[{"year":"2020","page":"119","abstract":[{"lang":"eng","text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry."}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","date_created":"2020-07-23T09:51:29Z","type":"dissertation","degree_awarded":"PhD","file":[{"date_updated":"2020-07-27T12:44:51Z","file_size":1061740,"creator":"savvakum","file_id":"8178","content_type":"application/zip","date_created":"2020-07-27T12:44:51Z","file_name":"source.zip","relation":"source_file","access_level":"closed"},{"date_updated":"2020-07-27T12:46:53Z","file_size":1336501,"file_id":"8179","content_type":"application/pdf","creator":"savvakum","success":1,"file_name":"thesis_pdfa.pdf","relation":"main_file","date_created":"2020-07-27T12:46:53Z","access_level":"open_access"}],"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey"}],"article_processing_charge":"No","_id":"8156","publication_status":"published","day":"24","related_material":{"record":[{"relation":"part_of_dissertation","id":"8182","status":"public"},{"status":"public","id":"8183","relation":"part_of_dissertation"},{"status":"public","id":"8185","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8184","status":"public"},{"relation":"part_of_dissertation","id":"6355","status":"public"},{"id":"75","relation":"part_of_dissertation","status":"public"}]},"ddc":["514"],"oa":1,"month":"07","has_accepted_license":"1","date_published":"2020-07-24T00:00:00Z","status":"public","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-27T12:46:53Z","date_updated":"2023-12-18T10:51:01Z","language":[{"iso":"eng"}],"citation":{"apa":"Avvakumov, S. (2020). <i>Topological methods in geometry and discrete mathematics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","mla":"Avvakumov, Sergey. <i>Topological Methods in Geometry and Discrete Mathematics</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020."},"alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:8156","title":"Topological methods in geometry and discrete mathematics"},{"year":"2020","external_id":{"isi":["000579698700006"]},"scopus_import":"1","page":"1160-1179.e9","abstract":[{"text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.","lang":"eng"}],"publication_identifier":{"issn":["0896-6273"]},"oa_version":"Published Version","project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF","grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-07-23T16:03:12Z","volume":107,"type":"journal_article","file":[{"file_id":"8828","content_type":"application/pdf","creator":"dernst","checksum":"7becdc16a6317304304631087ae7dd7f","date_updated":"2020-12-02T09:26:46Z","file_size":8911830,"access_level":"open_access","file_name":"2020_Neuron_Laukoter.pdf","success":1,"relation":"main_file","date_created":"2020-12-02T09:26:46Z"}],"article_type":"original","author":[{"orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter"},{"last_name":"Pauler","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J"},{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Penz","full_name":"Penz, Thomas"},{"full_name":"Bock, Christoph","orcid":"0000-0001-6091-3088","last_name":"Bock","first_name":"Christoph"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"ec_funded":1,"intvolume":"       107","article_processing_charge":"No","_id":"8162","publication_status":"published","day":"23","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/","relation":"press_release","description":"News on IST Website"}]},"issue":"6","publication":"Neuron","isi":1,"ddc":["570"],"oa":1,"month":"09","has_accepted_license":"1","date_published":"2020-09-23T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","department":[{"_id":"SiHi"}],"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 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.","file_date_updated":"2020-12-02T09:26:46Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-08-22T08:20:11Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"citation":{"short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9.","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>.","ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. 2020;107(6):1160-1179.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>","ieee":"S. Laukoter <i>et al.</i>, “Cell-type specificity of genomic imprinting in cerebral cortex,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020."},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"doi":"10.1016/j.neuron.2020.06.031","title":"Cell-type specificity of genomic imprinting in cerebral cortex"},{"scopus_import":"1","page":"193-199","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"year":"2020","external_id":{"isi":["000570978400005"]},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"volume":57,"date_created":"2020-07-24T07:09:18Z","type":"journal_article","publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"oa_version":"Published Version","article_type":"original","ec_funded":1,"author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"file":[{"file_id":"8164","creator":"mwintrae","content_type":"application/pdf","file_size":1476072,"date_updated":"2020-07-24T07:09:06Z","access_level":"open_access","relation":"main_file","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_created":"2020-07-24T07:09:06Z"}],"_id":"8163","article_processing_charge":"No","intvolume":"        57","publication":"Studia Scientiarum Mathematicarum Hungarica","isi":1,"ddc":["510"],"oa":1,"month":"07","publication_status":"published","day":"24","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Akadémiai Kiadó","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","department":[{"_id":"HeEd"}],"has_accepted_license":"1","date_published":"2020-07-24T00:00:00Z","status":"public","date_updated":"2023-10-10T13:05:27Z","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-24T07:09:06Z","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"doi":"10.1556/012.2020.57.2.1454","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","citation":{"apa":"Vegter, G., &#38; Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó, 2020. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>.","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. 2020;57(2):193-199. doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020."}},{"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2020-07-12T00:00:00Z","month":"07","oa":1,"isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","issue":"1806","pmid":1,"day":"12","publication_status":"published","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","doi":"10.1098/rstb.2019.0545","article_number":"20190545","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"citation":{"short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>.","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., &#38; Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>","ieee":"S. Stankowski <i>et al.</i>, “The evolution of strong reproductive isolation between sympatric intertidal snails,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020."},"language":[{"iso":"eng"}],"date_updated":"2023-08-22T08:22:13Z","quality_controlled":"1","type":"journal_article","date_created":"2020-07-26T22:01:01Z","volume":375,"oa_version":"Published Version","publication_identifier":{"eissn":["1471-2970"]},"abstract":[{"text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.","lang":"eng"}],"scopus_import":"1","external_id":{"pmid":["32654639"],"isi":["000552662100014"]},"year":"2020","article_processing_charge":"No","_id":"8167","intvolume":"       375","author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"full_name":"Eyres, Isobel","last_name":"Eyres","first_name":"Isobel"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"article_type":"original"},{"article_type":"original","author":[{"first_name":"Jonna","last_name":"Kulmuni","full_name":"Kulmuni, Jonna"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Lucek, Kay","last_name":"Lucek","first_name":"Kay"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M"}],"ec_funded":1,"article_processing_charge":"No","_id":"8168","intvolume":"       375","scopus_import":"1","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"year":"2020","external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"volume":375,"date_created":"2020-07-26T22:01:01Z","type":"journal_article","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2023-08-22T08:21:31Z","quality_controlled":"1","doi":"10.1098/rstb.2019.0528","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"article_number":"20190528","citation":{"chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., &#38; Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>.","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society Series B: Biological sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” <i>Philosophical Transactions of the Royal Society. Series B: Biological sciences</i>, vol. 375, no. 1806. The Royal Society, 2020."},"isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","oa":1,"month":"07","day":"12","publication_status":"published","issue":"1806","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","status":"public","date_published":"2020-07-12T00:00:00Z"},{"month":"07","isi":1,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","issue":"1806","pmid":1,"publication_status":"published","day":"12","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2020-07-12T00:00:00Z","status":"public","date_updated":"2023-08-22T08:23:24Z","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","doi":"10.1098/rstb.2019.0544","citation":{"ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>.","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &#38; Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>.","ieee":"H. Shang <i>et al.</i>, “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020."},"article_number":"20190544","abstract":[{"lang":"eng","text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation."}],"scopus_import":"1","external_id":{"isi":["000552662100013"],"pmid":["32654641"]},"year":"2020","type":"journal_article","date_created":"2020-07-26T22:01:02Z","volume":375,"oa_version":"Published Version","publication_identifier":{"eissn":["14712970"]},"author":[{"last_name":"Shang","first_name":"Huiying","full_name":"Shang, Huiying"},{"full_name":"Hess, Jaqueline","first_name":"Jaqueline","last_name":"Hess"},{"last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","first_name":"David","last_name":"Field"},{"full_name":"Ingvarsson, Pär K.","last_name":"Ingvarsson","first_name":"Pär K."},{"first_name":"Jianquan","last_name":"Liu","full_name":"Liu, Jianquan"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"}],"article_type":"original","_id":"8169","article_processing_charge":"No","intvolume":"       375"},{"scopus_import":"1","abstract":[{"text":"Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function\r\nof time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct\r\npeaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and\r\ncentrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For\r\nCS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the\r\ngas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in\r\ndetail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in\r\nhelium droplets introduced here should apply to a range of molecules and complexes.","lang":"eng"}],"year":"2020","external_id":{"isi":["000544526900006"],"arxiv":["2006.02694"]},"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"date_created":"2020-07-26T22:01:02Z","volume":125,"type":"journal_article","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"arxiv":1,"oa_version":"Preprint","article_type":"original","author":[{"full_name":"Chatterley, Adam S.","last_name":"Chatterley","first_name":"Adam S."},{"full_name":"Christiansen, Lars","first_name":"Lars","last_name":"Christiansen"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"full_name":"Jørgensen, Anders V.","last_name":"Jørgensen","first_name":"Anders V."},{"first_name":"Benjamin","last_name":"Shepperson","full_name":"Shepperson, Benjamin"},{"full_name":"Cherepanov, Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","first_name":"Igor"},{"last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert E.","last_name":"Zillich","full_name":"Zillich, Robert E."},{"last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"}],"ec_funded":1,"article_processing_charge":"No","_id":"8170","intvolume":"       125","isi":1,"publication":"Physical Review Letters","oa":1,"month":"07","publication_status":"published","day":"03","issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"H. S. acknowledges support from the European Research Council-AdG (Project No. 320459, DropletControl)\r\nand from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support\r\nby the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council\r\n(ERC) Starting Grant No. 801770 (ANGULON). G. B. acknowledges support from the Austrian Science Fund\r\n(FWF), under Project No. M2641-N27. I. C. acknowledges support by the European Union’s Horizon 2020 research and\r\ninnovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Computational resources for\r\nthe PIMC simulations were provided by the division for scientific computing at the Johannes Kepler University.","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","status":"public","date_published":"2020-07-03T00:00:00Z","date_updated":"2024-08-07T07:16:52Z","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1103/PhysRevLett.125.013001","title":"Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains","citation":{"chicago":"Chatterley, Adam S., Lars Christiansen, Constant A. Schouder, Anders V. Jørgensen, Benjamin Shepperson, Igor Cherepanov, Giacomo Bighin, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>.","apa":"Chatterley, A. S., Christiansen, L., Schouder, C. A., Jørgensen, A. V., Shepperson, B., Cherepanov, I., … Stapelfeldt, H. (2020). Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">https://doi.org/10.1103/PhysRevLett.125.013001</a>","short":"A.S. Chatterley, L. Christiansen, C.A. Schouder, A.V. Jørgensen, B. Shepperson, I. Cherepanov, G. Bighin, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 125 (2020).","ama":"Chatterley AS, Christiansen L, Schouder CA, et al. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. <i>Physical Review Letters</i>. 2020;125(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>","ista":"Chatterley AS, Christiansen L, Schouder CA, Jørgensen AV, Shepperson B, Cherepanov I, Bighin G, Zillich RE, Lemeshko M, Stapelfeldt H. 2020. Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains. Physical Review Letters. 125(1), 013001.","mla":"Chatterley, Adam S., et al. “Rotational Coherence Spectroscopy of Molecules in Helium Nanodroplets: Reconciling the Time and the Frequency Domains.” <i>Physical Review Letters</i>, vol. 125, no. 1, 013001, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.125.013001\">10.1103/PhysRevLett.125.013001</a>.","ieee":"A. S. Chatterley <i>et al.</i>, “Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains,” <i>Physical Review Letters</i>, vol. 125, no. 1. American Physical Society, 2020."},"article_number":"013001","main_file_link":[{"url":"https://arxiv.org/abs/2006.02694","open_access":"1"}]},{"scopus_import":"1","publication":"Photoswitching Proteins","page":"233-246","month":"07","abstract":[{"lang":"eng","text":"Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware."}],"day":"11","publication_status":"published","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2173,"date_created":"2020-07-26T22:01:03Z","editor":[{"last_name":"Niopek","first_name":"Dominik","full_name":"Niopek, Dominik"}],"department":[{"_id":"CaGu"}],"publisher":"Springer Nature","type":"book_chapter","publication_identifier":{"eisbn":["9781071607558"],"eissn":["19406029"]},"date_published":"2020-07-11T00:00:00Z","status":"public","oa_version":"None","date_updated":"2021-01-12T08:17:17Z","author":[{"first_name":"Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"series_title":"MIMB","_id":"8173","article_processing_charge":"No","doi":"10.1007/978-1-0716-0755-8_16","title":"Design and application of light-regulated receptor tyrosine kinases","citation":{"chicago":"Kainrath, Stephanie, and Harald L Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” In <i>Photoswitching Proteins</i>, edited by Dominik Niopek, 2173:233–46. MIMB. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>.","apa":"Kainrath, S., &#38; Janovjak, H. L. (2020). Design and application of light-regulated receptor tyrosine kinases. In D. Niopek (Ed.), <i>Photoswitching Proteins</i> (Vol. 2173, pp. 233–246). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">https://doi.org/10.1007/978-1-0716-0755-8_16</a>","short":"S. Kainrath, H.L. Janovjak, in:, D. Niopek (Ed.), Photoswitching Proteins, Springer Nature, 2020, pp. 233–246.","ista":"Kainrath S, Janovjak HL. 2020.Design and application of light-regulated receptor tyrosine kinases. In: Photoswitching Proteins. Methods in Molecular Biology, vol. 2173, 233–246.","ama":"Kainrath S, Janovjak HL. Design and application of light-regulated receptor tyrosine kinases. In: Niopek D, ed. <i>Photoswitching Proteins</i>. Vol 2173. MIMB. Springer Nature; 2020:233-246. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>","mla":"Kainrath, Stephanie, and Harald L. Janovjak. “Design and Application of Light-Regulated Receptor Tyrosine Kinases.” <i>Photoswitching Proteins</i>, edited by Dominik Niopek, vol. 2173, Springer Nature, 2020, pp. 233–46, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0755-8_16\">10.1007/978-1-0716-0755-8_16</a>.","ieee":"S. Kainrath and H. L. Janovjak, “Design and application of light-regulated receptor tyrosine kinases,” in <i>Photoswitching Proteins</i>, vol. 2173, D. Niopek, Ed. Springer Nature, 2020, pp. 233–246."},"intvolume":"      2173","alternative_title":["Methods in Molecular Biology"]},{"file_date_updated":"2020-08-24T15:43:52Z","file":[{"date_updated":"2020-08-24T15:43:49Z","file_size":6577,"checksum":"878c60885ce30afb59a884dd5eef451c","file_id":"8290","creator":"rhauschild","content_type":"text/plain","date_created":"2020-08-24T15:43:49Z","success":1,"file_name":"centriolesDistance.m","relation":"main_file","access_level":"open_access"},{"content_type":"text/plain","file_id":"8291","creator":"rhauschild","file_size":2680,"date_updated":"2020-08-24T15:43:52Z","checksum":"5a93ac7be2b66b28e4bd8b113ee6aade","access_level":"open_access","date_created":"2020-08-24T15:43:52Z","relation":"main_file","file_name":"goTracking.m","success":1}],"date_updated":"2021-01-11T15:29:08Z","author":[{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"}],"citation":{"ieee":"R. Hauschild, “Amplified centrosomes in dendritic cells promote immune cell effector functions.” IST Austria, 2020.","chicago":"Hauschild, Robert. “Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>.","apa":"Hauschild, R. (2020). Amplified centrosomes in dendritic cells promote immune cell effector functions. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">https://doi.org/10.15479/AT:ISTA:8181</a>","short":"R. Hauschild, (2020).","ama":"Hauschild R. Amplified centrosomes in dendritic cells promote immune cell effector functions. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>","mla":"Hauschild, Robert. <i>Amplified Centrosomes in Dendritic Cells Promote Immune Cell Effector Functions</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>.","ista":"Hauschild R. 2020. Amplified centrosomes in dendritic cells promote immune cell effector functions, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8181\">10.15479/AT:ISTA:8181</a>."},"_id":"8181","tmp":{"legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","name":"The 3-Clause BSD License","short":"3-Clause BSD"},"title":"Amplified centrosomes in dendritic cells promote immune cell effector functions","doi":"10.15479/AT:ISTA:8181","day":"24","year":"2020","license":"https://opensource.org/licenses/BSD-3-Clause","month":"08","oa":1,"has_accepted_license":"1","date_published":"2020-08-24T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"type":"software","publisher":"IST Austria","date_created":"2020-07-28T16:24:37Z"},{"arxiv":1,"publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"conference":{"end_date":"2020-06-19","start_date":"2020-06-14","location":"Virtual","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"oa_version":"Submitted Version","type":"conference","date_created":"2020-07-31T16:53:49Z","external_id":{"arxiv":["2004.04180"]},"year":"2020","scopus_import":"1","page":"7498-7507","abstract":[{"lang":"eng","text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n  A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n  We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes."}],"_id":"8186","article_processing_charge":"No","file":[{"date_updated":"2020-07-31T16:57:12Z","file_size":10262773,"content_type":"application/pdf","creator":"phenders","file_id":"8187","success":1,"file_name":"paper.pdf","relation":"main_file","date_created":"2020-07-31T16:57:12Z","access_level":"open_access"}],"author":[{"first_name":"Paul M","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M"},{"full_name":"Tsiminaki, Vagia","last_name":"Tsiminaki","first_name":"Vagia"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"has_accepted_license":"1","status":"public","date_published":"2020-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"publisher":"IEEE","publication_status":"published","day":"01","ddc":["004"],"publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","month":"07","oa":1,"citation":{"ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Virtual, 2020, pp. 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., &#38; Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 7498–7507). Virtual: IEEE. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 7498–7507. IEEE, 2020. <a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">https://doi.org/10.1109/CVPR42600.2020.00752</a>.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2020:7498-7507. doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2020, pp. 7498–507, doi:<a href=\"https://doi.org/10.1109/CVPR42600.2020.00752\">10.1109/CVPR42600.2020.00752</a>.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507."},"main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"title":"Leveraging 2D data to learn textured 3D mesh generation","doi":"10.1109/CVPR42600.2020.00752","file_date_updated":"2020-07-31T16:57:12Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-10-17T07:37:11Z"},{"oa":1,"month":"07","publication":"34th Conference on Neural Information Processing Systems","publication_status":"published","day":"07","publisher":"Curran Associates","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-07T00:00:00Z","status":"public","date_updated":"2023-04-25T09:49:58Z","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Unsupervised object-centric video generation and decomposition in 3D","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06705"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Curran Associates, 2020, pp. 3106–3117.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Curran Associates, 2020, pp. 3106–3117.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Curran Associates; 2020:3106–3117.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:3106–3117. Curran Associates, 2020.","apa":"Henderson, P. M., &#38; Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 3106–3117). Vancouver, Canada: Curran Associates.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117."},"abstract":[{"text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.","lang":"eng"}],"page":"3106–3117","year":"2020","external_id":{"arxiv":["2007.06705"]},"date_created":"2020-07-31T16:59:19Z","volume":33,"type":"conference","oa_version":"Preprint","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","end_date":"2020-12-12","start_date":"2020-12-06"},"publication_identifier":{"isbn":["9781713829546"]},"arxiv":1,"author":[{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M","first_name":"Paul M","last_name":"Henderson"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"_id":"8188","article_processing_charge":"No","intvolume":"        33"},{"article_type":"original","author":[{"last_name":"Yu","first_name":"Xiaoting","full_name":"Yu, Xiaoting"},{"first_name":"Junfeng","last_name":"Liu","full_name":"Liu, Junfeng"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Luo, Zhishan","first_name":"Zhishan","last_name":"Luo"},{"first_name":"Yong","last_name":"Zuo","full_name":"Zuo, Yong"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Nasiou, Déspina","last_name":"Nasiou","first_name":"Déspina"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Pan","first_name":"Kai","full_name":"Pan, Kai"},{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias"},{"last_name":"Xie","first_name":"Ying","full_name":"Xie, Ying"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"intvolume":"        77","article_processing_charge":"No","_id":"8189","year":"2020","external_id":{"isi":["000581738300030"]},"abstract":[{"lang":"eng","text":"Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface."}],"scopus_import":"1","oa_version":"None","publication_identifier":{"issn":["2211-2855"]},"volume":77,"date_created":"2020-08-02T22:00:57Z","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-08-22T08:24:05Z","citation":{"ieee":"X. Yu <i>et al.</i>, “Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation,” <i>Nano Energy</i>, vol. 77, no. 11. Elsevier, 2020.","short":"X. Yu, J. Liu, J. Li, Z. Luo, Y. Zuo, C. Xing, J. Llorca, D. Nasiou, J. Arbiol, K. Pan, T. Kleinhanns, Y. Xie, A. Cabot, Nano Energy 77 (2020).","ama":"Yu X, Liu J, Li J, et al. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. 2020;77(11). doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>","mla":"Yu, Xiaoting, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>, vol. 77, no. 11, 105116, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">10.1016/j.nanoen.2020.105116</a>.","ista":"Yu X, Liu J, Li J, Luo Z, Zuo Y, Xing C, Llorca J, Nasiou D, Arbiol J, Pan K, Kleinhanns T, Xie Y, Cabot A. 2020. Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. Nano Energy. 77(11), 105116.","chicago":"Yu, Xiaoting, Junfeng Liu, Junshan Li, Zhishan Luo, Yong Zuo, Congcong Xing, Jordi Llorca, et al. “Phosphorous Incorporation in Pd2Sn Alloys for Electrocatalytic Ethanol Oxidation.” <i>Nano Energy</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>.","apa":"Yu, X., Liu, J., Li, J., Luo, Z., Zuo, Y., Xing, C., … Cabot, A. (2020). Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation. <i>Nano Energy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nanoen.2020.105116\">https://doi.org/10.1016/j.nanoen.2020.105116</a>"},"article_number":"105116","doi":"10.1016/j.nanoen.2020.105116","title":"Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation","issue":"11","publication_status":"published","day":"01","month":"11","isi":1,"publication":"Nano Energy","status":"public","date_published":"2020-11-01T00:00:00Z","publisher":"Elsevier","department":[{"_id":"MaIb"}],"acknowledgement":"This work was supported by the European Regional Development Funds and by the Spanish Ministerio de Economía y Competitividad through the project SEHTOP, ENE2016- 77798-C4-3-R, and ENE2017-85087-C3. X. Y. thanks the China Scholarship Council for the scholarship support. J. Liu acknowledges support from the Jiangsu University Foundation (4111510011). J. Li obtained International Postdoctoral Exchange Fellowship Program (Talent-Introduction program) in 2019 and is grateful for the project (2019M663468) funded by the China Postdoctoral Science Foundation. Authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246, and from IST Austria. ICN2 acknowledges the support from the Severo Ochoa Programme (MINECO, grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. J. Llorca is a Serra Húnter Fellow and is grateful to MICINN/FEDER RTI2018-093996-B-C31, GC 2017 SGR 128 and to ICREA Academia program.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_published":"2020-07-22T00:00:00Z","status":"public","has_accepted_license":"1","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","day":"22","publication_status":"published","month":"07","oa":1,"ddc":["570"],"publication":"The Journal of Cell Biology","isi":1,"citation":{"short":"M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).","ista":"Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context. The Journal of Cell Biology. 219(8), e202007029.","mla":"Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>, vol. 219, no. 8, e202007029, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>.","ama":"Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. 2020;219(8). doi:<a href=\"https://doi.org/10.1083/jcb.202007029\">10.1083/jcb.202007029</a>","chicago":"Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology in Context.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>.","apa":"Sixt, M. K., &#38; Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology in context. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202007029\">https://doi.org/10.1083/jcb.202007029</a>","ieee":"M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,” <i>The Journal of Cell Biology</i>, vol. 219, no. 8. Rockefeller University Press, 2020."},"article_number":"e202007029","title":"Zena Werb (1945-2020): Cell biology in context","doi":"10.1083/jcb.202007029","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"file_date_updated":"2021-02-02T23:30:03Z","date_updated":"2023-10-17T10:04:49Z","language":[{"iso":"eng"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1540-8140"]},"type":"journal_article","date_created":"2020-08-02T22:00:57Z","volume":219,"external_id":{"isi":["000573631000004"]},"year":"2020","scopus_import":"1","intvolume":"       219","article_processing_charge":"No","_id":"8190","file":[{"access_level":"open_access","relation":"main_file","file_name":"2020_JCB_Sixt.pdf","date_created":"2020-08-04T13:11:52Z","file_id":"8200","creator":"dernst","content_type":"application/pdf","embargo":"2021-02-01","checksum":"30016d778d266b8e17d01094917873b8","file_size":830725,"date_updated":"2021-02-02T23:30:03Z"}],"author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Huttenlocher, Anna","first_name":"Anna","last_name":"Huttenlocher"}],"article_type":"letter_note"},{"date_created":"2020-08-02T22:00:58Z","publisher":"Association for Computing Machinery","type":"conference","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","status":"public","date_published":"2020-07-06T00:00:00Z","conference":{"end_date":"2020-07-17","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Virtual Event, United States"},"publication_identifier":{"isbn":["9781450369350"]},"month":"07","abstract":[{"text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures.","lang":"eng"}],"scopus_import":"1","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","page":"37-49","isi":1,"year":"2020","issue":"7","external_id":{"isi":["000744436200004"]},"publication_status":"published","day":"06","doi":"10.1145/3350755.3400213","title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","article_processing_charge":"No","_id":"8191","citation":{"ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, Virtual Event, United States, 2020, no. 7, pp. 37–49.","apa":"Alistarh, D.-A., Brown, T. A., &#38; Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 37–49. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3350755.3400213\">https://doi.org/10.1145/3350755.3400213</a>.","mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>.","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2020:37-49. doi:<a href=\"https://doi.org/10.1145/3350755.3400213\">10.1145/3350755.3400213</a>","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49.","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49."},"date_updated":"2024-02-28T12:56:32Z","language":[{"iso":"eng"}],"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A"},{"last_name":"Singhal","first_name":"Nandini","full_name":"Singhal, Nandini"}],"quality_controlled":"1"},{"quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:16:18Z","citation":{"short":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, A. Royer, in:, Proceedings of the 30th International Conference on Automated Planning and Scheduling, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","ama":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. Multiple-environment Markov decision processes: Efficient analysis and applications. In: <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>. Vol 30. Association for the Advancement of Artificial Intelligence; 2020:48-56.","ista":"Chatterjee K, Chmelik M, Karkhanis D, Novotný P, Royer A. 2020. Multiple-environment Markov decision processes: Efficient analysis and applications. Proceedings of the 30th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 30, 48–56.","mla":"Chatterjee, Krishnendu, et al. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, vol. 30, Association for the Advancement of Artificial Intelligence, 2020, pp. 48–56.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Deep Karkhanis, Petr Novotný, and Amélie Royer. “Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications.” In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, 30:48–56. Association for the Advancement of Artificial Intelligence, 2020.","apa":"Chatterjee, K., Chmelik, M., Karkhanis, D., Novotný, P., &#38; Royer, A. (2020). Multiple-environment Markov decision processes: Efficient analysis and applications. In <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i> (Vol. 30, pp. 48–56). Nancy, France: Association for the Advancement of Artificial Intelligence.","ieee":"K. Chatterjee, M. Chmelik, D. Karkhanis, P. Novotný, and A. Royer, “Multiple-environment Markov decision processes: Efficient analysis and applications,” in <i>Proceedings of the 30th International Conference on Automated Planning and Scheduling</i>, Nancy, France, 2020, vol. 30, pp. 48–56."},"title":"Multiple-environment Markov decision processes: Efficient analysis and applications","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8390"}]},"publication_status":"published","day":"01","month":"06","publication":"Proceedings of the 30th International Conference on Automated Planning and Scheduling","status":"public","date_published":"2020-06-01T00:00:00Z","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian ScienceFund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE),and COST Action GAMENET. Petr Novotn ́y is supported bythe Czech Science Foundation grant No. GJ19-15134Y.","department":[{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Karkhanis, Deep","last_name":"Karkhanis","first_name":"Deep"},{"first_name":"Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"}],"intvolume":"        30","article_processing_charge":"No","_id":"8193","year":"2020","abstract":[{"lang":"eng","text":"Multiple-environment Markov decision processes (MEMDPs) are MDPs equipped with not one, but multiple probabilistic transition functions, which represent the various possible unknown environments. While the previous research on MEMDPs focused on theoretical properties for long-run average payoff, we study them with discounted-sum payoff and focus on their practical advantages and applications. MEMDPs can be viewed as a special case of Partially observable and Mixed observability MDPs: the state of the system is perfectly observable, but not the environment. We show that the specific structure of MEMDPs allows for more efficient algorithmic analysis, in particular for faster belief updates. We demonstrate the applicability of MEMDPs in several domains. In particular, we formalize the sequential decision-making approach to contextual recommendation systems as MEMDPs and substantially improve over the previous MDP approach."}],"page":"48-56","scopus_import":"1","oa_version":"None","publication_identifier":{"eissn":["23340843"],"issn":["23340835"]},"conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"Nancy, France","end_date":"2020-10-30","start_date":"2020-10-26"},"type":"conference","volume":30,"date_created":"2020-08-02T22:00:58Z","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"}]},{"isi":1,"publication":"Automated Reasoning","oa":1,"month":"06","publication_status":"published","day":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"date_published":"2020-06-24T00:00:00Z","status":"public","language":[{"iso":"eng"}],"date_updated":"2023-08-22T08:27:25Z","quality_controlled":"1","doi":"10.1007/978-3-030-51074-9_2","title":"An SMT theory of fixed-point arithmetic","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-030-51074-9_2"}],"citation":{"apa":"Baranowski, M., He, S., Lechner, M., Nguyen, T. S., &#38; Rakamarić, Z. (2020). An SMT theory of fixed-point arithmetic. In <i>Automated Reasoning</i> (Vol. 12166, pp. 13–31). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>","chicago":"Baranowski, Marek, Shaobo He, Mathias Lechner, Thanh Son Nguyen, and Zvonimir Rakamarić. “An SMT Theory of Fixed-Point Arithmetic.” In <i>Automated Reasoning</i>, 12166:13–31. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">https://doi.org/10.1007/978-3-030-51074-9_2</a>.","mla":"Baranowski, Marek, et al. “An SMT Theory of Fixed-Point Arithmetic.” <i>Automated Reasoning</i>, vol. 12166, Springer Nature, 2020, pp. 13–31, doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>.","ista":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. 2020. An SMT theory of fixed-point arithmetic. Automated Reasoning. IJCAR: International Joint Conference on Automated Reasoning, LNCS, vol. 12166, 13–31.","ama":"Baranowski M, He S, Lechner M, Nguyen TS, Rakamarić Z. An SMT theory of fixed-point arithmetic. In: <i>Automated Reasoning</i>. Vol 12166. Springer Nature; 2020:13-31. doi:<a href=\"https://doi.org/10.1007/978-3-030-51074-9_2\">10.1007/978-3-030-51074-9_2</a>","short":"M. Baranowski, S. He, M. Lechner, T.S. Nguyen, Z. Rakamarić, in:, Automated Reasoning, Springer Nature, 2020, pp. 13–31.","ieee":"M. Baranowski, S. He, M. Lechner, T. S. Nguyen, and Z. Rakamarić, “An SMT theory of fixed-point arithmetic,” in <i>Automated Reasoning</i>, Paris, France, 2020, vol. 12166, pp. 13–31."},"alternative_title":["LNCS"],"page":"13-31","scopus_import":"1","abstract":[{"text":"Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.","lang":"eng"}],"year":"2020","external_id":{"isi":["000884318000002"]},"project":[{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-08-02T22:00:59Z","volume":12166,"type":"conference","conference":{"name":"IJCAR: International Joint Conference on Automated Reasoning","location":"Paris, France","end_date":"2020-07-04","start_date":"2020-07-01"},"publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030510732"]},"oa_version":"Published Version","author":[{"full_name":"Baranowski, Marek","last_name":"Baranowski","first_name":"Marek"},{"first_name":"Shaobo","last_name":"He","full_name":"He, Shaobo"},{"last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nguyen","first_name":"Thanh Son","full_name":"Nguyen, Thanh Son"},{"first_name":"Zvonimir","last_name":"Rakamarić","full_name":"Rakamarić, Zvonimir"}],"_id":"8194","article_processing_charge":"No","intvolume":"     12166"},{"_id":"8195","article_processing_charge":"No","intvolume":"     12224","author":[{"first_name":"Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"file":[{"access_level":"open_access","date_created":"2020-08-06T08:14:54Z","success":1,"file_name":"2020_LNCS_Kragl.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"8201","date_updated":"2020-08-06T08:14:54Z","file_size":804237}],"type":"conference","volume":12224,"date_created":"2020-08-03T11:45:35Z","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_identifier":{"isbn":["9783030532871"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783030532888"]},"abstract":[{"lang":"eng","text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier."}],"page":"275-298","scopus_import":"1","external_id":{"isi":["000695276000014"]},"year":"2020","title":"Refinement for structured concurrent programs","doi":"10.1007/978-3-030-53288-8_14","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LNCS"],"citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in <i>Computer Aided Verification</i>, 2020, vol. 12224, pp. 275–298.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: <i>Computer Aided Verification</i>. Vol 12224. Springer Nature; 2020:275-298. doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” <i>Computer Aided Verification</i>, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">10.1007/978-3-030-53288-8_14</a>.","ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2020). Refinement for structured concurrent programs. In <i>Computer Aided Verification</i> (Vol. 12224, pp. 275–298). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In <i>Computer Aided Verification</i>, 12224:275–98. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-53288-8_14\">https://doi.org/10.1007/978-3-030-53288-8_14</a>."},"language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:18:00Z","file_date_updated":"2020-08-06T08:14:54Z","quality_controlled":"1","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2020-07-14T00:00:00Z","status":"public","has_accepted_license":"1","month":"07","oa":1,"ddc":["000"],"publication":"Computer Aided Verification","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8332"}]},"day":"14","publication_status":"published"},{"has_accepted_license":"1","status":"public","date_published":"2020-07-29T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaSe"}],"acknowledgement":"N.L., T.G. and E.B. acknowledge support from the European Research Council (ERC) under\r\nthe European Union Horizon 2020 Research and Innovation Programme (Grant Agreement\r\nNo. 639172). T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G.\r\nacknowledges funding from the Institute of Science and Technology (IST) Austria, and from\r\nthe European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411. N.L. acknowledges support from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework 546 Programme (FP7/20072013), under REA Grant Agreement No. 631696, and by the Israeli Center\r\nof Research Excellence (I-CORE) Circle of Light funded by the Israel Science Foundation (Grant\r\nNo. 1802/12). M.R. gratefully acknowledges the support of the European Research Council\r\n(ERC) under the European Union Horizon 2020 Research and Innovation Programme (Grant\r\nAgreement No. 678862). M.R. acknowledges the support of the Villum Foundation. M.R. and\r\nE.B. acknowledge support from CRC 183 of the Deutsche Forschungsgemeinschaft","publisher":"SciPost Foundation","publication_status":"published","day":"29","publication":"SciPost Physics","isi":1,"ddc":["530"],"oa":1,"month":"07","article_number":"015","citation":{"ieee":"T. Gulden, E. Berg, M. S. Rudner, and N. Lindner, “Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps,” <i>SciPost Physics</i>, vol. 9. SciPost Foundation, 2020.","chicago":"Gulden, Tobias, Erez Berg, Mark Spencer Rudner, and Netanel Lindner. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>. SciPost Foundation, 2020. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>.","apa":"Gulden, T., Berg, E., Rudner, M. S., &#38; Lindner, N. (2020). Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">https://doi.org/10.21468/scipostphys.9.1.015</a>","short":"T. Gulden, E. Berg, M.S. Rudner, N. Lindner, SciPost Physics 9 (2020).","ama":"Gulden T, Berg E, Rudner MS, Lindner N. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. <i>SciPost Physics</i>. 2020;9. doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>","mla":"Gulden, Tobias, et al. “Exponentially Long Lifetime of Universal Quasi-Steady States in Topological Floquet Pumps.” <i>SciPost Physics</i>, vol. 9, 015, SciPost Foundation, 2020, doi:<a href=\"https://doi.org/10.21468/scipostphys.9.1.015\">10.21468/scipostphys.9.1.015</a>.","ista":"Gulden T, Berg E, Rudner MS, Lindner N. 2020. Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps. SciPost Physics. 9, 015."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.21468/scipostphys.9.1.015","title":"Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps","quality_controlled":"1","file_date_updated":"2020-08-06T08:56:06Z","date_updated":"2023-08-22T08:28:24Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2542-4653"]},"oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"volume":9,"date_created":"2020-08-04T13:04:15Z","type":"journal_article","year":"2020","external_id":{"isi":["000557362300008"]},"scopus_import":"1","abstract":[{"text":"We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.","lang":"eng"}],"intvolume":"         9","_id":"8199","article_processing_charge":"No","file":[{"date_created":"2020-08-06T08:56:06Z","file_name":"2020_SciPostPhys_Gulden.pdf","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2020-08-06T08:56:06Z","file_size":531137,"content_type":"application/pdf","file_id":"8202","creator":"dernst"}],"article_type":"original","ec_funded":1,"author":[{"first_name":"Tobias","last_name":"Gulden","id":"1083E038-9F73-11E9-A4B5-532AE6697425","orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"last_name":"Rudner","first_name":"Mark Spencer","full_name":"Rudner, Mark Spencer"},{"full_name":"Lindner, Netanel","first_name":"Netanel","last_name":"Lindner"}]},{"_id":"8203","article_processing_charge":"Yes (via OA deal)","intvolume":"        20","article_type":"original","author":[{"last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","first_name":"Lada"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger"},{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"first_name":"Ting","last_name":"Wang","orcid":"0000-0002-4619-9575","full_name":"Wang, Ting"},{"full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun","last_name":"Zhang"},{"full_name":"Held, Karsten","first_name":"Karsten","last_name":"Held"}],"ec_funded":1,"file":[{"creator":"dernst","file_id":"8204","content_type":"application/pdf","file_size":3308906,"date_updated":"2020-08-06T09:35:37Z","access_level":"open_access","relation":"main_file","file_name":"2020_NanoLetters_Katsaros.pdf","success":1,"date_created":"2020-08-06T09:35:37Z"}],"project":[{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"date_created":"2020-08-06T09:25:04Z","volume":20,"type":"journal_article","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"oa_version":"Published Version","scopus_import":"1","page":"5201-5206","abstract":[{"lang":"eng","text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits."}],"year":"2020","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1021/acs.nanolett.0c01466","title":"Zero field splitting of heavy-hole states in quantum dots","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"citation":{"ieee":"G. Katsaros <i>et al.</i>, “Zero field splitting of heavy-hole states in quantum dots,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">https://doi.org/10.1021/acs.nanolett.0c01466</a>.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. <i>Nano Letters</i>. 2020;20(7):5201-5206. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01466\">10.1021/acs.nanolett.0c01466</a>","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206."},"language":[{"iso":"eng"}],"date_updated":"2024-02-21T12:44:01Z","file_date_updated":"2020-08-06T09:35:37Z","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","department":[{"_id":"GeKa"}],"publisher":"American Chemical Society","has_accepted_license":"1","date_published":"2020-06-01T00:00:00Z","status":"public","publication":"Nano Letters","isi":1,"ddc":["530"],"oa":1,"month":"06","publication_status":"published","day":"01","related_material":{"record":[{"status":"public","relation":"research_data","id":"7689"}]},"issue":"7","pmid":1},{"file":[{"date_created":"2020-08-10T06:50:28Z","file_name":"2020_PNAS_Corominas.pdf","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2020-08-10T06:50:28Z","file_size":1111604,"creator":"dernst","file_id":"8223","content_type":"application/pdf"}],"article_type":"original","ec_funded":1,"author":[{"last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","last_name":"Kishi"},{"last_name":"Ellenbroek","first_name":"Saskia I.J.","full_name":"Ellenbroek, Saskia I.J."},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"}],"intvolume":"       117","article_processing_charge":"No","_id":"8220","year":"2020","external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"scopus_import":"1","page":"16969-16975","oa_version":"Published Version","publication_identifier":{"eissn":["10916490"]},"volume":117,"date_created":"2020-08-09T22:00:52Z","type":"journal_article","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2020-08-10T06:50:28Z","quality_controlled":"1","date_updated":"2023-08-22T08:29:30Z","language":[{"iso":"eng"}],"citation":{"ieee":"B. Corominas-Murtra <i>et al.</i>, “Stem cell lineage survival as a noisy competition for niche access,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>.","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., &#38; Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921205117\">https://doi.org/10.1073/pnas.1921205117</a>","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>.","ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(29):16969-16975. doi:<a href=\"https://doi.org/10.1073/pnas.1921205117\">10.1073/pnas.1921205117</a>","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975."},"doi":"10.1073/pnas.1921205117","title":"Stem cell lineage survival as a noisy competition for niche access","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/order-from-noise/"}]},"pmid":1,"issue":"29","publication_status":"published","day":"21","oa":1,"month":"07","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"ddc":["570"],"date_published":"2020-07-21T00:00:00Z","status":"public","has_accepted_license":"1","acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]