Finally, we provide the first\r\nexperimental measurements of the large-scale flow around an oblique turbulent band."}],"ec_funded":1,"publisher":"Cambridge University Press","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-02-28T23:01:25Z","ddc":["530"],"volume":912,"file_date_updated":"2021-03-03T09:49:34Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Fluid Mechanics","month":"02","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","full_name":"Klotz, Lukasz","first_name":"Lukasz","last_name":"Klotz"},{"last_name":"Pavlenko","first_name":"A. M.","full_name":"Pavlenko, A. M."},{"full_name":"Wesfreid, J. E.","first_name":"J. E.","last_name":"Wesfreid"}],"type":"journal_article"}]