[{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"department":[{"_id":"BeVi"}],"author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Tomas","full_name":"Larsson, Tomas","last_name":"Larsson"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"last_name":"Mehlig","full_name":"Mehlig, Bernhard","first_name":"Bernhard"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"isi":1,"year":"2018","oa_version":"Published Version","doi":"10.1002/evl3.74","day":"20","publisher":"Wiley","language":[{"iso":"eng"}],"pmid":1,"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","ieee":"A. M. Westram <i>et al.</i>, “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” <i>Evolution Letters</i>, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. 2018;2(4):297-309. doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>."},"file":[{"date_created":"2021-08-16T07:48:03Z","creator":"asandaue","file_id":"9918","access_level":"open_access","success":1,"file_name":"2018_EvolutionLetters_Westram.pdf","file_size":764299,"content_type":"application/pdf","date_updated":"2021-08-16T07:48:03Z","checksum":"8524e72507d521416be3f8ccfcd5e3f5","relation":"main_file"}],"article_type":"letter_note","ddc":["570"],"month":"08","title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","date_updated":"2023-09-19T15:08:25Z","date_published":"2018-08-20T00:00:00Z","article_processing_charge":"Yes","page":"297-309","file_date_updated":"2021-08-16T07:48:03Z","publication":"Evolution Letters","date_created":"2021-08-16T07:45:38Z","external_id":{"pmid":["30283683"],"isi":["000446774400004"]},"_id":"9917","volume":2,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9930"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","oa":1,"intvolume":"         2"},{"abstract":[{"text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.","lang":"eng"}],"related_material":{"record":[{"id":"9915","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.51sd2p5","open_access":"1"}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"citation":{"apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","ieee":"J. Hollander <i>et al.</i>, “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>.","mla":"Hollander, Johan, et al. <i>Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?</i> Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>."},"type":"research_data_reference","date_updated":"2023-09-19T15:08:53Z","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","department":[{"_id":"BeVi"}],"month":"10","author":[{"last_name":"Hollander","full_name":"Hollander, Johan","first_name":"Johan"},{"last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio","first_name":"Mauricio"},{"first_name":"Giuseppe","full_name":"Bianco, Giuseppe","last_name":"Bianco"},{"full_name":"Yang, Xi","last_name":"Yang","first_name":"Xi"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Ludovic","last_name":"Duvaux","full_name":"Duvaux, Ludovic"},{"first_name":"David G.","last_name":"Reid","full_name":"Reid, David G."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"date_published":"2018-10-17T00:00:00Z","article_processing_charge":"No","year":"2018","doi":"10.5061/dryad.51sd2p5","oa_version":"Published Version","publisher":"Dryad","_id":"9929","date_created":"2021-08-17T08:51:06Z","day":"17"},{"doi":"10.5061/dryad.bp25b65","oa_version":"Published Version","publisher":"Dryad","_id":"9930","day":"23","date_created":"2021-08-17T08:58:47Z","department":[{"_id":"BeVi"}],"title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","date_updated":"2023-09-19T15:08:24Z","month":"07","article_processing_charge":"No","year":"2018","date_published":"2018-07-23T00:00:00Z","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Larsson","full_name":"Larsson, Tomas","first_name":"Tomas"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"full_name":"Blomberg, Anders","last_name":"Blomberg","first_name":"Anders"},{"first_name":"Bernhard","last_name":"Mehlig","full_name":"Mehlig, Bernhard"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"type":"research_data_reference","citation":{"ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, <a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","mla":"Westram, Anja M., et al. <i>Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>","ieee":"A. M. Westram <i>et al.</i>, “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>"},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9917"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.bp25b65"}],"abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"status":"public","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"title":"Absorption and directed Jónsson terms","date_updated":"2023-09-05T15:37:18Z","month":"03","article_processing_charge":"No","date_published":"2018-03-21T00:00:00Z","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","page":"203-220","_id":"10864","external_id":{"arxiv":["1502.01072"]},"date_created":"2022-03-18T10:30:32Z","main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"volume":16,"place":"Cham","intvolume":"        16","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","scopus_import":"1","publication_identifier":{"isbn":["9783319747712"],"issn":["2211-2758"],"eisbn":["9783319747729"],"eissn":["2211-2766"]},"department":[{"_id":"VlKo"}],"year":"2018","author":[{"first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","last_name":"Kazda"},{"last_name":"Kozik","full_name":"Kozik, Marcin","first_name":"Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"editor":[{"first_name":"J","full_name":"Czelakowski, J","last_name":"Czelakowski"}],"doi":"10.1007/978-3-319-74772-9_7","oa_version":"Preprint","arxiv":1,"publisher":"Springer Nature","series_title":"OCTR","day":"21","publication_status":"published","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_chapter","citation":{"mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","apa":"Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>"}},{"main_file_link":[{"url":"https://doi.org/10.1093/bfgp/ely007","open_access":"1"}],"volume":17,"intvolume":"        17","oa":1,"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"5","scopus_import":"1","month":"09","date_updated":"2023-09-19T15:11:22Z","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"article_processing_charge":"No","date_published":"2018-09-01T00:00:00Z","page":"329-338","publication":"Briefings in Functional Genomics","external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"date_created":"2022-03-18T12:40:35Z","_id":"10880","pmid":1,"status":"public","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"publication_status":"published","quality_controlled":"1","type":"journal_article","citation":{"mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338."},"article_type":"original","department":[{"_id":"CaHe"}],"publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"year":"2018","isi":1,"author":[{"full_name":"Yuuta, Moriyama","orcid":"0000-0002-2853-8051","last_name":"Yuuta","first_name":"Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko","first_name":"Kazuko"}],"oa_version":"Published Version","doi":"10.1093/bfgp/ely007","day":"01","publisher":"Oxford University Press"},{"type":"journal_article","citation":{"apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>."},"article_type":"original","language":[{"iso":"eng"}],"status":"public","pmid":1,"publication_status":"published","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"quality_controlled":"1","oa_version":"None","doi":"10.1093/jxb/ery097","day":"13","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"author":[{"full_name":"Moturu, Taraka Ramji","last_name":"Moturu","first_name":"Taraka Ramji"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar","last_name":"Singh"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"isi":1,"year":"2018","scopus_import":"1","volume":69,"issue":"9","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        69","page":"2367-2378","publication":"Journal of Experimental Botany","date_created":"2022-03-18T12:43:22Z","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"_id":"10881","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"month":"04","title":"Molecular evolution and diversification of the SMXL gene family","date_updated":"2025-05-07T11:12:33Z","ec_funded":1,"date_published":"2018-04-13T00:00:00Z","keyword":["Plant Science","Physiology"],"article_processing_charge":"No"},{"date_published":"2018-12-17T00:00:00Z","article_processing_charge":"No","month":"12","date_updated":"2023-09-19T15:11:49Z","title":"Learning intelligent dialogs for bounding box annotation","date_created":"2022-03-18T12:45:09Z","external_id":{"isi":["000457843609036"],"arxiv":["1712.08087"]},"_id":"10882","page":"9175-9184","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1712.08087"}],"scopus_import":"1","isi":1,"author":[{"first_name":"Jasper","full_name":"Uijlings, Jasper","last_name":"Uijlings"},{"first_name":"Ksenia","last_name":"Konyushkova","full_name":"Konyushkova, Ksenia"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"last_name":"Ferrari","full_name":"Ferrari, Vittorio","first_name":"Vittorio"}],"year":"2018","conference":{"end_date":"2018-06-23","start_date":"2018-06-18","location":"Salt Lake City, UT, United States","name":"CVF: Conference on Computer Vision and Pattern Recognition"},"department":[{"_id":"ChLa"}],"publication_identifier":{"eissn":["2575-7075"],"isbn":["9781538664209"]},"day":"17","publisher":"IEEE","arxiv":1,"oa_version":"Preprint","doi":"10.1109/cvpr.2018.00956","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.","lang":"eng"}],"publication_status":"published","type":"conference","citation":{"ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184."}},{"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvořák, Wolfgang","last_name":"Dvořák","first_name":"Wolfgang"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"year":"2018","conference":{"end_date":"2018-11-21","start_date":"2018-11-17","location":"Awassa, Ethiopia","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"},"department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["2398-7340"]},"day":"23","publisher":"EasyChair","arxiv":1,"oa_version":"Published Version","doi":"10.29007/5z5k","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"publication_status":"published","ddc":["000"],"type":"conference","citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53, doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253. doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, 57:233–53. EasyChair, 2018. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., &#38; Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253."},"file":[{"file_size":720893,"content_type":"application/pdf","date_updated":"2022-05-17T07:51:08Z","checksum":"1229aa8640bd6db610c85decf2265480","relation":"main_file","access_level":"open_access","success":1,"file_name":"2018_EPiCs_Chatterjee.pdf","file_id":"11392","creator":"dernst","date_created":"2022-05-17T07:51:08Z"}],"ec_funded":1,"date_published":"2018-10-23T00:00:00Z","article_processing_charge":"No","month":"10","title":"Quasipolynomial set-based symbolic algorithms for parity games","date_updated":"2022-07-29T09:24:31Z","date_created":"2022-03-18T12:46:32Z","external_id":{"arxiv":["1909.04983"]},"_id":"10883","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"page":"233-253","file_date_updated":"2022-05-17T07:51:08Z","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":"        57","oa":1,"alternative_title":["EPiC Series in Computing"],"volume":57,"scopus_import":"1"},{"date_published":"2018-10-27T00:00:00Z","ec_funded":1,"title":"Mean-field limits of particles in interaction with quantised radiation fields","date_updated":"2021-01-12T06:48:16Z","month":"10","_id":"11","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"arxiv":["1806.10843"]},"date_created":"2018-12-11T11:44:08Z","page":"185 - 214","intvolume":"       270","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"volume":270,"scopus_import":1,"conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","location":"Munich, Germany","start_date":"2017-03-30","end_date":"2017-04-01"},"year":"2018","author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"department":[{"_id":"RoSe"}],"publisher":"Springer","day":"27","doi":"10.1007/978-3-030-01602-9_9","oa_version":"Preprint","arxiv":1,"quality_controlled":"1","publist_id":"8045","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"citation":{"apa":"Leopold, N. K., &#38; Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>.","mla":"Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp. 185–214, doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"type":"conference"},{"pubrep_id":"1037","file_date_updated":"2020-07-14T12:44:38Z","publication":"ACM Transaction on Graphics","date_created":"2018-12-11T11:44:09Z","external_id":{"isi":["000448185000096"]},"_id":"12","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"name":"Distributed 3D Object Design","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"}],"month":"08","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","date_updated":"2023-09-11T12:48:09Z","ec_funded":1,"date_published":"2018-08-04T00:00:00Z","article_processing_charge":"No","scopus_import":"1","volume":37,"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"4","oa":1,"intvolume":"        37","article_number":"135","oa_version":"Submitted Version","doi":"10.1145/3197517.3201341","day":"04","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"first_name":"Kazutaka","full_name":"Nakashima, Kazutaka","last_name":"Nakashima"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","last_name":"Iarussi","full_name":"Iarussi, Emmanuel"},{"first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2018","citation":{"short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., &#38; Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4. ACM, 2018.","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>.","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4, 135, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135."},"type":"journal_article","file":[{"file_size":104225664,"date_updated":"2020-07-14T12:44:38Z","content_type":"application/pdf","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","file_id":"5360","date_created":"2018-12-12T10:18:38Z","creator":"system"},{"file_id":"5361","creator":"system","date_created":"2018-12-12T10:18:39Z","checksum":"3861e693ba47c51f3ec7b7867d573a61","relation":"main_file","file_size":377743553,"date_updated":"2020-07-14T12:44:38Z","content_type":"application/zip","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","access_level":"open_access"},{"file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","access_level":"open_access","checksum":"490040c685ed869536e2a18f5a906b94","relation":"main_file","content_type":"video/vnd.objectvideo","date_updated":"2020-07-14T12:44:38Z","file_size":162634396,"date_created":"2018-12-12T10:18:41Z","creator":"system","file_id":"5362"},{"file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","access_level":"open_access","checksum":"be7fc8b229adda727419b6504b3b9352","relation":"main_file","date_updated":"2020-07-14T12:44:38Z","content_type":"image/jpeg","file_size":527972,"creator":"system","date_created":"2018-12-12T10:18:42Z","file_id":"5363"}],"ddc":["004","516","670"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.","lang":"eng"}],"publication_status":"published","publist_id":"8044","quality_controlled":"1"},{"ddc":["570"],"article_type":"original","file":[{"file_id":"5715","creator":"dernst","date_created":"2018-12-17T15:41:57Z","checksum":"9fe2a63bd95a5067d896c087d07998f3","relation":"main_file","file_size":4651930,"date_updated":"2020-07-14T12:45:28Z","content_type":"application/pdf","file_name":"2018_NatureComm_Espinoza.pdf","access_level":"open_access"}],"type":"journal_article","citation":{"chicago":"Espinoza Martinez, Claudia , José Guzmán, Xiaomin Zhang, and Peter M Jonas. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>.","ama":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>","ista":"Espinoza Martinez C, Guzmán J, Zhang X, Jonas PM. 2018. Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. Nature Communications. 9(1), 4605.","mla":"Espinoza Martinez, Claudia, et al. “Parvalbumin+ Interneurons Obey Unique Connectivity Rules and Establish a Powerful Lateral-Inhibition Microcircuit in Dentate Gyrus.” <i>Nature Communications</i>, vol. 9, no. 1, 4605, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-06899-3\">10.1038/s41467-018-06899-3</a>.","apa":"Espinoza Martinez, C., Guzmán, J., Zhang, X., &#38; Jonas, P. M. (2018). Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-018-06899-3\">https://doi.org/10.1038/s41467-018-06899-3</a>","short":"C. Espinoza Martinez, J. Guzmán, X. Zhang, P.M. Jonas, Nature Communications 9 (2018).","ieee":"C. Espinoza Martinez, J. Guzmán, X. Zhang, and P. M. Jonas, “Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018."},"quality_controlled":"1","publist_id":"8034","abstract":[{"text":"Parvalbumin-positive (PV+) GABAergic interneurons in hippocampal microcircuits are thought to play a key role in several higher network functions, such as feedforward and feedback inhibition, network oscillations, and pattern separation. Fast lateral inhibition mediated by GABAergic interneurons may implement a winner-takes-all mechanism in the hippocampal input layer. However, it is not clear whether the functional connectivity rules of granule cells (GCs) and interneurons in the dentate gyrus are consistent with such a mechanism. Using simultaneous patch-clamp recordings from up to seven GCs and up to four PV+ interneurons in the dentate gyrus, we find that connectivity is structured in space, synapse-specific, and enriched in specific disynaptic motifs. In contrast to the neocortex, lateral inhibition in the dentate gyrus (in which a GC inhibits neighboring GCs via a PV+ interneuron) is ~ 10-times more abundant than recurrent inhibition (in which a GC inhibits itself). Thus, unique connectivity rules may enable the dentate gyrus to perform specific higher-order computations","lang":"eng"}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","day":"02","doi":"10.1038/s41467-018-06899-3","oa_version":"Published Version","year":"2018","author":[{"last_name":"Espinoza Martinez","orcid":"0000-0003-4710-2082","full_name":"Espinoza Martinez, Claudia ","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José"},{"last_name":"Zhang","full_name":"Zhang, Xiaomin","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"isi":1,"department":[{"_id":"PeJo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","article_number":"4605","intvolume":"         9","oa":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J..","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","related_material":{"record":[{"id":"6363","status":"public","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/lateral-inhibition-keeps-similar-memories-apart/","relation":"press_release"}]},"volume":9,"_id":"21","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize"}],"external_id":{"isi":["000449069700009"]},"date_created":"2018-12-11T11:44:12Z","publication":"Nature Communications","file_date_updated":"2020-07-14T12:45:28Z","article_processing_charge":"No","date_published":"2018-11-02T00:00:00Z","ec_funded":1,"title":"Parvalbumin+ interneurons obey unique connectivity rules and establish a powerful lateral-inhibition microcircuit in dentate gyrus","date_updated":"2024-03-25T23:30:16Z","month":"11"},{"day":"20","doi":"10.1364/OPTICA.5.001210","oa_version":"Published Version","year":"2018","author":[{"first_name":"Gabriel","full_name":"Botello, Gabriel","last_name":"Botello"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Abdalmalak","full_name":"Abdalmalak, Kerlos","first_name":"Kerlos"},{"last_name":"Brown","full_name":"Brown, Elliott","first_name":"Elliott"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Sascha","full_name":"Preu, Sascha","last_name":"Preu"},{"first_name":"Daniel","full_name":"Segovia Vargas, Daniel","last_name":"Segovia Vargas"},{"full_name":"Strekalov, Dmitry","last_name":"Strekalov","first_name":"Dmitry"},{"last_name":"Munoz","full_name":"Munoz, Luis","first_name":"Luis"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"isi":1,"department":[{"_id":"JoFi"}],"publication_identifier":{"issn":["23342536"]},"article_type":"original","citation":{"apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. <i>Optica</i>. <a href=\"https://doi.org/10.1364/OPTICA.5.001210\">https://doi.org/10.1364/OPTICA.5.001210</a>","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","ieee":"G. Botello <i>et al.</i>, “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” <i>Optica</i>, vol. 5, no. 10. pp. 1210–1219, 2018.","chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>, 2018. <a href=\"https://doi.org/10.1364/OPTICA.5.001210\">https://doi.org/10.1364/OPTICA.5.001210</a>.","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. <i>Optica</i>. 2018;5(10):1210-1219. doi:<a href=\"https://doi.org/10.1364/OPTICA.5.001210\">10.1364/OPTICA.5.001210</a>","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” <i>Optica</i>, vol. 5, no. 10, 2018, pp. 1210–19, doi:<a href=\"https://doi.org/10.1364/OPTICA.5.001210\">10.1364/OPTICA.5.001210</a>."},"type":"journal_article","quality_controlled":"1","publist_id":"8033","publication_status":"published","abstract":[{"text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.","lang":"eng"}],"status":"public","language":[{"iso":"eng"}],"_id":"22","external_id":{"isi":["000447853100007"]},"date_created":"2018-12-11T11:44:12Z","publication":"Optica","page":"1210 - 1219","article_processing_charge":"No","date_published":"2018-10-20T00:00:00Z","date_updated":"2023-10-17T12:12:40Z","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","month":"10","scopus_import":"1","oa":1,"intvolume":"         5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","main_file_link":[{"open_access":"1","url":"www.doi.org/10.1364/OPTICA.5.001210 "}],"volume":5},{"issue":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"        18","volume":18,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"id":"69","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"7996"}]},"scopus_import":"1","ec_funded":1,"date_published":"2018-10-25T00:00:00Z","article_processing_charge":"No","month":"10","date_updated":"2023-09-18T09:30:37Z","title":"Single-shot readout of hole spins in Ge","date_created":"2018-12-11T11:44:13Z","external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"project":[{"call_identifier":"FP7","grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires"}],"_id":"23","page":"7141 - 7145","file_date_updated":"2020-07-14T12:45:37Z","pubrep_id":"1065","publication":"Nano Letters","quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","pmid":1,"status":"public","publication_status":"published","abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}],"publist_id":"8032","ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"citation":{"ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” <i>Nano Letters</i>, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., &#38; Katsaros, G. (2018). Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. 2018;18(11):7141-7145. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>"},"type":"journal_article","file":[{"file_id":"5194","date_created":"2018-12-12T10:16:08Z","creator":"system","date_updated":"2020-07-14T12:45:37Z","content_type":"application/pdf","file_size":1361441,"relation":"main_file","checksum":"3e6034a94c6b5335e939145d88bdb371","access_level":"open_access","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf"}],"author":[{"full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636","last_name":"Vukušić","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","last_name":"Watzinger"},{"first_name":"Joshua M","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","full_name":"Milem, Joshua M","last_name":"Milem"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["15306984"]},"department":[{"_id":"GeKa"}],"day":"25","publisher":"American Chemical Society","oa_version":"Published Version","doi":"10.1021/acs.nanolett.8b03217"},{"month":"07","date_updated":"2025-06-02T08:53:48Z","title":"Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives","ec_funded":1,"article_processing_charge":"No","date_published":"2018-07-01T00:00:00Z","page":"4692 - 4699","external_id":{"arxiv":["1804.10601"],"isi":["000764175404117"]},"date_created":"2018-12-11T11:44:13Z","_id":"24","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"main_file_link":[{"url":"https://arxiv.org/abs/1804.10601","open_access":"1"}],"volume":2018,"intvolume":"      2018","oa":1,"acknowledgement":"This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2018","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2018-07-13","location":"Stockholm, Sweden","end_date":"2018-07-19"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","last_name":"Elgyütt","full_name":"Elgyütt, Adrian"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Owen","last_name":"Rouillé","full_name":"Rouillé, Owen"}],"isi":1,"oa_version":"Preprint","arxiv":1,"doi":"10.24963/ijcai.2018/652","day":"01","publisher":"IJCAI","status":"public","language":[{"iso":"eng"}],"publist_id":"8031","publication_status":"published","abstract":[{"text":"Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it.","lang":"eng"}],"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives</i>. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>.","ista":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.","ama":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>","chicago":"Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>.","ieee":"K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699.","apa":"Chatterjee, K., Elgyütt, A., Novotný, P., &#38; Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>","short":"K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699."},"type":"conference"},{"article_processing_charge":"No","date_published":"2018-07-01T00:00:00Z","ec_funded":1,"title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","date_updated":"2025-06-02T08:53:40Z","month":"07","_id":"25","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"external_id":{"isi":["000764175404127"]},"date_created":"2018-12-11T11:44:13Z","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","page":"4764 - 4770","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2018/662","open_access":"1"}],"volume":"2018-July","scopus_import":"1","conference":{"location":"Stockholm, Sweden","start_date":"2018-07-13","end_date":"2018-07-19","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"year":"2018","isi":1,"author":[{"full_name":"Horák, Karel","last_name":"Horák","first_name":"Karel"},{"first_name":"Branislav","last_name":"Bošanský","full_name":"Bošanský, Branislav"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"department":[{"_id":"KrCh"}],"publisher":"IJCAI","day":"01","doi":"10.24963/ijcai.2018/662","oa_version":"Published Version","quality_controlled":"1","publist_id":"8030","publication_status":"published","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples."}],"status":"public","language":[{"iso":"eng"}],"type":"conference","citation":{"ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>. Vol 2018-July. IJCAI; 2018:4764-4770. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, 2018–July:4764–70. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>.","ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>.","apa":"Horák, K., Bošanský, B., &#38; Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i> (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770."}},{"author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719","last_name":"Steinrück"}],"year":"2018","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"CaGu"}],"day":"30","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th1059","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.","lang":"eng"}],"publication_status":"published","publist_id":"8029","ddc":["576","579"],"citation":{"chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018."},"type":"dissertation","file":[{"file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","access_level":"closed","file_name":"Thesis_Steinrueck_final.docx","embargo_to":"open_access","file_id":"5941","date_created":"2019-02-08T10:51:22Z","creator":"dernst"},{"creator":"dernst","embargo":"2019-11-02","date_created":"2019-02-08T10:51:22Z","file_id":"5942","file_name":"Thesis_Steinrueck_final.pdf","access_level":"open_access","checksum":"3def8b7854c8b42d643597ce0215efac","relation":"main_file","content_type":"application/pdf","date_updated":"2021-02-11T11:17:14Z","file_size":7521973}],"date_published":"2018-10-30T00:00:00Z","article_processing_charge":"No","month":"10","date_updated":"2023-09-07T12:48:43Z","title":"The influence of sequence context on the evolution of bacterial gene expression","date_created":"2018-12-11T11:44:14Z","_id":"26","page":"109","file_date_updated":"2021-02-11T11:17:14Z","pubrep_id":"1059","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"704"}]}},{"title":"Efficient optimization for rank-based loss functions","date_updated":"2023-09-11T13:24:43Z","month":"06","date_published":"2018-06-28T00:00:00Z","article_processing_charge":"No","ec_funded":1,"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","page":"3693-3701","_id":"273","project":[{"call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"date_created":"2018-12-11T11:45:33Z","external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]},"main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"scopus_import":"1","department":[{"_id":"VlKo"}],"publication_identifier":{"isbn":["9781538664209"]},"isi":1,"author":[{"first_name":"Pritish","full_name":"Mohapatra, Pritish","last_name":"Mohapatra"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"},{"full_name":"Jawahar, C V","last_name":"Jawahar","first_name":"C V"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kumar, M Pawan","last_name":"Kumar","first_name":"M Pawan"}],"conference":{"location":"Salt Lake City, UT, USA","start_date":"2018-06-18","end_date":"2018-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"year":"2018","doi":"10.1109/cvpr.2018.00389","arxiv":1,"oa_version":"Preprint","publisher":"IEEE","day":"28","abstract":[{"lang":"eng","text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","citation":{"ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701."},"type":"conference"},{"publist_id":"7627","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"publication_status":"published","pmid":1,"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"date_created":"2018-12-17T12:50:07Z","creator":"dernst","file_id":"5704","file_name":"2018_JournalCellBiology_Brown.pdf","access_level":"open_access","checksum":"9c7eba51a35c62da8c13f98120b64df4","relation":"main_file","file_size":2252043,"date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf"}],"citation":{"short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>","ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>."},"type":"journal_article","ddc":["570"],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","author":[{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"full_name":"Johnson, Louise","last_name":"Johnson","first_name":"Louise"},{"last_name":"Leone","full_name":"Leone, Dario","first_name":"Dario"},{"first_name":"Peter","full_name":"Májek, Peter","last_name":"Májek"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"last_name":"Bukosza","full_name":"Bukosza, Nora","first_name":"Nora"},{"first_name":"Helga","full_name":"Schachner, Helga","last_name":"Schachner"},{"last_name":"Asfour","full_name":"Asfour, Gabriele","first_name":"Gabriele"},{"first_name":"Brigitte","last_name":"Langer","full_name":"Langer, Brigitte"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Parapatics","full_name":"Parapatics, Katja","first_name":"Katja"},{"full_name":"Hong, Young","last_name":"Hong","first_name":"Young"},{"last_name":"Bennett","full_name":"Bennett, Keiryn","first_name":"Keiryn"},{"first_name":"Renate","full_name":"Kain, Renate","last_name":"Kain"},{"last_name":"Detmar","full_name":"Detmar, Michael","first_name":"Michael"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Jackson, David","last_name":"Jackson","first_name":"David"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"}],"isi":1,"doi":"10.1083/jcb.201612051","oa_version":"Published Version","publisher":"Rockefeller University Press","day":"12","volume":217,"intvolume":"       217","oa":1,"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","scopus_import":"1","date_updated":"2023-09-13T08:51:29Z","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","month":"04","article_processing_charge":"No","date_published":"2018-04-12T00:00:00Z","ec_funded":1,"publication":"Journal of Cell Biology","file_date_updated":"2020-07-14T12:45:45Z","page":"2205 - 2221","_id":"275","project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"date_created":"2018-12-11T11:45:33Z"},{"month":"06","date_updated":"2023-09-13T09:00:15Z","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","article_processing_charge":"No","date_published":"2018-06-07T00:00:00Z","publication":"PLoS One","file_date_updated":"2020-07-14T12:45:45Z","external_id":{"isi":["000434384900031"]},"date_created":"2018-12-11T11:45:34Z","_id":"276","volume":13,"intvolume":"        13","oa":1,"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_number":"e0198330","scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"MiSi"}],"year":"2018","author":[{"first_name":"Corina","full_name":"Frick, Corina","last_name":"Frick"},{"first_name":"Philip","full_name":"Dettinger, Philip","last_name":"Dettinger"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"},{"last_name":"Jauch","full_name":"Jauch, Annaïse","first_name":"Annaïse"},{"first_name":"Christoph","last_name":"Berger","full_name":"Berger, Christoph"},{"full_name":"Recher, Mike","last_name":"Recher","first_name":"Mike"},{"last_name":"Schroeder","full_name":"Schroeder, Timm","first_name":"Timm"},{"last_name":"Mehling","full_name":"Mehling, Matthias","first_name":"Matthias"}],"isi":1,"oa_version":"Published Version","doi":"10.1371/journal.pone.0198330","day":"07","publisher":"Public Library of Science","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7626","publication_status":"published","abstract":[{"lang":"eng","text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo."}],"quality_controlled":"1","type":"journal_article","citation":{"ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>."},"file":[{"creator":"dernst","date_created":"2018-12-17T14:10:32Z","file_id":"5709","file_name":"2018_Plos_Frick.pdf","access_level":"open_access","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","relation":"main_file","file_size":7682167,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z"}],"article_type":"original","ddc":["570"]},{"page":"407 - 420","publication":"Plant Molecular Biology","file_date_updated":"2020-07-14T12:45:45Z","external_id":{"isi":["000438981700009"]},"date_created":"2018-12-11T11:45:34Z","_id":"277","month":"06","date_updated":"2023-09-08T13:21:05Z","title":"An armadillo-domain protein participates in a telomerase interaction network","article_processing_charge":"No","date_published":"2018-06-12T00:00:00Z","scopus_import":"1","volume":97,"oa":1,"intvolume":"        97","issue":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","doi":"10.1007/s11103-018-0747-4","day":"12","publisher":"Springer","department":[{"_id":"EvBe"}],"year":"2018","author":[{"first_name":"Ladislav","full_name":"Dokládal, Ladislav","last_name":"Dokládal"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Honys, David","last_name":"Honys","first_name":"David"},{"last_name":"Dupláková","full_name":"Dupláková, Nikoleta","first_name":"Nikoleta"},{"first_name":"Lan","full_name":"Lee, Lan","last_name":"Lee"},{"last_name":"Gelvin","full_name":"Gelvin, Stanton","first_name":"Stanton"},{"first_name":"Eva","last_name":"Sýkorová","full_name":"Sýkorová, Eva"}],"isi":1,"citation":{"ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018."},"type":"journal_article","file":[{"creator":"dernst","date_created":"2020-05-14T12:23:08Z","file_id":"7834","file_name":"2018_PlantMolecBio_Dokladal.pdf","access_level":"open_access","checksum":"451ae47616e6af2533099f596b2a47fb","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","file_size":1150679}],"article_type":"original","ddc":["580"],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"7625","publication_status":"published","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"quality_controlled":"1"}]