[{"language":[{"iso":"eng"}],"year":"2019","author":[{"id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","last_name":"Raices","first_name":"Julia","full_name":"Raices, Julia"},{"first_name":"Paulo","last_name":"Otto","full_name":"Otto, Paulo"},{"first_name":"Maria","last_name":"Vibranovski","full_name":"Vibranovski, Maria"}],"department":[{"_id":"BeVi"}],"status":"public","OA_embargo":"6 months","ddc":["576"],"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"oa":1,"publisher":"Cold Spring Harbor Laboratory Press","date_created":"2019-07-21T21:59:15Z","file_date_updated":"2020-07-14T12:47:35Z","abstract":[{"text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. ","lang":"eng"}],"issue":"7","publication_identifier":{"eissn":[" 1549-5469"],"issn":["1088-9051"]},"volume":29,"OA_place":"publisher","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","page":"1115-1122","title":"Haploid selection drives new gene male germline expression","type":"journal_article","oa_version":"Published Version","citation":{"ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. <i>Genome Research</i>. 2019;29(7):1115-1122. doi:<a href=\"https://doi.org/10.1101/gr.238824.118\">10.1101/gr.238824.118</a>","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” <i>Genome Research</i>, vol. 29, no. 7, Cold Spring Harbor Laboratory Press, 2019, pp. 1115–22, doi:<a href=\"https://doi.org/10.1101/gr.238824.118\">10.1101/gr.238824.118</a>.","chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2019. <a href=\"https://doi.org/10.1101/gr.238824.118\">https://doi.org/10.1101/gr.238824.118</a>.","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” <i>Genome Research</i>, vol. 29, no. 7. Cold Spring Harbor Laboratory Press, pp. 1115–1122, 2019.","apa":"Raices, J., Otto, P., &#38; Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.238824.118\">https://doi.org/10.1101/gr.238824.118</a>","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122."},"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:35Z","file_id":"6670","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","relation":"main_file","creator":"apreinsp","access_level":"open_access","date_created":"2019-07-24T08:05:56Z","file_name":"2019_GenomeResearch_Raices.pdf","file_size":2319022}],"isi":1,"external_id":{"isi":["000473730600007"]},"day":"01","publication":"Genome Research","doi":"10.1101/gr.238824.118","article_processing_charge":"No","OA_type":"hybrid","date_published":"2019-07-01T00:00:00Z","quality_controlled":"1","intvolume":"        29","month":"07","publication_status":"published","date_updated":"2025-05-20T06:25:39Z","_id":"6658"},{"scopus_import":"1","title":"Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins","type":"journal_article","page":"995-1000","oa_version":"Published Version","citation":{"ista":"Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000.","chicago":"Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” <i>Bulletin of the Chemical Society of Japan</i>. Bulletin of the Chemical Society of Japan, 2019. <a href=\"https://doi.org/10.1246/bcsj.20190034\">https://doi.org/10.1246/bcsj.20190034</a>.","ama":"Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. <i>Bulletin of the Chemical Society of Japan</i>. 2019;92(5):995-1000. doi:<a href=\"https://doi.org/10.1246/bcsj.20190034\">10.1246/bcsj.20190034</a>","mla":"Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” <i>Bulletin of the Chemical Society of Japan</i>, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:<a href=\"https://doi.org/10.1246/bcsj.20190034\">10.1246/bcsj.20190034</a>.","short":"N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000.","apa":"Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. <i>Bulletin of the Chemical Society of Japan</i>. Bulletin of the Chemical Society of Japan. <a href=\"https://doi.org/10.1246/bcsj.20190034\">https://doi.org/10.1246/bcsj.20190034</a>","ieee":"N. Zenmyo <i>et al.</i>, “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” <i>Bulletin of the Chemical Society of Japan</i>, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019."},"isi":1,"external_id":{"isi":["000468101800007"]},"day":"15","publication":"Bulletin of the Chemical Society of Japan","doi":"10.1246/bcsj.20190034","article_processing_charge":"No","OA_type":"free access","date_published":"2019-05-15T00:00:00Z","ec_funded":1,"intvolume":"        92","month":"05","quality_controlled":"1","_id":"6659","date_updated":"2025-09-10T10:37:21Z","publication_status":"published","author":[{"full_name":"Zenmyo, Naoki","first_name":"Naoki","last_name":"Zenmyo"},{"last_name":"Tokumaru","first_name":"Hiroki","full_name":"Tokumaru, Hiroki"},{"full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya","first_name":"Shohei"},{"full_name":"Fuchida, Hirokazu","first_name":"Hirokazu","last_name":"Fuchida"},{"id":"4427179E-F248-11E8-B48F-1D18A9856A87","last_name":"Tabata","first_name":"Shigekazu","full_name":"Tabata, Shigekazu"},{"full_name":"Hamachi, Itaru","last_name":"Hamachi","first_name":"Itaru"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Ojida, Akio","first_name":"Akio","last_name":"Ojida"}],"language":[{"iso":"eng"}],"year":"2019","department":[{"_id":"RySh"}],"status":"public","ddc":["570"],"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"has_accepted_license":"1","date_created":"2019-07-21T21:59:16Z","oa":1,"publisher":"Bulletin of the Chemical Society of Japan","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1246/bcsj.20190034"}],"abstract":[{"lang":"eng","text":"Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research."}],"issue":"5","acknowledgement":"his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation.","volume":92,"publication_identifier":{"issn":["0009-2673"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original"},{"article_processing_charge":"No","article_number":"111","doi":"10.1145/3306346.3322992","quality_controlled":"1","intvolume":"        38","month":"07","publication_status":"published","date_updated":"2025-03-31T15:58:17Z","_id":"6660","ec_funded":1,"date_published":"2019-07-04T00:00:00Z","oa_version":"Submitted Version","scopus_import":"1","type":"journal_article","title":"Geometry-aware scattering compensation for 3D printing","external_id":{"isi":["000475740600085"]},"publication":"ACM Transactions on Graphics","day":"04","citation":{"mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 111, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3322992\">10.1145/3306346.3322992</a>.","ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3322992\">10.1145/3306346.3322992</a>","chicago":"Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3322992\">https://doi.org/10.1145/3306346.3322992</a>.","ista":"Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111.","ieee":"D. Sumin <i>et al.</i>, “Geometry-aware scattering compensation for 3D printing,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","short":"D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).","apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3322992\">https://doi.org/10.1145/3306346.3322992</a>"},"file":[{"date_updated":"2020-07-14T12:47:36Z","content_type":"application/pdf","date_created":"2019-07-24T07:36:08Z","file_name":"2019_ACM_Sumin_AuthorVersion.pdf","access_level":"open_access","file_size":10109800,"checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","relation":"main_file","file_id":"6669","creator":"dernst"},{"file_size":11051245,"access_level":"open_access","date_created":"2019-10-11T06:51:07Z","file_name":"sumin19geometry-aware-suppl.zip","creator":"dernst","file_id":"6938","relation":"supplementary_material","checksum":"f80f365a04e35855fa467ea7ab26b16c","date_updated":"2020-07-14T12:47:36Z","content_type":"application/zip"}],"isi":1,"publisher":"ACM","oa":1,"date_created":"2019-07-22T07:22:28Z","file_date_updated":"2020-07-14T12:47:36Z","project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","volume":38,"publication_identifier":{"issn":["0730-0301"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers."}],"issue":"4","department":[{"_id":"BeBi"}],"year":"2019","language":[{"iso":"eng"}],"author":[{"full_name":"Sumin, Denis","first_name":"Denis","last_name":"Sumin"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"first_name":"Tobias","last_name":"Rittig","full_name":"Rittig, Tobias"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"full_name":"Nindel, Thomas","first_name":"Thomas","last_name":"Nindel"},{"first_name":"Alexander","last_name":"Wilkie","full_name":"Wilkie, Alexander"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"},{"last_name":"Křivánek","first_name":"Jaroslav","full_name":"Křivánek, Jaroslav"},{"full_name":"Myszkowski, Karol","first_name":"Karol","last_name":"Myszkowski"}],"ddc":["000"],"status":"public"},{"status":"public","ddc":["000"],"author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Lieutier","first_name":"André","full_name":"Lieutier, André"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken"}],"year":"2019","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"corr_author":"1","issue":"1-2","abstract":[{"text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","volume":3,"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file_date_updated":"2020-07-14T12:47:36Z","date_created":"2019-07-24T08:37:29Z","oa":1,"publisher":"Springer Nature","file":[{"file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","access_level":"open_access","date_created":"2019-07-31T08:09:56Z","file_size":2215157,"checksum":"a5b244db9f751221409cf09c97ee0935","relation":"main_file","file_id":"6741","creator":"dernst","date_updated":"2020-07-14T12:47:36Z","content_type":"application/pdf"}],"citation":{"ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. <i>Journal of Applied and Computational Topology</i>. 2019;3(1-2):29–58. doi:<a href=\"https://doi.org/10.1007/s41468-019-00029-8\">10.1007/s41468-019-00029-8</a>","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” <i>Journal of Applied and Computational Topology</i>, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:<a href=\"https://doi.org/10.1007/s41468-019-00029-8\">10.1007/s41468-019-00029-8</a>.","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s41468-019-00029-8\">https://doi.org/10.1007/s41468-019-00029-8</a>.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” <i>Journal of Applied and Computational Topology</i>, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","apa":"Boissonnat, J.-D., Lieutier, A., &#38; Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-019-00029-8\">https://doi.org/10.1007/s41468-019-00029-8</a>"},"publication":"Journal of Applied and Computational Topology","day":"01","title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","type":"journal_article","page":"29–58","scopus_import":"1","oa_version":"Published Version","date_published":"2019-06-01T00:00:00Z","ec_funded":1,"_id":"6671","publication_status":"published","date_updated":"2025-04-14T07:44:06Z","intvolume":"         3","month":"06","quality_controlled":"1","doi":"10.1007/s41468-019-00029-8","article_processing_charge":"Yes (via OA deal)"},{"conference":{"name":"STOC: Symposium on Theory of Computing","location":"Phoenix, AZ, United States","start_date":"2019-06-23","end_date":"2019-06-26"},"status":"public","language":[{"iso":"eng"}],"year":"2019","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"first_name":"Leqi","last_name":"Zhu","full_name":"Zhu, Leqi"}],"department":[{"_id":"DaAl"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"abstract":[{"lang":"eng","text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power."}],"arxiv":1,"publication_identifier":{"isbn":["9781450367059"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"14364"}]},"oa":1,"publisher":"ACM","date_created":"2019-07-24T09:13:05Z","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>, 986–96. ACM, 2019. <a href=\"https://doi.org/10.1145/3313276.3316407\">https://doi.org/10.1145/3313276.3316407</a>.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>. ACM; 2019:986-996. doi:<a href=\"https://doi.org/10.1145/3313276.3316407\">10.1145/3313276.3316407</a>","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>, ACM, 2019, pp. 986–96, doi:<a href=\"https://doi.org/10.1145/3313276.3316407\">10.1145/3313276.3316407</a>.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2019). Why extension-based proofs fail. In <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i> (pp. 986–996). Phoenix, AZ, United States: ACM. <a href=\"https://doi.org/10.1145/3313276.3316407\">https://doi.org/10.1145/3313276.3316407</a>","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM, 2019, pp. 986–996.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in <i>Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>, Phoenix, AZ, United States, 2019, pp. 986–996."},"isi":1,"external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"day":"01","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","scopus_import":"1","page":"986-996","title":"Why extension-based proofs fail","type":"conference","oa_version":"Preprint","date_published":"2019-06-01T00:00:00Z","quality_controlled":"1","month":"06","date_updated":"2025-05-14T11:26:07Z","publication_status":"published","_id":"6676","doi":"10.1145/3313276.3316407","article_processing_charge":"No"},{"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"volume":73,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"research_data","status":"public","id":"9802"}]},"abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"issue":"9","date_created":"2019-07-25T09:08:28Z","publisher":"Wiley","oa":1,"file_date_updated":"2020-07-14T12:47:37Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["576"],"status":"public","corr_author":"1","department":[{"_id":"NiBa"}],"author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani"}],"language":[{"iso":"eng"}],"year":"2019","intvolume":"        73","month":"09","quality_controlled":"1","_id":"6680","date_updated":"2024-10-09T20:58:56Z","publication_status":"published","date_published":"2019-09-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/evo.13812","external_id":{"isi":["000481300600001"]},"day":"01","publication":"Evolution","citation":{"ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. <i>Evolution</i>. 2019;73(9):1729-1745. doi:<a href=\"https://doi.org/10.1111/evo.13812\">10.1111/evo.13812</a>","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” <i>Evolution</i>, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:<a href=\"https://doi.org/10.1111/evo.13812\">10.1111/evo.13812</a>.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” <i>Evolution</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/evo.13812\">https://doi.org/10.1111/evo.13812</a>.","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” <i>Evolution</i>, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.13812\">https://doi.org/10.1111/evo.13812</a>","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745."},"isi":1,"file":[{"creator":"kschuh","file_id":"6881","checksum":"772ce7035965153959b946a1033de1ca","relation":"main_file","file_size":937573,"date_created":"2019-09-17T10:56:27Z","file_name":"2019_Evolution_Sachdeva.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:37Z"}],"oa_version":"Published Version","scopus_import":"1","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","type":"journal_article","page":"1729-1745"},{"status":"public","department":[{"_id":"BeVi"}],"author":[{"full_name":"Cossard, Guillaume","last_name":"Cossard","first_name":"Guillaume"},{"orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Pannell, John ","first_name":"John ","last_name":"Pannell"}],"year":"2019","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","volume":123,"publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"issue":"7","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"abstract":[{"lang":"eng","text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species."}],"date_created":"2019-07-28T21:59:15Z","oa":1,"publisher":"Oxford University Press","publication":"Annals of botany","day":"04","external_id":{"isi":["000493043500004"],"pmid":["30289430"]},"isi":1,"citation":{"apa":"Cossard, G., Toups, M. A., &#38; Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcy183\">https://doi.org/10.1093/aob/mcy183</a>","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” <i>Annals of botany</i>, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","chicago":"Cossard, Guillaume, Melissa A Toups, and John  Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” <i>Annals of Botany</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/aob/mcy183\">https://doi.org/10.1093/aob/mcy183</a>.","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. <i>Annals of botany</i>. 2019;123(7):1119-1131. doi:<a href=\"https://doi.org/10.1093/aob/mcy183\">10.1093/aob/mcy183</a>","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” <i>Annals of Botany</i>, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:<a href=\"https://doi.org/10.1093/aob/mcy183\">10.1093/aob/mcy183</a>.","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131."},"oa_version":"Published Version","type":"journal_article","pmid":1,"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","page":"1119-1131","scopus_import":"1","_id":"6710","date_updated":"2023-08-29T06:42:22Z","publication_status":"published","intvolume":"       123","month":"06","quality_controlled":"1","date_published":"2019-06-04T00:00:00Z","article_processing_charge":"No","doi":"10.1093/aob/mcy183"},{"scopus_import":"1","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","type":"journal_article","oa_version":"Published Version","citation":{"apa":"Igler, C., &#38; Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2019.01171\">https://doi.org/10.3389/fmicb.2019.01171</a>","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” <i>Frontiers in Microbiology</i>, vol. 10. Frontiers, 2019.","chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” <i>Frontiers in Microbiology</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fmicb.2019.01171\">https://doi.org/10.3389/fmicb.2019.01171</a>.","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” <i>Frontiers in Microbiology</i>, vol. 10, 1171, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fmicb.2019.01171\">10.3389/fmicb.2019.01171</a>.","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. <i>Frontiers in Microbiology</i>. 2019;10. doi:<a href=\"https://doi.org/10.3389/fmicb.2019.01171\">10.3389/fmicb.2019.01171</a>","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171."},"file":[{"file_size":246151,"date_created":"2019-07-29T07:51:54Z","file_name":"2019_Frontiers_Igler.pdf","access_level":"open_access","creator":"apreinsp","relation":"main_file","checksum":"317a06067e9a8e717bb55f23e0d77ba7","file_id":"6722","date_updated":"2020-07-14T12:47:38Z","content_type":"application/pdf"}],"isi":1,"external_id":{"isi":["000470131200001"]},"day":"03","publication":"Frontiers in Microbiology","article_number":"1171","doi":"10.3389/fmicb.2019.01171","article_processing_charge":"Yes (via OA deal)","date_published":"2019-06-03T00:00:00Z","quality_controlled":"1","intvolume":"        10","month":"06","date_updated":"2025-04-14T13:38:17Z","publication_status":"published","_id":"6717","language":[{"iso":"eng"}],"year":"2019","author":[{"full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"full_name":"Abedon, Stephen T.","last_name":"Abedon","first_name":"Stephen T."}],"department":[{"_id":"CaGu"}],"status":"public","ddc":["570"],"project":[{"name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","oa":1,"publisher":"Frontiers","date_created":"2019-07-28T21:59:18Z","file_date_updated":"2020-07-14T12:47:38Z","abstract":[{"lang":"eng","text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple."}],"volume":10,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2019-07-29T12:23:29Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"file_date_updated":"2020-07-14T12:47:38Z","abstract":[{"text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.","lang":"eng"}],"arxiv":1,"volume":132,"publication_identifier":{"isbn":["978-3-95977-109-2"],"issn":["1868-8969"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"language":[{"iso":"eng"}],"year":"2019","department":[{"_id":"VlKo"}],"conference":{"name":"ICALP: Automata, Languages and Programming","location":"Patras, Greece","start_date":"2019-07-08","end_date":"2019-07-12"},"alternative_title":["LIPIcs"],"status":"public","ddc":["000"],"doi":"10.4230/LIPICS.ICALP.2019.77","article_processing_charge":"No","date_published":"2019-07-01T00:00:00Z","ec_funded":1,"month":"07","intvolume":"       132","quality_controlled":"1","_id":"6725","date_updated":"2025-07-10T11:53:47Z","publication_status":"published","scopus_import":"1","title":"Testing the complexity of a valued CSP language","type":"conference","page":"77:1-77:12","oa_version":"Published Version","citation":{"ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.","chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In <i>46th International Colloquium on Automata, Languages and Programming</i>, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.77\">https://doi.org/10.4230/LIPICS.ICALP.2019.77</a>.","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: <i>46th International Colloquium on Automata, Languages and Programming</i>. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.77\">10.4230/LIPICS.ICALP.2019.77</a>","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” <i>46th International Colloquium on Automata, Languages and Programming</i>, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:<a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.77\">10.4230/LIPICS.ICALP.2019.77</a>.","short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In <i>46th International Colloquium on Automata, Languages and Programming</i> (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ICALP.2019.77\">https://doi.org/10.4230/LIPICS.ICALP.2019.77</a>","ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in <i>46th International Colloquium on Automata, Languages and Programming</i>, Patras, Greece, 2019, vol. 132, p. 77:1-77:12."},"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:38Z","creator":"dernst","file_id":"6738","relation":"main_file","checksum":"f5ebee8eec6ae09e30365578ee63a492","file_size":575475,"access_level":"open_access","date_created":"2019-07-31T07:01:45Z","file_name":"2019_LIPICS_Kolmogorov.pdf"}],"external_id":{"arxiv":["1803.02289"]},"day":"01","publication":"46th International Colloquium on Automata, Languages and Programming"},{"date_published":"2019-06-29T00:00:00Z","ec_funded":1,"_id":"6726","date_updated":"2025-09-10T10:38:28Z","publication_status":"published","month":"06","intvolume":"     11627","quality_controlled":"1","editor":[{"full_name":"Buchmann, J","first_name":"J","last_name":"Buchmann"},{"full_name":"Nitaj, A","last_name":"Nitaj","first_name":"A"},{"full_name":"Rachidi, T","last_name":"Rachidi","first_name":"T"}],"place":"Cham","doi":"10.1007/978-3-030-23696-0_9","article_processing_charge":"No","isi":1,"citation":{"ieee":"M. Walter, “Sampling the integers with low relative error,” in <i>Progress in Cryptology – AFRICACRYPT 2019</i>, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.","short":"M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.","apa":"Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, &#38; T. Rachidi (Eds.), <i>Progress in Cryptology – AFRICACRYPT 2019</i> (Vol. 11627, pp. 157–180). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-23696-0_9\">https://doi.org/10.1007/978-3-030-23696-0_9</a>","mla":"Walter, Michael. “Sampling the Integers with Low Relative Error.” <i>Progress in Cryptology – AFRICACRYPT 2019</i>, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:<a href=\"https://doi.org/10.1007/978-3-030-23696-0_9\">10.1007/978-3-030-23696-0_9</a>.","ama":"Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. <i>Progress in Cryptology – AFRICACRYPT 2019</i>. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:<a href=\"https://doi.org/10.1007/978-3-030-23696-0_9\">10.1007/978-3-030-23696-0_9</a>","chicago":"Walter, Michael. “Sampling the Integers with Low Relative Error.” In <i>Progress in Cryptology – AFRICACRYPT 2019</i>, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-23696-0_9\">https://doi.org/10.1007/978-3-030-23696-0_9</a>.","ista":"Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180."},"publication":"Progress in Cryptology – AFRICACRYPT 2019","day":"29","external_id":{"isi":["001299240700009"]},"title":"Sampling the integers with low relative error","type":"book_chapter","page":"157-180","scopus_import":"1","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2019/068","open_access":"1"}],"abstract":[{"lang":"eng","text":"Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1611-3349"],"eisbn":["978-3-0302-3696-0"],"isbn":["978-3-0302-3695-3"],"issn":["0302-9743"]},"volume":11627,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"date_created":"2019-07-29T12:25:31Z","oa":1,"publisher":"Springer Nature","status":"public","series_title":"LNCS","conference":{"start_date":"2019-07-09","end_date":"2019-07-11","location":"Rabat, Morocco","name":"AFRICACRYPT: International Conference on Cryptology in Africa"},"author":[{"first_name":"Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482"}],"language":[{"iso":"eng"}],"year":"2019","department":[{"_id":"KrPi"}]},{"status":"public","language":[{"iso":"eng"}],"year":"2019","author":[{"last_name":"Hashemi","first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali"},{"last_name":"Condo","first_name":"Carlo","full_name":"Condo, Carlo"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"},{"full_name":"Gross, Warren J","first_name":"Warren J","last_name":"Gross"}],"department":[{"_id":"MaMo"}],"issue":"22","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.09203"}],"abstract":[{"text":"Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. ","lang":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1053-587X"]},"volume":67,"oa":1,"publisher":"IEEE","date_created":"2019-07-31T09:51:14Z","citation":{"apa":"Hashemi, S. A., Condo, C., Mondelli, M., &#38; Gross, W. J. (2019). Rate-flexible fast polar decoders. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href=\"https://doi.org/10.1109/TSP.2019.2944738\">https://doi.org/10.1109/TSP.2019.2944738</a>","short":"S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019).","ieee":"S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” <i>IEEE Transactions on Signal Processing</i>, vol. 67, no. 22. IEEE, 2019.","chicago":"Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/TSP.2019.2944738\">https://doi.org/10.1109/TSP.2019.2944738</a>.","ama":"Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. <i>IEEE Transactions on Signal Processing</i>. 2019;67(22). doi:<a href=\"https://doi.org/10.1109/TSP.2019.2944738\">10.1109/TSP.2019.2944738</a>","mla":"Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” <i>IEEE Transactions on Signal Processing</i>, vol. 67, no. 22, 8854897, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/TSP.2019.2944738\">10.1109/TSP.2019.2944738</a>.","ista":"Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897."},"day":"15","publication":"IEEE Transactions on Signal Processing","external_id":{"arxiv":["1903.09203"]},"title":"Rate-flexible fast polar decoders","type":"journal_article","scopus_import":"1","oa_version":"Preprint","date_published":"2019-11-15T00:00:00Z","publication_status":"published","date_updated":"2025-01-14T14:34:26Z","_id":"6750","quality_controlled":"1","month":"11","intvolume":"        67","article_number":"8854897","doi":"10.1109/TSP.2019.2944738","article_processing_charge":"No"},{"publisher":"ACM","oa":1,"date_created":"2019-08-04T21:59:16Z","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"publication_identifier":{"issn":["0004-5411"],"eissn":["1557-735X"]},"volume":66,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"950"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1705.01433","open_access":"1"}],"abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players."}],"arxiv":1,"issue":"4","department":[{"_id":"ToHe"}],"year":"2019","language":[{"iso":"eng"}],"author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K"}],"status":"public","article_processing_charge":"No","article_number":"31","doi":"10.1145/3340295","quality_controlled":"1","intvolume":"        66","month":"07","publication_status":"published","date_updated":"2025-07-10T11:53:47Z","_id":"6752","date_published":"2019-07-16T00:00:00Z","oa_version":"Preprint","scopus_import":"1","title":"Infinite-duration bidding games","type":"journal_article","external_id":{"isi":["000487714900008"],"arxiv":["1705.01433"]},"publication":"Journal of the ACM","day":"16","citation":{"apa":"Avni, G., Henzinger, T. A., &#38; Chonev, V. K. (2019). Infinite-duration bidding games. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3340295\">https://doi.org/10.1145/3340295</a>","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” <i>Journal of the ACM</i>, vol. 66, no. 4. ACM, 2019.","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3340295\">https://doi.org/10.1145/3340295</a>.","mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” <i>Journal of the ACM</i>, vol. 66, no. 4, 31, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3340295\">10.1145/3340295</a>.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. <i>Journal of the ACM</i>. 2019;66(4). doi:<a href=\"https://doi.org/10.1145/3340295\">10.1145/3340295</a>","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31."},"isi":1},{"status":"public","ddc":["570"],"language":[{"iso":"eng"}],"year":"2019","author":[{"last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Roquis, David","first_name":"David","last_name":"Roquis"},{"full_name":"Bulla, Ingo","last_name":"Bulla","first_name":"Ingo"},{"full_name":"Augusto, Ronaldo C.","last_name":"Augusto","first_name":"Ronaldo C."},{"last_name":"Arancibia","first_name":"Nathalie","full_name":"Arancibia, Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"full_name":"Boissier, Jérôme","last_name":"Boissier","first_name":"Jérôme"},{"full_name":"Cosseau, Céline","first_name":"Céline","last_name":"Cosseau"}],"department":[{"_id":"BeVi"}],"abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"issue":"7","acknowledged_ssus":[{"_id":"CampIT"}],"publication_identifier":{"eissn":["1759-6653"]},"volume":11,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"publisher":"Oxford University Press","date_created":"2019-08-04T21:59:18Z","file_date_updated":"2020-07-14T12:47:39Z","citation":{"ieee":"M. A. L. Picard <i>et al.</i>, “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome biology and evolution</i>. 2019;11(7):1909-1922. doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>."},"file":[{"date_updated":"2020-07-14T12:47:39Z","content_type":"application/pdf","date_created":"2019-08-05T07:55:02Z","access_level":"open_access","file_name":"2019_GenomeBiology_Picard.pdf","file_size":580205,"relation":"main_file","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_id":"6765","creator":"dernst"}],"isi":1,"external_id":{"isi":["000484039500018"],"pmid":["31273378"]},"day":"01","publication":"Genome biology and evolution","scopus_import":"1","page":"1909-1922","pmid":1,"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","type":"journal_article","oa_version":"Published Version","date_published":"2019-07-01T00:00:00Z","quality_controlled":"1","month":"07","intvolume":"        11","date_updated":"2025-05-14T11:08:50Z","publication_status":"published","_id":"6755","doi":"10.1093/gbe/evz133","article_processing_charge":"No"},{"status":"public","ddc":["520","530"],"language":[{"iso":"eng"}],"year":"2019","author":[{"full_name":"Pranav, Pratyush","first_name":"Pratyush","last_name":"Pranav"},{"last_name":"Adler","first_name":"Robert J.","full_name":"Adler, Robert J."},{"first_name":"Thomas","last_name":"Buchert","full_name":"Buchert, Thomas"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Bernard J.T.","last_name":"Jones","full_name":"Jones, Bernard J.T."},{"full_name":"Schwartzman, Armin","first_name":"Armin","last_name":"Schwartzman"},{"first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"},{"last_name":"Van De Weygaert","first_name":"Rien","full_name":"Van De Weygaert, Rien"}],"department":[{"_id":"HeEd"}],"acknowledgement":"PP is grateful to Julian Borill from the Planck consortium for providing the data, and for the illuminating discussions and inputs. PP also thanks Hans Kristen Eriksen, Anne Ducout, and Francois R. Bouchet for significantly helpful discussions at various stages. The authors collectively thank the anonymous referee for the invaluable comments and suggestions that have added significant value to the contents of the manuscript. PP and RA acknowledge the support of ERC advanced grant Understanding Random Systems through Algebraic Topology (URSAT) (no: 320422, PI: RA). This work is also part of a project that has received funding for PP and TB from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC advanced grant 740021– Advances in Research on THeories of the dark UniverSe (ARTHUS), PI: TB). HE and HW acknowledge the support by the Office of Naval Research, through grant N62909-18-1-2038, and by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”, through grant I02979-N35 of the Austrian Science Fund (FWF). PP acknowledges the support and use of resources at the NERSC computing center.","arxiv":1,"abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"article_type":"original","OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":627,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","project":[{"grant_number":"M62909-18-1-2038","_id":"265683E4-B435-11E9-9278-68D0E5697425","name":"Toward Computational Information Topology"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:39Z","oa":1,"publisher":"EDP Sciences","date_created":"2019-08-04T21:59:18Z","file":[{"date_updated":"2020-07-14T12:47:39Z","content_type":"application/pdf","access_level":"open_access","file_name":"2019_AstronomyAstrophysics_Pranav.pdf","date_created":"2019-08-05T08:08:59Z","file_size":14420451,"file_id":"6766","checksum":"83b9209ed9eefbdcefd89019c5a97805","relation":"main_file","creator":"dernst"}],"isi":1,"citation":{"ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. <i>Astronomy and Astrophysics</i>. 2019;627. doi:<a href=\"https://doi.org/10.1051/0004-6361/201834916\">10.1051/0004-6361/201834916</a>","mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” <i>Astronomy and Astrophysics</i>, vol. 627, A163, EDP Sciences, 2019, doi:<a href=\"https://doi.org/10.1051/0004-6361/201834916\">10.1051/0004-6361/201834916</a>.","chicago":"Pranav, Pratyush, Robert J. Adler, Thomas Buchert, Herbert Edelsbrunner, Bernard J.T. Jones, Armin Schwartzman, Hubert Wagner, and Rien Van De Weygaert. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2019. <a href=\"https://doi.org/10.1051/0004-6361/201834916\">https://doi.org/10.1051/0004-6361/201834916</a>.","ista":"Pranav P, Adler RJ, Buchert T, Edelsbrunner H, Jones BJT, Schwartzman A, Wagner H, Van De Weygaert R. 2019. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 627, A163.","ieee":"P. Pranav <i>et al.</i>, “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” <i>Astronomy and Astrophysics</i>, vol. 627. EDP Sciences, 2019.","short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201834916\">https://doi.org/10.1051/0004-6361/201834916</a>"},"publication":"Astronomy and Astrophysics","day":"17","external_id":{"isi":["000475839300003"],"arxiv":["1812.07678"]},"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","type":"journal_article","scopus_import":"1","oa_version":"Published Version","date_published":"2019-07-17T00:00:00Z","publication_status":"published","date_updated":"2025-05-20T08:01:55Z","_id":"6756","quality_controlled":"1","month":"07","intvolume":"       627","article_number":"A163","doi":"10.1051/0004-6361/201834916","OA_type":"hybrid","article_processing_charge":"No"},{"file":[{"date_updated":"2020-07-14T12:47:39Z","content_type":"application/pdf","file_name":"2019_eJourCombinatorics_Jelinek.pdf","date_created":"2019-08-05T06:46:55Z","access_level":"open_access","file_size":533697,"file_id":"6764","checksum":"20fc366fc6683ef0b074a019b73a663a","relation":"main_file","creator":"dernst"}],"citation":{"apa":"Jelínek, V., &#38; Töpfer, M. (2019). On grounded L-graphs and their relatives. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/8096\">https://doi.org/10.37236/8096</a>","short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” <i>Electronic Journal of Combinatorics</i>, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019.","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2019. <a href=\"https://doi.org/10.37236/8096\">https://doi.org/10.37236/8096</a>.","ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. <i>Electronic Journal of Combinatorics</i>. 2019;26(3). doi:<a href=\"https://doi.org/10.37236/8096\">10.37236/8096</a>","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” <i>Electronic Journal of Combinatorics</i>, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:<a href=\"https://doi.org/10.37236/8096\">10.37236/8096</a>.","ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17."},"publication":"Electronic Journal of Combinatorics","day":"19","external_id":{"arxiv":["1808.04148"]},"title":"On grounded L-graphs and their relatives","type":"journal_article","scopus_import":"1","oa_version":"Published Version","date_published":"2019-07-19T00:00:00Z","ec_funded":1,"_id":"6759","publication_status":"published","date_updated":"2025-06-26T12:25:39Z","intvolume":"        26","month":"07","quality_controlled":"1","doi":"10.37236/8096","article_number":"P3.17","OA_type":"gold","article_processing_charge":"Yes","status":"public","ddc":["510"],"author":[{"full_name":"Jelínek, Vít","first_name":"Vít","last_name":"Jelínek"},{"full_name":"Töpfer, Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87","last_name":"Töpfer","first_name":"Martin"}],"year":"2019","language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"corr_author":"1","DOAJ_listed":"1","arxiv":1,"issue":"3","abstract":[{"lang":"eng","text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","article_type":"original","publication_identifier":{"eissn":["1077-8926"]},"volume":26,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:39Z","date_created":"2019-08-04T21:59:20Z","publisher":"Electronic Journal of Combinatorics","oa":1},{"author":[{"full_name":"Friesecke, Gero","first_name":"Gero","last_name":"Friesecke"},{"last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael"}],"language":[{"iso":"eng"}],"year":"2019","department":[{"_id":"JuFi"}],"status":"public","date_created":"2019-08-04T21:59:21Z","publisher":"SIAM","oa":1,"issue":"3","arxiv":1,"abstract":[{"text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":17,"publication_identifier":{"eissn":["1540-3467"],"issn":["1540-3459"]},"title":"New optimal control problems in density functional theory motivated by photovoltaics","type":"journal_article","page":"926-947","scopus_import":"1","oa_version":"Preprint","isi":1,"citation":{"ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” <i>Multiscale Modeling and Simulation</i>, vol. 17, no. 3. SIAM, pp. 926–947, 2019.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","apa":"Friesecke, G., &#38; Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. <i>Multiscale Modeling and Simulation</i>. SIAM. <a href=\"https://doi.org/10.1137/18M1207272\">https://doi.org/10.1137/18M1207272</a>","ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. <i>Multiscale Modeling and Simulation</i>. 2019;17(3):926-947. doi:<a href=\"https://doi.org/10.1137/18M1207272\">10.1137/18M1207272</a>","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” <i>Multiscale Modeling and Simulation</i>, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:<a href=\"https://doi.org/10.1137/18M1207272\">10.1137/18M1207272</a>.","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” <i>Multiscale Modeling and Simulation</i>. SIAM, 2019. <a href=\"https://doi.org/10.1137/18M1207272\">https://doi.org/10.1137/18M1207272</a>."},"day":"16","publication":"Multiscale Modeling and Simulation","external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"doi":"10.1137/18M1207272","article_processing_charge":"No","date_published":"2019-07-16T00:00:00Z","_id":"6762","publication_status":"published","date_updated":"2025-07-10T11:53:49Z","month":"07","intvolume":"        17","quality_controlled":"1"},{"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"volume":15,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics."}],"issue":"29","publisher":"Royal Society of Chemistry","date_created":"2019-08-04T21:59:21Z","status":"public","department":[{"_id":"ScWa"}],"year":"2019","language":[{"iso":"eng"}],"author":[{"first_name":"Hamza K.","last_name":"Khattak","full_name":"Khattak, Hamza K."},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R"},{"last_name":"Slepkov","first_name":"Aaron D.","full_name":"Slepkov, Aaron D."}],"quality_controlled":"1","intvolume":"        15","month":"07","date_updated":"2025-07-10T11:53:49Z","publication_status":"published","_id":"6763","date_published":"2019-07-15T00:00:00Z","article_processing_charge":"No","doi":"10.1039/c9sm00756c","external_id":{"pmid":["31305853"],"isi":["000476909200002"]},"publication":"Soft Matter","day":"15","citation":{"apa":"Khattak, H. K., Waitukaitis, S. R., &#38; Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” <i>Soft Matter</i>, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c9sm00756c\">https://doi.org/10.1039/c9sm00756c</a>.","ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. <i>Soft Matter</i>. 2019;15(29):5804-5809. doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>","mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” <i>Soft Matter</i>, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:<a href=\"https://doi.org/10.1039/c9sm00756c\">10.1039/c9sm00756c</a>.","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809."},"isi":1,"oa_version":"None","scopus_import":"1","page":"5804-5809","pmid":1,"title":"Microwave induced mechanical activation of hydrogel dimers","type":"journal_article"},{"intvolume":"        10","month":"08","quality_controlled":"1","_id":"6778","publication_status":"published","date_updated":"2025-04-14T07:45:04Z","date_published":"2019-08-02T00:00:00Z","ec_funded":1,"article_processing_charge":"No","doi":"10.1038/s41467-019-11471-8","article_number":"3480","external_id":{"pmid":["31375675"],"isi":["000478576500012"]},"publication":"Nature Communications","day":"02","citation":{"ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., &#38; Friml, J. (2019). Evolution of fast root gravitropism in seed plants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-11471-8\">https://doi.org/10.1038/s41467-019-11471-8</a>","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” <i>Nature Communications</i>, vol. 10, 3480, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-11471-8\">10.1038/s41467-019-11471-8</a>.","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-11471-8\">10.1038/s41467-019-11471-8</a>","chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-11471-8\">https://doi.org/10.1038/s41467-019-11471-8</a>."},"isi":1,"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","checksum":"d2c654fdb97f33078f606fe0c298bf6e","relation":"main_file","file_id":"6798","creator":"dernst","date_created":"2019-08-12T07:09:20Z","access_level":"open_access","file_name":"2019_NatureComm_Zhang.pdf","file_size":6406141}],"oa_version":"Published Version","scopus_import":"1","type":"journal_article","title":"Evolution of fast root gravitropism in seed plants","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"volume":10,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/","description":"News on IST Homepage","relation":"press_release"}]},"article_type":"original","abstract":[{"lang":"eng","text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land."}],"date_created":"2019-08-09T08:46:26Z","publisher":"Springer Nature","oa":1,"file_date_updated":"2020-07-14T12:47:40Z","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","ddc":["580"],"status":"public","department":[{"_id":"JiFr"}],"author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"full_name":"Xiao, G","first_name":"G","last_name":"Xiao"},{"first_name":"X","last_name":"Wang","full_name":"Wang, X"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"year":"2019","language":[{"iso":"eng"}]},{"department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"year":"2019","author":[{"full_name":"Suri, Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"full_name":"Pallantla, Ravi Kumar","last_name":"Pallantla","first_name":"Ravi Kumar"},{"full_name":"Schatz, Michael F.","first_name":"Michael F.","last_name":"Schatz"},{"first_name":"Roman O.","last_name":"Grigoriev","full_name":"Grigoriev, Roman O."}],"ddc":["532"],"status":"public","publisher":"American Physical Society","oa":1,"date_created":"2019-08-09T09:40:41Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"volume":100,"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}],"issue":"1","arxiv":1,"oa_version":"Preprint","scopus_import":"1","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","type":"journal_article","external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"day":"25","publication":"Physical Review E","citation":{"short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., &#38; Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 100, no. 1. American Physical Society, 2019.","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physreve.100.013112\">https://doi.org/10.1103/physreve.100.013112</a>.","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. <i>Physical Review E</i>. 2019;100(1). doi:<a href=\"https://doi.org/10.1103/physreve.100.013112\">10.1103/physreve.100.013112</a>"},"isi":1,"article_processing_charge":"No","article_number":"013112","doi":"10.1103/physreve.100.013112","quality_controlled":"1","intvolume":"       100","month":"07","date_updated":"2025-04-15T06:50:28Z","publication_status":"published","_id":"6779","ec_funded":1,"date_published":"2019-07-25T00:00:00Z"},{"article_number":"e1007168","doi":"10.1371/journal.pcbi.1007168","article_processing_charge":"No","date_published":"2019-07-02T00:00:00Z","quality_controlled":"1","intvolume":"        15","month":"07","date_updated":"2025-04-14T13:46:26Z","publication_status":"published","_id":"6784","scopus_import":"1","title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","type":"journal_article","oa_version":"Published Version","citation":{"ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. <i>PLoS Computational Biology</i>. 2019;15(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">10.1371/journal.pcbi.1007168</a>","mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” <i>PLoS Computational Biology</i>, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">10.1371/journal.pcbi.1007168</a>.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">https://doi.org/10.1371/journal.pcbi.1007168</a>.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” <i>PLoS Computational Biology</i>, vol. 15, no. 7. Public Library of Science, 2019.","apa":"Ruess, J., Pleska, M., Guet, C. C., &#38; Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007168\">https://doi.org/10.1371/journal.pcbi.1007168</a>","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019)."},"file":[{"checksum":"7ded4721b41c2a0fc66a1c634540416a","relation":"main_file","file_id":"6803","creator":"dernst","file_name":"2019_PlosComputBiology_Ruess.pdf","access_level":"open_access","date_created":"2019-08-12T12:27:26Z","file_size":2200003,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z"}],"isi":1,"external_id":{"isi":["000481577700032"]},"publication":"PLoS Computational Biology","day":"02","project":[{"grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","date_created":"2019-08-11T21:59:19Z","file_date_updated":"2020-07-14T12:47:40Z","abstract":[{"lang":"eng","text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems."}],"issue":"7","publication_identifier":{"eissn":["1553-7358"]},"volume":15,"article_type":"original","related_material":{"record":[{"id":"9786","status":"public","relation":"research_data"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"year":"2019","author":[{"orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"status":"public","ddc":["570"]}]