[{"year":"2019","publication_status":"published","isi":1,"publication_identifier":{"issn":["0955-0674"]},"publication":"Current Opinion in Cell Biology","language":[{"iso":"eng"}],"day":"01","page":"114-120","date_created":"2019-07-14T21:59:17Z","date_published":"2019-10-01T00:00:00Z","doi":"10.1016/j.ceb.2019.05.007","volume":60,"abstract":[{"lang":"eng","text":"The spatiotemporal organization of cell divisions constitutes an integral part in the development of multicellular organisms, and mis-regulation of cell divisions can lead to severe developmental defects. Cell divisions have an important morphogenetic function in development by regulating growth and shape acquisition of developing tissues, and, conversely, tissue morphogenesis is known to affect both the rate and orientation of cell divisions. Moreover, cell divisions are associated with an extensive reorganization of the cytoskeleton and adhesion apparatus in the dividing cells that in turn can affect large-scale tissue rheological properties. Thus, the interplay between cell divisions and tissue morphogenesis plays a key role in embryo and tissue morphogenesis."}],"oa_version":"None","quality_controlled":"1","scopus_import":"1","publisher":"Elsevier","intvolume":" 60","month":"10","citation":{"ista":"Godard BG, Heisenberg C-PJ. 2019. Cell division and tissue mechanics. Current Opinion in Cell Biology. 60, 114–120.","chicago":"Godard, Benoit G, and Carl-Philipp J Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology. Elsevier, 2019. https://doi.org/10.1016/j.ceb.2019.05.007.","ama":"Godard BG, Heisenberg C-PJ. Cell division and tissue mechanics. Current Opinion in Cell Biology. 2019;60:114-120. doi:10.1016/j.ceb.2019.05.007","apa":"Godard, B. G., & Heisenberg, C.-P. J. (2019). Cell division and tissue mechanics. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2019.05.007","short":"B.G. Godard, C.-P.J. Heisenberg, Current Opinion in Cell Biology 60 (2019) 114–120.","ieee":"B. G. Godard and C.-P. J. Heisenberg, “Cell division and tissue mechanics,” Current Opinion in Cell Biology, vol. 60. Elsevier, pp. 114–120, 2019.","mla":"Godard, Benoit G., and Carl-Philipp J. Heisenberg. “Cell Division and Tissue Mechanics.” Current Opinion in Cell Biology, vol. 60, Elsevier, 2019, pp. 114–20, doi:10.1016/j.ceb.2019.05.007."},"date_updated":"2023-08-29T06:33:14Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000486545800016"]},"author":[{"first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G","last_name":"Godard"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"Cell division and tissue mechanics","department":[{"_id":"CaHe"}],"_id":"6631","type":"journal_article","status":"public"},{"title":"Geometry-aware scattering compensation for 3D printing","article_processing_charge":"No","external_id":{"isi":["000475740600085"]},"author":[{"first_name":"Denis","full_name":"Sumin, Denis","last_name":"Sumin"},{"last_name":"Weyrich","full_name":"Weyrich, Tim","first_name":"Tim"},{"full_name":"Rittig, Tobias","last_name":"Rittig","first_name":"Tobias"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"first_name":"Thomas","last_name":"Nindel","full_name":"Nindel, Thomas"},{"full_name":"Wilkie, Alexander","last_name":"Wilkie","first_name":"Alexander"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Křivánek","full_name":"Křivánek, Jaroslav","first_name":"Jaroslav"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992.","ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992","apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, 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).","mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992."},"project":[{"grant_number":"642841","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"article_number":"111","date_created":"2019-07-22T07:22:28Z","doi":"10.1145/3306346.3322992","date_published":"2019-07-04T00:00:00Z","publication":"ACM Transactions on Graphics","day":"04","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"ACM","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:36Z","ddc":["000"],"date_updated":"2023-08-29T06:40:49Z","status":"public","type":"journal_article","_id":"6660","ec_funded":1,"volume":38,"issue":"4","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6669","checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","date_updated":"2020-07-14T12:47:36Z","file_size":10109800,"creator":"dernst","date_created":"2019-07-24T07:36:08Z","file_name":"2019_ACM_Sumin_AuthorVersion.pdf"},{"content_type":"application/zip","relation":"supplementary_material","access_level":"open_access","checksum":"f80f365a04e35855fa467ea7ab26b16c","file_id":"6938","file_size":11051245,"date_updated":"2020-07-14T12:47:36Z","creator":"dernst","file_name":"sumin19geometry-aware-suppl.zip","date_created":"2019-10-11T06:51:07Z"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"intvolume":" 38","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"publisher":"CSH Press","quality_controlled":"1","oa":1,"date_published":"2019-07-01T00:00:00Z","doi":"10.1101/gr.238824.118","date_created":"2019-07-21T21:59:15Z","page":"1115-1122","day":"01","publication":"Genome Research","has_accepted_license":"1","isi":1,"year":"2019","title":"Haploid selection drives new gene male germline expression","author":[{"first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","full_name":"Raices, Julia","last_name":"Raices"},{"full_name":"Otto, Paulo","last_name":"Otto","first_name":"Paulo"},{"full_name":"Vibranovski, Maria","last_name":"Vibranovski","first_name":"Maria"}],"article_processing_charge":"No","external_id":{"isi":["000473730600007"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118","ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118.","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118."},"month":"07","intvolume":" 29","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"volume":29,"issue":"7","license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","file_id":"6670","file_size":2319022,"date_updated":"2020-07-14T12:47:35Z","creator":"apreinsp","file_name":"2019_GenomeResearch_Raices.pdf","date_created":"2019-07-24T08:05:56Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"6658","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:35Z","ddc":["576"],"date_updated":"2023-08-29T06:35:05Z"},{"ec_funded":1,"related_material":{"link":[{"description":"YouTube Video","url":"https://youtu.be/SO349S8-x_w","relation":"supplementary_material"}]},"issue":"4","volume":38,"language":[{"iso":"eng"}],"file":[{"file_size":74316182,"date_updated":"2020-07-14T12:47:35Z","creator":"dernst","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","date_created":"2019-07-19T06:18:53Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b4562af94672b44d2a501046427412af","file_id":"6651"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"intvolume":" 38","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry."}],"file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"BeBi"}],"ddc":["000"],"date_updated":"2023-08-29T06:35:52Z","status":"public","type":"journal_article","_id":"6650","date_created":"2019-07-19T06:18:15Z","doi":"10.1145/3306346.3322981","date_published":"2019-07-01T00:00:00Z","publication":"ACM Transactions on Graphics","day":"01","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"publisher":"ACM","quality_controlled":"1","title":"Volume-aware design of composite molds","article_processing_charge":"No","external_id":{"isi":["000475740600084"]},"author":[{"last_name":"Alderighi","full_name":"Alderighi, Thomas","first_name":"Thomas"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"first_name":"Daniela","full_name":"Giorgi, Daniela","last_name":"Giorgi"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981","ama":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","ieee":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","mla":"Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981."},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"110"},{"file":[{"file_size":246151,"date_updated":"2020-07-14T12:47:38Z","creator":"apreinsp","file_name":"2019_Frontiers_Igler.pdf","date_created":"2019-07-29T07:51:54Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6722","checksum":"317a06067e9a8e717bb55f23e0d77ba7"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10,"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","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."}],"month":"06","intvolume":" 10","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-29T06:41:20Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:38Z","_id":"6717","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"03","publication":"Frontiers in Microbiology","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-06-03T00:00:00Z","doi":"10.3389/fmicb.2019.01171","date_created":"2019-07-28T21:59:18Z","publisher":"Frontiers","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171","ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019)."},"title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","author":[{"id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","last_name":"Igler","full_name":"Igler, Claudia"},{"first_name":"Stephen T.","full_name":"Abedon, Stephen T.","last_name":"Abedon"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000470131200001"]},"article_number":"1171","project":[{"grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}]},{"year":"2019","isi":1,"has_accepted_license":"1","publication":"Evolution","day":"01","page":"1729-1745","date_created":"2019-07-25T09:08:28Z","doi":"10.1111/evo.13812","date_published":"2019-09-01T00:00:00Z","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000481300600001"]},"author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","publication_status":"published","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"language":[{"iso":"eng"}],"file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:37Z","file_size":937573,"date_created":"2019-09-17T10:56:27Z","file_name":"2019_Evolution_Sachdeva.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"772ce7035965153959b946a1033de1ca","file_id":"6881"}],"volume":73,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9802"}]},"issue":"9","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 73","month":"09","date_updated":"2023-08-29T06:43:58Z","ddc":["576"],"file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"NiBa"}],"_id":"6680","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public"},{"citation":{"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,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.","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.","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.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000493043500004"],"pmid":["30289430"]},"author":[{"last_name":"Cossard","full_name":"Cossard, Guillaume","first_name":"Guillaume"},{"last_name":"Toups","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"full_name":"Pannell, John ","last_name":"Pannell","first_name":"John "}],"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","year":"2019","isi":1,"publication":"Annals of botany","day":"04","page":"1119-1131","date_created":"2019-07-28T21:59:15Z","date_published":"2019-06-04T00:00:00Z","doi":"10.1093/aob/mcy183","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","date_updated":"2023-08-29T06:42:22Z","department":[{"_id":"BeVi"}],"_id":"6710","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1095-8290"],"issn":["0305-7364"]},"language":[{"iso":"eng"}],"volume":123,"issue":"7","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."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"scopus_import":"1","intvolume":" 123","month":"06"},{"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"first_name":"Michelle N.","full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie"},{"last_name":"Marchini","full_name":"Marchini, Marta","first_name":"Marta"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"last_name":"Kučka","full_name":"Kučka, Marek","first_name":"Marek"},{"last_name":"Beluch","full_name":"Beluch, William H.","first_name":"William H."},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"}],"article_processing_charge":"No","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","department":[{"_id":"NiBa"}],"citation":{"ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk."},"date_updated":"2023-08-29T06:41:51Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9804","doi":"10.5061/dryad.0q2h6tk","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]},"date_published":"2019-06-06T00:00:00Z","date_created":"2021-08-06T11:52:54Z","year":"2019","day":"06","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"oa":1,"month":"06","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"oa_version":"Published Version"},{"day":"16","year":"2019","date_created":"2021-08-06T11:45:11Z","related_material":{"record":[{"status":"public","id":"6680","relation":"used_in_publication"}]},"doi":"10.5061/dryad.8tp0900","date_published":"2019-07-16T00:00:00Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"oa":1,"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","short":"H. Sachdeva, (2019).","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900."},"date_updated":"2023-08-29T06:43:57Z","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"_id":"9802","status":"public","type":"research_data_reference"},{"scopus_import":"1","intvolume":" 627","month":"07","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":627,"publication_status":"published","publication_identifier":{"issn":["00046361"],"eissn":["14320746"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2019_AstronomyAstrophysics_Pranav.pdf","date_created":"2019-08-05T08:08:59Z","file_size":14420451,"date_updated":"2020-07-14T12:47:39Z","creator":"dernst","file_id":"6766","checksum":"83b9209ed9eefbdcefd89019c5a97805","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"6756","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:39Z","date_updated":"2023-08-29T07:01:48Z","ddc":["520","530"],"oa":1,"quality_controlled":"1","publisher":"EDP Sciences","date_created":"2019-08-04T21:59:18Z","doi":"10.1051/0004-6361/201834916","date_published":"2019-07-17T00:00:00Z","year":"2019","has_accepted_license":"1","isi":1,"publication":"Astronomy and Astrophysics","day":"17","project":[{"name":"Toward Computational Information Topology","grant_number":"M62909-18-1-2038","_id":"265683E4-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"article_number":"A163","external_id":{"isi":["000475839300003"],"arxiv":["1812.07678"]},"article_processing_charge":"No","author":[{"first_name":"Pratyush","full_name":"Pranav, Pratyush","last_name":"Pranav"},{"last_name":"Adler","full_name":"Adler, Robert J.","first_name":"Robert J."},{"first_name":"Thomas","last_name":"Buchert","full_name":"Buchert, Thomas"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Jones","full_name":"Jones, Bernard J.T.","first_name":"Bernard J.T."},{"last_name":"Schwartzman","full_name":"Schwartzman, Armin","first_name":"Armin"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","full_name":"Wagner, Hubert","last_name":"Wagner"},{"first_name":"Rien","last_name":"Van De Weygaert","full_name":"Van De Weygaert, Rien"}],"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","citation":{"mla":"Pranav, Pratyush, et al. “Unexpected Topology of the Temperature Fluctuations in the Cosmic Microwave Background.” Astronomy and Astrophysics, vol. 627, A163, EDP Sciences, 2019, doi:10.1051/0004-6361/201834916.","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).","ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 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. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834916","ama":"Pranav P, Adler RJ, Buchert T, et al. Unexpected topology of the temperature fluctuations in the cosmic microwave background. Astronomy and Astrophysics. 2019;627. doi:10.1051/0004-6361/201834916","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.” Astronomy and Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834916.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]