[{"department":[{"_id":"SiHi"}],"article_processing_charge":"No","year":"2021","language":[{"iso":"eng"}],"acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","publisher":"Cold Spring Harbor Laboratory","month":"01","date_published":"2021-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Anderson, Donovan J.","last_name":"Anderson","first_name":"Donovan J."},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"McKenna","first_name":"Aaron","full_name":"McKenna, Aaron"},{"full_name":"Shendure, Jay","first_name":"Jay","last_name":"Shendure"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","date_updated":"2021-02-04T07:29:53Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.12.31.425016"}],"publication_status":"submitted","doi":"10.1101/2020.12.31.425016","publication":"bioRxiv","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","ec_funded":1,"type":"preprint","abstract":[{"text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.","lang":"eng"}],"citation":{"chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>.","ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>","short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.).","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>"},"status":"public","day":"01","date_created":"2021-02-04T07:23:23Z","_id":"9082"},{"has_accepted_license":"1","publisher":"SciPost Foundation","title":"Shape of a sound wave in a weakly-perturbed Bose gas","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Marchukov, Oleksandr","first_name":"Oleksandr","last_name":"Marchukov"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"file":[{"file_size":666512,"creator":"dernst","content_type":"application/pdf","file_id":"9105","access_level":"open_access","relation":"main_file","checksum":"9fd614b7ab49999e7267874df2582f7e","file_name":"2021_SciPostPhysics_Marchukov.pdf","success":1,"date_created":"2021-02-09T07:06:22Z","date_updated":"2021-02-09T07:06:22Z"}],"article_processing_charge":"No","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"Marchukov, O., &#38; Volosniev, A. (2021). Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>","mla":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>, vol. 10, no. 2, 025, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>.","ama":"Marchukov O, Volosniev A. Shape of a sound wave in a weakly-perturbed Bose gas. <i>SciPost Physics</i>. 2021;10(2). doi:<a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">10.21468/scipostphys.10.2.025</a>","short":"O. Marchukov, A. Volosniev, SciPost Physics 10 (2021).","ieee":"O. Marchukov and A. Volosniev, “Shape of a sound wave in a weakly-perturbed Bose gas,” <i>SciPost Physics</i>, vol. 10, no. 2. SciPost Foundation, 2021.","ista":"Marchukov O, Volosniev A. 2021. Shape of a sound wave in a weakly-perturbed Bose gas. SciPost Physics. 10(2), 025.","chicago":"Marchukov, Oleksandr, and Artem Volosniev. “Shape of a Sound Wave in a Weakly-Perturbed Bose Gas.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.10.2.025\">https://doi.org/10.21468/scipostphys.10.2.025</a>."},"publication_identifier":{"issn":["2542-4653"]},"abstract":[{"text":"We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation.","lang":"eng"}],"arxiv":1,"type":"journal_article","file_date_updated":"2021-02-09T07:06:22Z","_id":"9093","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","date_published":"2021-02-03T00:00:00Z","intvolume":"        10","month":"02","acknowledgement":"We acknowledge fruitful discussions with Dr. Simos Mistakidis regarding beyond mean-field\r\neffects in our system. We also thank Prof. Maxim Olshanii for valuable suggestions to improve\r\nthe manuscript.O.V.M acknowledges the support from the National Science Foundation\r\nthrough grants No. PHY-1402249, No. PHY-1607221, and No. PHY-1912542 and the\r\nBinational (US-Israel) Science Foundation through grant No. 2015616, as well as by the Israel\r\nScience Foundation (grant No. 1287/17) and from the German Aeronautics and Space Administration\r\n(DLR) through Grant No. 50WM1957. This work has also received funding from\r\nthe DFG Project No.413495248 [VO 2437/1-1] and European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411\r\n(A. G. V.)","article_number":"025","date_updated":"2023-08-07T13:39:37Z","oa":1,"issue":"2","external_id":{"isi":["000646783100027"],"arxiv":["2004.08075"]},"year":"2021","volume":10,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-04T12:39:24Z","ddc":["530"],"day":"03","status":"public","publication":"SciPost Physics","doi":"10.21468/scipostphys.10.2.025","oa_version":"Published Version","ec_funded":1,"isi":1},{"year":"2021","external_id":{"isi":["000626365700001"],"pmid":["33533935"]},"date_updated":"2023-09-05T13:57:53Z","oa":1,"issue":"4","date_published":"2021-04-05T00:00:00Z","intvolume":"       220","month":"04","article_number":"e202006081","oa_version":"Published Version","isi":1,"publication":"Journal of Cell Biology","doi":"10.1083/jcb.202006081","date_created":"2021-02-05T10:08:04Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"ddc":["570"],"day":"05","status":"public","volume":220,"pmid":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MiSi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse","author":[{"orcid":"0000-0002-1073-744X","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"full_name":"Altenburger, LM","last_name":"Altenburger","first_name":"LM"},{"full_name":"Hauschild, R","last_name":"Hauschild","first_name":"R"},{"last_name":"Assen","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","first_name":"Frank P","full_name":"Assen, Frank P"},{"full_name":"Rottner, K","first_name":"K","last_name":"Rottner"},{"full_name":"TEB, Stradal","first_name":"Stradal","last_name":"TEB"},{"last_name":"Diz-Muñoz","first_name":"A","full_name":"Diz-Muñoz, A"},{"last_name":"Stein","first_name":"JV","full_name":"Stein, JV"},{"full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/pdf","file_id":"11367","file_size":5102328,"creator":"dernst","access_level":"open_access","checksum":"843ebc153847c8626e13c9c5ce71d533","relation":"main_file","success":1,"file_name":"2021_JournCellBiology_Leithner.pdf","date_updated":"2022-05-12T14:16:21Z","date_created":"2022-05-12T14:16:21Z"}],"has_accepted_license":"1","publisher":"Rockefeller University Press","publication_status":"published","_id":"9094","quality_controlled":"1","citation":{"chicago":"Leithner, Alexander F, LM Altenburger, R Hauschild, Frank P Assen, K Rottner, Stradal TEB, A Diz-Muñoz, JV Stein, and Michael K Sixt. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>.","short":"A.F. Leithner, L. Altenburger, R. Hauschild, F.P. Assen, K. Rottner, S. TEB, A. Diz-Muñoz, J. Stein, M.K. Sixt, Journal of Cell Biology 220 (2021).","ista":"Leithner AF, Altenburger L, Hauschild R, Assen FP, Rottner K, TEB S, Diz-Muñoz A, Stein J, Sixt MK. 2021. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. Journal of Cell Biology. 220(4), e202006081.","ieee":"A. F. Leithner <i>et al.</i>, “Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","ama":"Leithner AF, Altenburger L, Hauschild R, et al. Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>","mla":"Leithner, Alexander F., et al. “Dendritic Cell Actin Dynamics Control Contact Duration and Priming Efficiency at the Immunological Synapse.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202006081, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202006081\">10.1083/jcb.202006081</a>.","apa":"Leithner, A. F., Altenburger, L., Hauschild, R., Assen, F. P., Rottner, K., TEB, S., … Sixt, M. K. (2021). Dendritic cell actin dynamics control contact duration and priming efficiency at the immunological synapse. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202006081\">https://doi.org/10.1083/jcb.202006081</a>"},"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"scopus_import":"1","abstract":[{"text":"Dendritic cells (DCs) are crucial for the priming of naive T cells and the initiation of adaptive immunity. Priming is initiated at a heterologous cell–cell contact, the immunological synapse (IS). While it is established that F-actin dynamics regulates signaling at the T cell side of the contact, little is known about the cytoskeletal contribution on the DC side. Here, we show that the DC actin cytoskeleton is decisive for the formation of a multifocal synaptic structure, which correlates with T cell priming efficiency. DC actin at the IS appears in transient foci that are dynamized by the WAVE regulatory complex (WRC). The absence of the WRC in DCs leads to stabilized contacts with T cells, caused by an increase in ICAM1-integrin–mediated cell–cell adhesion. This results in lower numbers of activated and proliferating T cells, demonstrating an important role for DC actin in the regulation of immune synapse functionality.","lang":"eng"}],"file_date_updated":"2022-05-12T14:16:21Z","type":"journal_article"},{"status":"public","day":"26","date_created":"2021-02-07T23:01:12Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"volume":11,"oa_version":"Published Version","doi":"10.1038/s41598-020-80507-7","publication":"Scientific Reports","oa":1,"date_updated":"2022-08-19T07:22:23Z","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).","article_number":"2204","intvolume":"        11","month":"01","date_published":"2021-01-26T00:00:00Z","year":"2021","quality_controlled":"1","_id":"9097","type":"journal_article","file_date_updated":"2021-02-09T07:33:23Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"citation":{"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>.","short":"R. Pandey, Y. Al-Nuaimi, R.K. Mishra, S.K. Spurgeon, M. Goodfellow, Scientific Reports 11 (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.","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.","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>","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>.","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>"},"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","file":[{"file_name":"2021_ScientificReports_Pandey.pdf","success":1,"date_updated":"2021-02-09T07:33:23Z","date_created":"2021-02-09T07:33:23Z","file_size":2885056,"creator":"dernst","content_type":"application/pdf","file_id":"9106","checksum":"e8a68df48750712671f5c47b0228e531","access_level":"open_access","relation":"main_file"}],"title":"Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis","author":[{"last_name":"Pandey","first_name":"Rakesh","full_name":"Pandey, Rakesh"},{"full_name":"Al-Nuaimi, Yusur","first_name":"Yusur","last_name":"Al-Nuaimi"},{"last_name":"Mishra","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar"},{"full_name":"Spurgeon, Sarah K.","first_name":"Sarah K.","last_name":"Spurgeon"},{"full_name":"Goodfellow, Marc","last_name":"Goodfellow","first_name":"Marc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"article_processing_charge":"No"},{"publication_status":"published","quality_controlled":"1","_id":"9098","arxiv":1,"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."}],"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":["0012365X"]},"citation":{"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>.","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>","short":"G. Ivanov, Discrete Mathematics 344 (2021).","ista":"Ivanov G. 2021. On the volume of projections of the cross-polytope. Discrete Mathematics. 344(5), 112312.","ieee":"G. Ivanov, “On the volume of projections of the cross-polytope,” <i>Discrete Mathematics</i>, vol. 344, no. 5. Elsevier, 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>.","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>"},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"article_processing_charge":"No","author":[{"first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory"}],"title":"On the volume of projections of the cross-polytope","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","oa_version":"Preprint","isi":1,"publication":"Discrete Mathematics","main_file_link":[{"url":"https://arxiv.org/abs/1808.09165","open_access":"1"}],"doi":"10.1016/j.disc.2021.112312","day":"01","status":"public","date_created":"2021-02-07T23:01:12Z","volume":344,"year":"2021","external_id":{"arxiv":["1808.09165"],"isi":["000633365200001"]},"oa":1,"issue":"5","date_updated":"2023-08-07T13:40:37Z","article_number":"112312","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).","date_published":"2021-05-01T00:00:00Z","intvolume":"       344","month":"05"},{"quality_controlled":"1","_id":"9099","arxiv":1,"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","type":"journal_article","citation":{"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>.","short":"T.K. Srivastava, Archiv Der Mathematik 116 (2021) 515–527.","ista":"Srivastava TK. 2021. Lifting automorphisms on Abelian varieties as derived autoequivalences. Archiv der Mathematik. 116(5), 515–527.","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.","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>","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>.","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>"},"publication_identifier":{"issn":["0003889X"],"eissn":["14208938"]},"publication_status":"published","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","last_name":"Srivastava","full_name":"Srivastava, Tanya K"}],"title":"Lifting automorphisms on Abelian varieties as derived autoequivalences","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"article_processing_charge":"No","status":"public","day":"01","date_created":"2021-02-07T23:01:13Z","volume":116,"ec_funded":1,"oa_version":"Preprint","isi":1,"publication":"Archiv der Mathematik","main_file_link":[{"url":"https://arxiv.org/abs/2001.07762","open_access":"1"}],"doi":"10.1007/s00013-020-01564-y","oa":1,"issue":"5","date_updated":"2023-08-07T13:42:38Z","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.","date_published":"2021-05-01T00:00:00Z","intvolume":"       116","month":"05","year":"2021","page":"515-527","external_id":{"isi":["000612580200001"],"arxiv":["2001.07762"]}},{"date_updated":"2023-08-07T13:42:08Z","issue":"1","oa":1,"intvolume":"        34","month":"01","date_published":"2021-01-18T00:00:00Z","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.","year":"2021","external_id":{"isi":["000608367500001"]},"page":"4-15","date_created":"2021-02-07T23:01:13Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"status":"public","day":"18","volume":34,"isi":1,"oa_version":"Published Version","doi":"10.1111/jeb.13756","publication":"Journal of Evolutionary Biology","file":[{"relation":"main_file","access_level":"open_access","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","creator":"dernst","file_size":561340,"file_id":"9108","content_type":"application/pdf","date_created":"2021-02-09T09:04:02Z","date_updated":"2021-02-09T09:04:02Z","file_name":"2021_JourEvolBiology_Faria.pdf","success":1}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean"}],"title":"Speciation in marine environments: Diving under the surface","has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"NiBa"}],"_id":"9100","quality_controlled":"1","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"citation":{"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>","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 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>.","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>","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>."},"file_date_updated":"2021-02-09T09:04:02Z","type":"journal_article","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"}],"scopus_import":"1","publication_status":"published"},{"volume":24,"ddc":["590"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-07T23:01:13Z","day":"01","status":"public","publication":"Animal Cognition","doi":"10.1007/s10071-020-01461-5","oa_version":"Published Version","isi":1,"date_published":"2021-07-01T00:00:00Z","month":"07","intvolume":"        24","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.","date_updated":"2023-08-07T13:41:08Z","oa":1,"issue":"4","page":"753-764","external_id":{"isi":["000608382100001"]},"year":"2021","citation":{"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>.","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>","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.","short":"S.A. Reber, J. Oh, J. Janisch, C. Stevenson, S. Foggett, A. Wilkinson, Animal Cognition 24 (2021) 753–764.","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.","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>.","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>"},"publication_identifier":{"eissn":["14359456"],"issn":["14359448"]},"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file_date_updated":"2021-02-09T07:40:14Z","_id":"9101","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Springer Nature","title":"Early life differences in behavioral predispositions in two Alligatoridae species","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Stephan A.","last_name":"Reber","full_name":"Reber, Stephan A."},{"orcid":"0000-0001-7425-2372","last_name":"Oh","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook","full_name":"Oh, Jinook"},{"first_name":"Judith","last_name":"Janisch","full_name":"Janisch, Judith"},{"full_name":"Stevenson, Colin","first_name":"Colin","last_name":"Stevenson"},{"full_name":"Foggett, Shaun","last_name":"Foggett","first_name":"Shaun"},{"full_name":"Wilkinson, Anna","last_name":"Wilkinson","first_name":"Anna"}],"file":[{"date_updated":"2021-02-09T07:40:14Z","date_created":"2021-02-09T07:40:14Z","success":1,"file_name":"2021_AnimalCognition_Reber.pdf","relation":"main_file","access_level":"open_access","checksum":"d9dfa0d1de6d684692b041d936dd858e","content_type":"application/pdf","file_id":"9107","creator":"dernst","file_size":1117991}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"article_type":"original"},{"day":"01","status":"public","date_created":"2021-02-11T14:41:02Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"volume":5,"oa_version":"Published Version","ec_funded":1,"doi":"10.1007/s41468-020-00063-x","publication":"Journal of Applied and Computational Topology","issue":"1","oa":1,"date_updated":"2023-09-05T15:37:56Z","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).","intvolume":"         5","month":"03","date_published":"2021-03-01T00:00:00Z","year":"2021","external_id":{"arxiv":["1909.03488"]},"page":"99-140","quality_controlled":"1","_id":"9111","type":"journal_article","file_date_updated":"2021-02-11T14:43:59Z","arxiv":1,"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."}],"scopus_import":"1","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"citation":{"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>","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>.","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.","short":"A. Brown, O. Bobrowski, E. Munch, B. Wang, Journal of Applied and Computational Topology 5 (2021) 99–140.","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>","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","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"file":[{"file_id":"9112","content_type":"application/pdf","creator":"dernst","file_size":2090265,"relation":"main_file","access_level":"open_access","checksum":"3f02e9d47c428484733da0f588a3c069","success":1,"file_name":"2020_JourApplCompTopology_Brown.pdf","date_updated":"2021-02-11T14:43:59Z","date_created":"2021-02-11T14:43:59Z"}],"title":"Probabilistic convergence and stability of random mapper graphs","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Brown, Adam","first_name":"Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","last_name":"Brown"},{"full_name":"Bobrowski, Omer","last_name":"Bobrowski","first_name":"Omer"},{"last_name":"Munch","first_name":"Elizabeth","full_name":"Munch, Elizabeth"},{"full_name":"Wang, Bei","last_name":"Wang","first_name":"Bei"}],"publisher":"Springer Nature","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"article_processing_charge":"Yes (via OA deal)"},{"volume":6,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["540"],"date_created":"2021-02-14T23:01:14Z","day":"20","status":"public","publication":"ACS Energy Letters","doi":"10.1021/acsenergylett.0c02448","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12885"}]},"ec_funded":1,"oa_version":"Published Version","isi":1,"date_published":"2021-01-20T00:00:00Z","intvolume":"         6","month":"01","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).","date_updated":"2023-08-07T13:46:00Z","oa":1,"issue":"2","page":"581-587","external_id":{"isi":["000619803400036"]},"year":"2021","publication_identifier":{"eissn":["2380-8195"]},"citation":{"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>.","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>.","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>","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.","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.","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."},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2021-02-17T07:36:52Z","_id":"9118","quality_controlled":"1","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","has_accepted_license":"1","publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Calcabrini, Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano"},{"last_name":"Genc","first_name":"Aziz","full_name":"Genc, Aziz"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"full_name":"Kleinhanns, Tobias","last_name":"Kleinhanns","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Dirin, Dmitry N.","last_name":"Dirin","first_name":"Dmitry N."},{"full_name":"Akkerman, Quinten A.","first_name":"Quinten A.","last_name":"Akkerman"},{"last_name":"Kovalenko","first_name":"Maksym V.","full_name":"Kovalenko, Maksym V."},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"}],"title":"Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites","file":[{"relation":"main_file","access_level":"open_access","checksum":"6fa7374bf8b95fdfe6e6c595322a6689","file_id":"9155","content_type":"application/pdf","file_size":5071201,"creator":"dernst","date_created":"2021-02-17T07:36:52Z","date_updated":"2021-02-17T07:36:52Z","success":1,"file_name":"2021_ACSEnergyLetters_Calcabrini.pdf"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"article_type":"original"},{"isi":1,"oa_version":"Preprint","doi":"10.1111/1755-0998.13323","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"publication":"Molecular Ecology Resources","date_created":"2021-02-14T23:01:14Z","status":"public","day":"15","volume":21,"year":"2021","page":"2629-2644","external_id":{"isi":["000614183100001"]},"date_updated":"2023-08-07T13:45:18Z","oa":1,"intvolume":"        21","month":"01","date_published":"2021-01-15T00:00:00Z","publication_status":"published","_id":"9119","quality_controlled":"1","publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"citation":{"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>.","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>","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.","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.","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>.","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>"},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"NiBa"}],"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","last_name":"Fraisse"},{"last_name":"Popovic","first_name":"Iva","full_name":"Popovic, Iva"},{"first_name":"Clément","last_name":"Mazoyer","full_name":"Mazoyer, Clément"},{"last_name":"Spataro","first_name":"Bruno","full_name":"Spataro, Bruno"},{"full_name":"Delmotte, Stéphane","last_name":"Delmotte","first_name":"Stéphane"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"first_name":"Étienne","last_name":"Loire","full_name":"Loire, Étienne"},{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"full_name":"Duret, Laurent","last_name":"Duret","first_name":"Laurent"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"},{"first_name":"Xavier","last_name":"Vekemans","full_name":"Vekemans, Xavier"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"DILS: Demographic inferences with linked selection by using ABC","publisher":"Wiley"},{"volume":111,"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-15T09:27:14Z","status":"public","day":"12","publication":"Letters in Mathematical Physics","doi":"10.1007/s11005-021-01358-5","oa_version":"Published Version","isi":1,"date_published":"2021-02-12T00:00:00Z","month":"02","intvolume":"       111","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)","article_number":"20","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"date_updated":"2023-09-05T15:17:16Z","oa":1,"external_id":{"isi":["000617531900001"]},"year":"2021","citation":{"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>.","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>","ieee":"A. B. Lauritsen, “The BCS energy gap at low density,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","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.","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>.","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>"},"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2021-02-15T09:31:07Z","type":"journal_article","_id":"9121","quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","has_accepted_license":"1","publisher":"Springer Nature","title":"The BCS energy gap at low density","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard"}],"file":[{"date_created":"2021-02-15T09:31:07Z","date_updated":"2021-02-15T09:31:07Z","success":1,"file_name":"2021_LettersMathPhysics_Lauritsen.pdf","relation":"main_file","checksum":"eaf1b3ff5026f120f0929a5c417dc842","access_level":"open_access","file_id":"9122","content_type":"application/pdf","creator":"dernst","file_size":329332}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"GradSch"}],"language":[{"iso":"eng"}],"article_type":"original"},{"oa_version":"Published Version","publication":"Journal of Advances in Modeling Earth Systems","doi":"10.1029/2020ms002256","status":"public","day":"01","date_created":"2021-02-15T15:10:01Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["550"],"volume":13,"year":"2021","oa":1,"issue":"2","keyword":["Global and Planetary Change","General Earth and Planetary Sciences","Environmental Chemistry"],"date_updated":"2022-01-24T12:26:01Z","article_number":"e2020MS002256","date_published":"2021-02-01T00:00:00Z","month":"02","intvolume":"        13","publication_status":"published","quality_controlled":"1","_id":"9151","scopus_import":"1","abstract":[{"lang":"eng","text":"We investigate how mesoscale circulations associated with convective aggregation can modulate the sensitivity of the hydrologic cycle to warming. We quantify changes in the full distribution of rain across radiative‐convective equilibrium states in a cloud‐resolving model. For a given SST, the shift in mean rainfall between disorganized and organized states is associated with a shift in atmospheric radiative cooling, and is roughly analogous to the effect of a 4K SST increase. With rising temperatures, the increase in mean rain rate is insensitive to the presence of organization, while extremes can intensify faster in the aggregated state, leading to a faster amplification in the sporadic nature of rain. When convection aggregates, heavy rain is enhanced by 20‐30% and nonlinear behaviors are observed as a function of SST and strength of aggregation feedbacks. First, radiative‐ and surface‐flux aggregation feedbacks have multiplicative effects on extremes, illustrating a non‐trivial sensitivity to the degree of organization. Second, alternating Clausius‐Clapeyron and super‐Clausius‐Clapeyron regimes in extreme rainfall are found as a function of SST, corresponding to varying thermodynamic and dynamic contributions, and a large sensitivity to precipitation efficiency variations in some SST ranges.\r\nThe potential for mesoscale circulations in amplifying the hydrologic cycle is established. However these nonlinear distortions question the quantitative relevance of idealized self‐aggregation. This calls for a deeper investigation of relationships which capture the coupling between global energetics, aggregation feedbacks and local convection, and for systematic tests of their sensitivity to domain configurations, surface boundary conditions, microphysics and turbulence schemes."}],"type":"journal_article","file_date_updated":"2021-08-11T12:23:01Z","publication_identifier":{"issn":["1942-2466","1942-2466"]},"extern":"1","citation":{"apa":"Fildier, B., Collins, W. D., &#38; Muller, C. J. (2021). Distortions of the rain distribution with warming, with and without self‐aggregation. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2020ms002256\">https://doi.org/10.1029/2020ms002256</a>","mla":"Fildier, Benjamin, et al. “Distortions of the Rain Distribution with Warming, with and without Self‐aggregation.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 13, no. 2, e2020MS002256, American Geophysical Union, 2021, doi:<a href=\"https://doi.org/10.1029/2020ms002256\">10.1029/2020ms002256</a>.","ama":"Fildier B, Collins WD, Muller CJ. Distortions of the rain distribution with warming, with and without self‐aggregation. <i>Journal of Advances in Modeling Earth Systems</i>. 2021;13(2). doi:<a href=\"https://doi.org/10.1029/2020ms002256\">10.1029/2020ms002256</a>","ista":"Fildier B, Collins WD, Muller CJ. 2021. Distortions of the rain distribution with warming, with and without self‐aggregation. Journal of Advances in Modeling Earth Systems. 13(2), e2020MS002256.","ieee":"B. Fildier, W. D. Collins, and C. J. Muller, “Distortions of the rain distribution with warming, with and without self‐aggregation,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 13, no. 2. American Geophysical Union, 2021.","short":"B. Fildier, W.D. Collins, C.J. Muller, Journal of Advances in Modeling Earth Systems 13 (2021).","chicago":"Fildier, Benjamin, William D. Collins, and Caroline J Muller. “Distortions of the Rain Distribution with Warming, with and without Self‐aggregation.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2021. <a href=\"https://doi.org/10.1029/2020ms002256\">https://doi.org/10.1029/2020ms002256</a>."},"article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"full_name":"Fildier, Benjamin","first_name":"Benjamin","last_name":"Fildier"},{"full_name":"Collins, William D.","last_name":"Collins","first_name":"William D."},{"full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350"}],"title":"Distortions of the rain distribution with warming, with and without self‐aggregation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"2021_JAMES_Fildier.pdf","success":1,"date_created":"2021-08-11T12:23:01Z","date_updated":"2021-08-11T12:23:01Z","creator":"kschuh","file_size":1947936,"file_id":"9881","content_type":"application/pdf","checksum":"591ce69b7a36f24346d2061ac712f0f4","relation":"main_file","access_level":"open_access"}],"publisher":"American Geophysical Union","has_accepted_license":"1"},{"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","doi":"10.1088/1742-5468/abc7c7","status":"public","day":"05","ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-17T17:48:46Z","volume":2021,"year":"2021","external_id":{"isi":["000605080300001"]},"oa":1,"issue":"1","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability","Statistical and Nonlinear Physics"],"date_updated":"2023-08-07T13:46:28Z","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.","article_number":"013101","date_published":"2021-01-05T00:00:00Z","intvolume":"      2021","month":"01","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","_id":"9158","abstract":[{"lang":"eng","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."}],"type":"journal_article","file_date_updated":"2021-02-19T14:04:40Z","publication_identifier":{"issn":["1742-5468"]},"citation":{"short":"S. De Nicola, Journal of Statistical Mechanics: Theory and Experiment 2021 (2021).","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.","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.","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>","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>.","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>","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>."},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"article_processing_charge":"No","author":[{"full_name":"De Nicola, Stefano","last_name":"De Nicola","orcid":"0000-0002-4842-6671","first_name":"Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87"}],"title":"Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2021-02-19T14:04:40Z","date_updated":"2021-02-19T14:04:40Z","file_name":"2021_JourStatMech_deNicola.pdf","success":1,"relation":"main_file","access_level":"open_access","checksum":"64e2aae4837790db26e1dd1986c69c07","file_size":1693609,"creator":"dernst","file_id":"9172","content_type":"application/pdf"}],"publisher":"IOP Publishing","has_accepted_license":"1"},{"publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"M02463","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"abstract":[{"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.","lang":"eng"}],"type":"journal_article","citation":{"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>","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.","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).","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>.","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>","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>."},"publication_identifier":{"issn":["1943-2631"]},"quality_controlled":"1","_id":"9168","department":[{"_id":"NiBa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"publication":"Genetics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"doi":"10.1093/genetics/iyaa025","oa_version":"Published Version","isi":1,"volume":217,"day":"01","status":"public","date_created":"2021-02-18T14:41:30Z","external_id":{"isi":["000637218100005"]},"year":"2021","article_number":"iyaa025","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).","date_published":"2021-02-01T00:00:00Z","intvolume":"       217","month":"02","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"issue":"2","date_updated":"2023-08-07T13:47:01Z"},{"article_number":"102957","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.","intvolume":"       167","month":"03","date_published":"2021-03-01T00:00:00Z","issue":"03","oa":1,"date_updated":"2023-08-07T13:47:48Z","external_id":{"arxiv":["2010.08976"],"isi":["000623881600009"]},"year":"2021","volume":167,"day":"01","status":"public","date_created":"2021-02-21T23:01:20Z","doi":"10.1016/j.bulsci.2021.102957","main_file_link":[{"url":"https://arxiv.org/abs/2010.08976","open_access":"1"}],"publication":"Bulletin des Sciences Mathematiques","isi":1,"ec_funded":1,"oa_version":"Preprint","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Pathologies of the Hilbert scheme of points of a supersingular Enriques surface","author":[{"full_name":"Srivastava, Tanya K","last_name":"Srivastava","first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"TaHa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","arxiv":1,"publication_identifier":{"issn":["0007-4497"]},"citation":{"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>.","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>","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>.","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.","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."},"quality_controlled":"1","_id":"9173","publication_status":"published","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}]},{"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"}],"quality_controlled":"1","_id":"9188","file_date_updated":"2021-08-11T12:30:38Z","type":"journal_article","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_identifier":{"issn":["0197-0186"]},"citation":{"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>.","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>.","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>","short":"F. Pauler, Q. Hudson, S. Laukoter, S. Hippenmeyer, Neurochemistry International 145 (2021).","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.","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."},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2021-08-11T12:30:38Z","date_created":"2021-08-11T12:30:38Z","success":1,"file_name":"2021_NCI_Pauler.pdf","relation":"main_file","checksum":"c6d7a40089cd29e289f9b22e75768304","access_level":"open_access","content_type":"application/pdf","file_id":"9883","file_size":7083499,"creator":"kschuh"}],"title":"Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond","author":[{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"},{"last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne","full_name":"Laukoter, Susanne"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","has_accepted_license":"1","isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.1016/j.neuint.2021.104986","publication":"Neurochemistry International","day":"01","status":"public","date_created":"2021-02-23T12:31:43Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["570"],"pmid":1,"volume":145,"year":"2021","external_id":{"isi":["000635575000005"],"pmid":["33600873"]},"issue":"5","oa":1,"date_updated":"2023-08-07T13:48:26Z","keyword":["Cell Biology","Cellular and Molecular Neuroscience"],"article_number":"104986","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.","month":"05","intvolume":"       145","date_published":"2021-05-01T00:00:00Z"},{"doi":"10.1111/pce.14029","publication":"Plant, Cell & Environment","isi":1,"oa_version":"Submitted Version","pmid":1,"volume":44,"ddc":["580"],"date_created":"2021-02-24T10:07:21Z","status":"public","day":"01","page":"1846-1857","external_id":{"isi":["000625398600001"],"pmid":["33576018"]},"year":"2021","month":"06","intvolume":"        44","date_published":"2021-06-01T00:00:00Z","date_updated":"2023-11-07T08:18:36Z","issue":"6","oa":1,"publication_status":"published","publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"citation":{"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>.","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>","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>.","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>","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.","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.","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."},"file_date_updated":"2023-11-02T17:02:11Z","type":"journal_article","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."}],"scopus_import":"1","_id":"9189","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Wiley","file":[{"access_level":"open_access","checksum":"a812418fede076741c9c4dc07f317068","relation":"main_file","file_size":8437528,"creator":"amally","content_type":"application/pdf","file_id":"14481","date_created":"2023-11-02T17:02:11Z","date_updated":"2023-11-02T17:02:11Z","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","success":1}],"title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Zhao, 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L","first_name":"L","last_name":"Zhang"},{"last_name":"Jiang","first_name":"X","full_name":"Jiang, X"},{"full_name":"Li, Y","first_name":"Y","last_name":"Li"},{"last_name":"Luo","first_name":"H","full_name":"Luo, H"},{"full_name":"Li, K","first_name":"K","last_name":"Li"},{"last_name":"Yang","first_name":"J","full_name":"Yang, J"},{"full_name":"Luo, Q","last_name":"Luo","first_name":"Q"},{"full_name":"Li, L","last_name":"Li","first_name":"L"},{"full_name":"Peng, S","first_name":"S","last_name":"Peng"},{"full_name":"Huang, H","first_name":"H","last_name":"Huang"},{"full_name":"Zuo, Z","first_name":"Z","last_name":"Zuo"},{"full_name":"Liu, C","last_name":"Liu","first_name":"C"},{"last_name":"Wang","first_name":"L","full_name":"Wang, L"},{"full_name":"Li, C","first_name":"C","last_name":"Li"},{"first_name":"X","last_name":"He","full_name":"He, X"},{"full_name":"Friml, 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fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"file_date_updated":"2021-02-24T17:45:13Z","type":"research_data","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>.","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.","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>.","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>","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>.","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>"},"status":"public","day":"26","_id":"9192","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-02-24T17:49:21Z","ddc":["576"],"doi":"10.15479/AT:ISTA:9192","oa_version":"Published Version","contributor":[{"contributor_type":"project_member","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"contributor_type":"project_member","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"contributor_type":"project_member","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett"},{"contributor_type":"project_member","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","last_name":"Pickup"},{"contributor_type":"project_leader","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11411"},{"id":"11321","relation":"later_version","status":"public"},{"status":"public","relation":"earlier_version","id":"8254"}]}},{"_id":"9200","quality_controlled":"1","publication_identifier":{"isbn":["9781450383394"]},"citation":{"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>","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>.","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>","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.","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.","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.","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>."},"arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","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."}],"type":"conference","file_date_updated":"2021-05-25T13:53:22Z","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"publication_status":"published","author":[{"first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","last_name":"Garcia Soto","orcid":"0000-0003-2936-5719","full_name":"Garcia Soto, Miriam"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"},{"full_name":"Schilling, Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Synthesis of hybrid automata with affine dynamics from time-series data","file":[{"file_name":"2021_HSCC_Soto.pdf","success":1,"date_updated":"2021-05-25T13:53:22Z","date_created":"2021-05-25T13:53:22Z","file_size":1474786,"creator":"kschuh","content_type":"application/pdf","file_id":"9424","access_level":"open_access","relation":"main_file","checksum":"4c1202c1abf71384c3ee6fea88c2f80e"}],"has_accepted_license":"1","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ToHe"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_created":"2021-02-26T16:30:39Z","day":"01","status":"public","ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control","doi":"10.1145/3447928.3456704","keyword":["hybrid automaton","membership","system identification"],"date_updated":"2023-08-07T13:49:33Z","oa":1,"date_published":"2021-05-01T00:00:00Z","month":"05","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.","year":"2021","page":"2102.12734","external_id":{"isi":["000932821700028"],"arxiv":["2102.12734"]},"conference":{"name":"HSCC: International Conference on Hybrid Systems Computation and Control","end_date":"2021-05-21","start_date":"2021-05-19","location":"Nashville, TN, United States"}}]