[{"_id":"106","external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"scopus_import":"1","type":"journal_article","oa_version":"Preprint","date_updated":"2023-09-13T08:49:16Z","department":[{"_id":"HeEd"}],"citation":{"ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>.","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"full_name":"Petrunin, Anton","first_name":"Anton","last_name":"Petrunin"}],"date_published":"2018-09-01T00:00:00Z","title":"Long geodesics on convex surfaces","quality_controlled":"1","date_created":"2018-12-11T11:44:40Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"year":"2018","publication":"Mathematical Intelligencer","article_processing_charge":"No","volume":40,"status":"public","issue":"3","publist_id":"7948","doi":"10.1007/s00283-018-9795-5","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"isi":1,"month":"09","publication_status":"published","day":"01","publisher":"Springer","intvolume":"        40","page":"26 - 31","arxiv":1,"language":[{"iso":"eng"}]},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","date_published":"2018-06-01T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","publication":"Discrete & Computational Geometry","article_processing_charge":"Yes (via OA deal)","volume":59,"ddc":["516","000"],"date_created":"2018-12-11T11:49:57Z","external_id":{"isi":["000432205500011"]},"file_date_updated":"2019-01-18T09:27:36Z","scopus_import":"1","_id":"1064","date_updated":"2023-09-20T12:08:51Z","oa_version":"Published Version","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"5844","date_created":"2019-01-18T09:27:36Z","success":1,"file_name":"2018_DiscreteComp_Akopyan.pdf","date_updated":"2019-01-18T09:27:36Z","content_type":"application/pdf","file_size":482518}],"department":[{"_id":"HeEd"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009."},"author":[{"last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"last_name":"Balitskiy","full_name":"Balitskiy, Alexey","first_name":"Alexey"},{"last_name":"Grigorev","first_name":"Mikhail","full_name":"Grigorev, Mikhail"}],"oa":1,"type":"journal_article","publisher":"Springer","language":[{"iso":"eng"}],"intvolume":"        59","page":"1001-1009","article_type":"original","license":"https://creativecommons.org/licenses/by/4.0/","issue":"4","publist_id":"6324","doi":"10.1007/s00454-017-9883-x","abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"status":"public","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"publication_status":"published","day":"01","ec_funded":1,"isi":1,"month":"06"},{"external_id":{"isi":["000448185000096"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:44:38Z","_id":"12","department":[{"_id":"BeBi"}],"file":[{"file_id":"5360","date_created":"2018-12-12T10:18:38Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z","file_size":104225664,"file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","creator":"system","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","relation":"main_file"},{"access_level":"open_access","file_id":"5361","date_created":"2018-12-12T10:18:39Z","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_updated":"2020-07-14T12:44:38Z","content_type":"application/zip","file_size":377743553,"checksum":"3861e693ba47c51f3ec7b7867d573a61","relation":"main_file","creator":"system"},{"file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","file_size":162634396,"content_type":"video/vnd.objectvideo","date_updated":"2020-07-14T12:44:38Z","access_level":"open_access","date_created":"2018-12-12T10:18:41Z","file_id":"5362","relation":"main_file","checksum":"490040c685ed869536e2a18f5a906b94","creator":"system"},{"creator":"system","checksum":"be7fc8b229adda727419b6504b3b9352","relation":"main_file","content_type":"image/jpeg","date_updated":"2020-07-14T12:44:38Z","file_size":527972,"file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","file_id":"5363","date_created":"2018-12-12T10:18:42Z","access_level":"open_access"}],"date_updated":"2023-09-11T12:48:09Z","oa_version":"Submitted Version","oa":1,"author":[{"full_name":"Nakashima, Kazutaka","first_name":"Kazutaka","last_name":"Nakashima"},{"first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","full_name":"Iarussi, Emmanuel","last_name":"Iarussi"},{"last_name":"Zhang","first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., &#38; Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4, 135, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. <i>ACM Transaction on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201341\">10.1145/3197517.3201341</a>","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” <i>ACM Transaction on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201341\">https://doi.org/10.1145/3197517.3201341</a>.","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” <i>ACM Transaction on Graphics</i>, vol. 37, no. 4. ACM, 2018."},"has_accepted_license":"1","pubrep_id":"1037","type":"journal_article","date_published":"2018-08-04T00:00:00Z","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design"}],"quality_controlled":"1","year":"2018","article_processing_charge":"No","volume":37,"publication":"ACM Transaction on Graphics","date_created":"2018-12-11T11:44:09Z","ddc":["004","516","670"],"issue":"4","publist_id":"8044","abstract":[{"text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.","lang":"eng"}],"doi":"10.1145/3197517.3201341","status":"public","publication_status":"published","ec_funded":1,"day":"04","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","description":"News on IST Homepage"}]},"month":"08","isi":1,"publisher":"ACM","language":[{"iso":"eng"}],"intvolume":"        37","article_number":"135"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2018-06-01T00:00:00Z","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"date_created":"2018-12-11T11:50:45Z","ddc":["519"],"article_processing_charge":"Yes (via OA deal)","volume":31,"publication":"Journal of Theoretical Probability","year":"2018","_id":"1215","scopus_import":1,"file_date_updated":"2020-07-14T12:44:39Z","type":"journal_article","pubrep_id":"712","author":[{"last_name":"Flandoli","full_name":"Flandoli, Franco","first_name":"Franco"},{"last_name":"Russo","first_name":"Francesco","full_name":"Russo, Francesco"},{"last_name":"Zanco","id":"47491882-F248-11E8-B48F-1D18A9856A87","first_name":"Giovanni A","full_name":"Zanco, Giovanni A"}],"oa":1,"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. 2018;31(2):789-826. doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2. Springer, pp. 789–826, 2018.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","apa":"Flandoli, F., Russo, F., &#38; Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. Springer. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>."},"file":[{"file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","file_size":671125,"access_level":"open_access","file_id":"5266","date_created":"2018-12-12T10:17:13Z","checksum":"47686d58ec21c164540f1a980ff2163f","relation":"main_file","creator":"system"}],"department":[{"_id":"JaMa"}],"date_updated":"2021-01-12T06:49:09Z","oa_version":"Published Version","publisher":"Springer","page":"789-826","intvolume":"        31","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/s10959-016-0724-2","publist_id":"6119","abstract":[{"lang":"eng","text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus."}],"issue":"2","month":"06","day":"01","publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA."},{"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"date_published":"2018-08-04T00:00:00Z","title":"Metamolds: Computational design of silicone molds","quality_controlled":"1","year":"2018","publication":"ACM Trans. Graph.","volume":37,"article_processing_charge":"No","ddc":["004"],"date_created":"2018-12-11T11:44:09Z","external_id":{"isi":["000448185000097"]},"file_date_updated":"2020-07-14T12:44:43Z","scopus_import":"1","_id":"13","oa_version":"Submitted Version","date_updated":"2023-09-13T08:56:07Z","file":[{"access_level":"open_access","date_created":"2018-12-12T10:18:52Z","file_id":"5374","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","file_size":91939066,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:43Z","relation":"main_file","checksum":"61d46273dca4de626accef1d17a0aaad","creator":"system"}],"department":[{"_id":"BeBi"}],"citation":{"ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” <i>ACM Trans. Graph.</i>, vol. 37, no. 4. ACM, 2018.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i> ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. <i>ACM Trans Graph</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2018). Metamolds: Computational design of silicone molds. <i>ACM Trans. Graph.</i> ACM. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i>, vol. 37, no. 4, 136, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>.","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"full_name":"Alderighi, Thomas","first_name":"Thomas","last_name":"Alderighi"},{"last_name":"Malomo","full_name":"Malomo, Luigi","first_name":"Luigi"},{"first_name":"Daniela","full_name":"Giorgi, Daniela","last_name":"Giorgi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"pubrep_id":"1038","type":"journal_article","publisher":"ACM","language":[{"iso":"eng"}],"article_number":"136","intvolume":"        37","issue":"4","publist_id":"8043","abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"doi":"10.1145/3197517.3201381","status":"public","publication_status":"published","day":"04","ec_funded":1,"isi":1,"month":"08","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/"}]}},{"date_published":"2018-11-03T00:00:00Z","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"year":"2018","article_processing_charge":"No","date_created":"2021-08-06T12:26:53Z","doi":"10.6084/m9.figshare.7295339.v1","abstract":[{"lang":"eng","text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb)."}],"_id":"9807","status":"public","department":[{"_id":"SiHi"}],"oa_version":"Published Version","date_updated":"2023-09-13T09:10:47Z","oa":1,"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"full_name":"Karbiener, Michael","first_name":"Michael","last_name":"Karbiener"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"citation":{"ieee":"J. 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Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>"},"author":[{"full_name":"Bod'ová, Katarína","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","last_name":"Bod'ová"},{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Pickup","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"oa":1,"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","id":"316","status":"public"}]},"month":"04","doi":"10.25386/genetics.6148304.v1","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"status":"public","_id":"9813"},{"publisher":"Public Library of Science","title":"Implementation of the inference method in Matlab","date_published":"2018-03-07T00:00:00Z","date_created":"2021-08-09T07:01:24Z","year":"2018","article_processing_charge":"No","_id":"9831","status":"public","doi":"10.1371/journal.pone.0193049.s001","abstract":[{"lang":"eng","text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish."}],"related_material":{"record":[{"id":"406","relation":"used_in_publication","status":"public"}]},"month":"03","type":"research_data_reference","department":[{"_id":"GaTk"}],"date_updated":"2023-09-15T12:06:18Z","oa_version":"Published Version","author":[{"last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína","first_name":"Katarína"},{"last_name":"Mitchell","first_name":"Gabriel","full_name":"Mitchell, Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., &#38; Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>","mla":"Bod’Ová, Katarína, et al. <i>Implementation of the Inference Method in Matlab</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">https://doi.org/10.1371/journal.pone.0193049.s001</a>.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pone.0193049.s001\">10.1371/journal.pone.0193049.s001</a>","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018."},"day":"07"},{"article_processing_charge":"No","year":"2018","main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"date_created":"2021-08-09T12:46:39Z","date_published":"2018-10-09T00:00:00Z","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publisher":"Dryad","oa":1,"author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"citation":{"chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>","ieee":"R. Faria <i>et al.</i>, “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","mla":"Faria, Rui, et al. <i>Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. <a href=\"https://doi.org/10.5061/dryad.72cg113\">https://doi.org/10.5061/dryad.72cg113</a>","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, <a href=\"https://doi.org/10.5061/dryad.72cg113\">10.5061/dryad.72cg113</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"09","department":[{"_id":"NiBa"}],"date_updated":"2023-08-24T14:50:26Z","oa_version":"Published Version","month":"10","related_material":{"record":[{"status":"public","id":"6095","relation":"used_in_publication"}]},"type":"research_data_reference","doi":"10.5061/dryad.72cg113","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"_id":"9837","status":"public"},{"publisher":"Dryad","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","date_published":"2018-06-14T00:00:00Z","date_created":"2021-08-09T12:54:35Z","year":"2018","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.f1s76f2"}],"article_processing_charge":"No","status":"public","_id":"9838","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"doi":"10.5061/dryad.f1s76f2","type":"research_data_reference","related_material":{"record":[{"id":"162","relation":"used_in_publication","status":"public"}]},"month":"06","date_updated":"2023-09-18T09:29:07Z","oa_version":"Published Version","department":[{"_id":"AnKi"}],"day":"14","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>","ieee":"M. Kaucka <i>et al.</i>, “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">https://doi.org/10.5061/dryad.f1s76f2</a>","mla":"Kaucka, Marketa, et al. <i>Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, <a href=\"https://doi.org/10.5061/dryad.f1s76f2\">10.5061/dryad.f1s76f2</a>."},"oa":1,"author":[{"last_name":"Kaucka","full_name":"Kaucka, Marketa","first_name":"Marketa"},{"last_name":"Petersen","first_name":"Julian","full_name":"Petersen, Julian"},{"full_name":"Tesarova, Marketa","first_name":"Marketa","last_name":"Tesarova"},{"last_name":"Szarowska","first_name":"Bara","full_name":"Szarowska, Bara"},{"last_name":"Kastriti","first_name":"Maria Eleni","full_name":"Kastriti, Maria Eleni"},{"last_name":"Xie","full_name":"Xie, Meng","first_name":"Meng"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"last_name":"Annusver","first_name":"Karl","full_name":"Annusver, Karl"},{"last_name":"Kasper","full_name":"Kasper, Maria","first_name":"Maria"},{"last_name":"Symmons","full_name":"Symmons, Orsolya","first_name":"Orsolya"},{"last_name":"Pan","full_name":"Pan, Leslie","first_name":"Leslie"},{"first_name":"Francois","full_name":"Spitz, Francois","last_name":"Spitz"},{"first_name":"Jozef","full_name":"Kaiser, Jozef","last_name":"Kaiser"},{"first_name":"Maria","full_name":"Hovorakova, Maria","last_name":"Hovorakova"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"first_name":"Michael P","full_name":"Matise, Michael P","last_name":"Matise"},{"last_name":"Wang","full_name":"Wang, Hui","first_name":"Hui"},{"last_name":"Marklund","first_name":"Ulrika","full_name":"Marklund, Ulrika"},{"last_name":"Abdo","full_name":"Abdo, Hind","first_name":"Hind"},{"last_name":"Ernfors","full_name":"Ernfors, Patrik","first_name":"Patrik"},{"last_name":"Maire","full_name":"Maire, Pascal","first_name":"Pascal"},{"first_name":"Maud","full_name":"Wurmser, Maud","last_name":"Wurmser"},{"full_name":"Chagin, Andrei S","first_name":"Andrei S","last_name":"Chagin"},{"last_name":"Fried","full_name":"Fried, Kaj","first_name":"Kaj"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"}]},{"abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"doi":"10.5061/dryad.42n44","status":"public","_id":"9840","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"12","citation":{"ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, <a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. <a href=\"https://doi.org/10.5061/dryad.42n44\">https://doi.org/10.5061/dryad.42n44</a>","mla":"Payne, Pavel, et al. <i>Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.42n44\">10.5061/dryad.42n44</a>."},"author":[{"last_name":"Payne","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel","first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas","full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback"}],"oa":1,"oa_version":"Published Version","date_updated":"2023-09-11T12:49:17Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"type":"research_data_reference","month":"03","related_material":{"record":[{"relation":"used_in_publication","id":"423","status":"public"}]},"date_published":"2018-03-12T00:00:00Z","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","publisher":"Dryad","article_processing_charge":"No","year":"2018","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"date_created":"2021-08-09T13:10:02Z"},{"abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"doi":"10.5061/dryad.51d4r","_id":"9841","status":"public","author":[{"full_name":"Harrison, Mark C.","first_name":"Mark C.","last_name":"Harrison"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh M.","first_name":"Hugh M.","last_name":"Robertson"},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"last_name":"Bitard-Feildel","first_name":"Tristan","full_name":"Bitard-Feildel, Tristan"},{"first_name":"Hsu","full_name":"Chao, Hsu","last_name":"Chao"},{"last_name":"Childers","first_name":"Christopher P.","full_name":"Childers, Christopher P."},{"full_name":"Dinh, Huyen","first_name":"Huyen","last_name":"Dinh"},{"full_name":"Doddapaneni, Harshavardhan","first_name":"Harshavardhan","last_name":"Doddapaneni"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"last_name":"Gowin","first_name":"Johannes","full_name":"Gowin, Johannes"},{"last_name":"Greiner","first_name":"Carolin","full_name":"Greiner, Carolin"},{"first_name":"Yi","full_name":"Han, Yi","last_name":"Han"},{"full_name":"Hu, Haofu","first_name":"Haofu","last_name":"Hu"},{"last_name":"Hughes","first_name":"Daniel S. T.","full_name":"Hughes, Daniel S. T."},{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961"},{"first_name":"Carsten","full_name":"Kemena, Carsten","last_name":"Kemena"},{"first_name":"Lukas P. M.","full_name":"Kremer, Lukas P. M.","last_name":"Kremer"},{"first_name":"Sandra L.","full_name":"Lee, Sandra L.","last_name":"Lee"},{"last_name":"Lopez-Ezquerra","first_name":"Alberto","full_name":"Lopez-Ezquerra, Alberto"},{"full_name":"Mallet, Ludovic","first_name":"Ludovic","last_name":"Mallet"},{"last_name":"Monroy-Kuhn","first_name":"Jose M.","full_name":"Monroy-Kuhn, Jose M."},{"last_name":"Moser","first_name":"Annabell","full_name":"Moser, Annabell"},{"full_name":"Murali, Shwetha C.","first_name":"Shwetha C.","last_name":"Murali"},{"last_name":"Muzny","first_name":"Donna M.","full_name":"Muzny, Donna M."},{"last_name":"Otani","full_name":"Otani, Saria","first_name":"Saria"},{"last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors","first_name":"Maria-Dolors"},{"last_name":"Poelchau","first_name":"Monica","full_name":"Poelchau, Monica"},{"last_name":"Qu","first_name":"Jiaxin","full_name":"Qu, Jiaxin"},{"first_name":"Florentine","full_name":"Schaub, Florentine","last_name":"Schaub"},{"last_name":"Wada-Katsumata","first_name":"Ayako","full_name":"Wada-Katsumata, Ayako"},{"full_name":"Worley, Kim C.","first_name":"Kim C.","last_name":"Worley"},{"first_name":"Qiaolin","full_name":"Xie, Qiaolin","last_name":"Xie"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"last_name":"Poulsen","first_name":"Michael","full_name":"Poulsen, Michael"},{"full_name":"Gibbs, Richard A.","first_name":"Richard A.","last_name":"Gibbs"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"},{"last_name":"Richards","first_name":"Stephen","full_name":"Richards, Stephen"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"full_name":"Korb, Judith","first_name":"Judith","last_name":"Korb"},{"full_name":"Bornberg-Bauer, Erich","first_name":"Erich","last_name":"Bornberg-Bauer"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ama":"Harrison MC, Jongepier E, Robertson HM, et al. 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Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>.","ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","apa":"Harrison, M. 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The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","publication_status":"published","day":"13","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9929"}]},"month":"12","issue":"6","doi":"10.1002/evl3.85","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. 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Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"doi":"10.1002/evl3.74","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9930"}]},"month":"08","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. 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We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}]},{"status":"public","_id":"9930","abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"doi":"10.5061/dryad.bp25b65","type":"research_data_reference","month":"07","related_material":{"record":[{"status":"public","id":"9917","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"23","citation":{"ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, <a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>","mla":"Westram, Anja M., et al. <i>Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>.","ieee":"A. M. Westram <i>et al.</i>, “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018."},"author":[{"last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","first_name":"Anja M"},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"last_name":"Blomberg","first_name":"Anders","full_name":"Blomberg, Anders"},{"last_name":"Mehlig","first_name":"Bernhard","full_name":"Mehlig, Bernhard"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"oa":1,"oa_version":"Published Version","date_updated":"2023-09-19T15:08:24Z","department":[{"_id":"BeVi"}],"publisher":"Dryad","title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","date_published":"2018-07-23T00:00:00Z","date_created":"2021-08-17T08:58:47Z","article_processing_charge":"No","year":"2018","main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}]}]