[{"publisher":"CSH Press","quality_controlled":"1","oa":1,"page":"1115-1122","date_published":"2019-07-01T00:00:00Z","doi":"10.1101/gr.238824.118","date_created":"2019-07-21T21:59:15Z","has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Genome Research","author":[{"first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","full_name":"Raices, Julia","last_name":"Raices"},{"first_name":"Paulo","last_name":"Otto","full_name":"Otto, Paulo"},{"first_name":"Maria","full_name":"Vibranovski, Maria","last_name":"Vibranovski"}],"article_processing_charge":"No","external_id":{"isi":["000473730600007"]},"title":"Haploid selection drives new gene male germline expression","citation":{"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.","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 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.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"07","intvolume":" 29","abstract":[{"text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. ","lang":"eng"}],"oa_version":"Published Version","volume":29,"issue":"7","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"published","file":[{"file_id":"6670","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-24T08:05:56Z","file_name":"2019_GenomeResearch_Raices.pdf","creator":"apreinsp","date_updated":"2020-07-14T12:47:35Z","file_size":2319022}],"language":[{"iso":"eng"}],"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)"},"status":"public","_id":"6658","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:35Z","date_updated":"2023-08-29T06:35:05Z","ddc":["576"]},{"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."}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 38","publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","file":[{"date_created":"2019-07-19T06:18:53Z","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","date_updated":"2020-07-14T12:47:35Z","file_size":74316182,"creator":"dernst","file_id":"6651","checksum":"b4562af94672b44d2a501046427412af","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://youtu.be/SO349S8-x_w","relation":"supplementary_material","description":"YouTube Video"}]},"issue":"4","volume":38,"ec_funded":1,"_id":"6650","type":"journal_article","status":"public","date_updated":"2023-08-29T06:35:52Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"BeBi"}],"quality_controlled":"1","publisher":"ACM","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"ACM Transactions on Graphics","date_published":"2019-07-01T00:00:00Z","doi":"10.1145/3306346.3322981","date_created":"2019-07-19T06:18:15Z","article_number":"110","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"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","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.","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"first_name":"Daniela","last_name":"Giorgi","full_name":"Giorgi, Daniela"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"}],"external_id":{"isi":["000475740600084"]},"article_processing_charge":"No","title":"Volume-aware design of composite molds"},{"volume":10,"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","file":[{"file_name":"2019_Frontiers_Igler.pdf","date_created":"2019-07-29T07:51:54Z","creator":"apreinsp","file_size":246151,"date_updated":"2020-07-14T12:47:38Z","file_id":"6722","checksum":"317a06067e9a8e717bb55f23e0d77ba7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:38Z","date_updated":"2023-08-29T06:41:20Z","ddc":["570"],"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)"},"status":"public","_id":"6717","doi":"10.3389/fmicb.2019.01171","date_published":"2019-06-03T00:00:00Z","date_created":"2019-07-28T21:59:18Z","isi":1,"has_accepted_license":"1","year":"2019","day":"03","publication":"Frontiers in Microbiology","publisher":"Frontiers","quality_controlled":"1","oa":1,"author":[{"full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"first_name":"Stephen T.","full_name":"Abedon, Stephen T.","last_name":"Abedon"}],"external_id":{"isi":["000470131200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","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.","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).","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"article_number":"1171"},{"oa_version":"Published Version","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."}],"month":"09","intvolume":" 73","scopus_import":"1","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"772ce7035965153959b946a1033de1ca","file_id":"6881","file_size":937573,"date_updated":"2020-07-14T12:47:37Z","creator":"kschuh","file_name":"2019_Evolution_Sachdeva.pdf","date_created":"2019-09-17T10:56:27Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"9802","relation":"research_data"}]},"issue":"9","volume":73,"_id":"6680","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)"},"ddc":["576"],"date_updated":"2023-08-29T06:43:58Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:37Z","quality_controlled":"1","publisher":"Wiley","oa":1,"day":"01","publication":"Evolution","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1111/evo.13812","date_published":"2019-09-01T00:00:00Z","date_created":"2019-07-25T09:08:28Z","page":"1729-1745","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","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","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.","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."},"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000481300600001"]}},{"publication":"Annals of botany","day":"04","year":"2019","isi":1,"date_created":"2019-07-28T21:59:15Z","date_published":"2019-06-04T00:00:00Z","doi":"10.1093/aob/mcy183","page":"1119-1131","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","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."},"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","article_processing_charge":"No","external_id":{"pmid":["30289430"],"isi":["000493043500004"]},"author":[{"first_name":"Guillaume","full_name":"Cossard, Guillaume","last_name":"Cossard"},{"last_name":"Toups","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pannell, John ","last_name":"Pannell","first_name":"John "}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"volume":123,"issue":"7","pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 123","month":"06","main_file_link":[{"url":"https://doi.org/10.1093/aob/mcy183","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-29T06:42:22Z","department":[{"_id":"BeVi"}],"_id":"6710","status":"public","type":"journal_article","article_type":"original"},{"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.","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.","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","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","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","author":[{"first_name":"João Pl","last_name":"Castro","full_name":"Castro, João Pl"},{"last_name":"Yancoskie","full_name":"Yancoskie, Michelle N.","first_name":"Michelle N."},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, 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"},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"last_name":"Beluch","full_name":"Beluch, William H.","first_name":"William H."},{"full_name":"Naumann, Ronald","last_name":"Naumann","first_name":"Ronald"},{"first_name":"Isabella","full_name":"Skuplik, Isabella","last_name":"Skuplik"},{"last_name":"Cobb","full_name":"Cobb, John","first_name":"John"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Rolian","full_name":"Rolian, Campbell","first_name":"Campbell"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","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"}],"_id":"9804","type":"research_data_reference","status":"public","year":"2019","day":"06","doi":"10.5061/dryad.0q2h6tk","related_material":{"record":[{"relation":"used_in_publication","id":"6713","status":"public"}]},"date_published":"2019-06-06T00:00:00Z","date_created":"2021-08-06T11:52:54Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"month":"06"},{"type":"research_data_reference","status":"public","_id":"9802","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"article_processing_charge":"No","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","department":[{"_id":"NiBa"}],"citation":{"ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","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.","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 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","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","short":"H. Sachdeva, (2019).","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."},"date_updated":"2023-08-29T06:43:57Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"month":"07","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","date_published":"2019-07-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"6680","status":"public"}]},"doi":"10.5061/dryad.8tp0900","date_created":"2021-08-06T11:45:11Z","year":"2019","day":"16"},{"quality_controlled":"1","publisher":"EDP Sciences","oa":1,"day":"17","publication":"Astronomy and Astrophysics","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1051/0004-6361/201834916","date_published":"2019-07-17T00:00:00Z","date_created":"2019-08-04T21:59:18Z","article_number":"A163","project":[{"name":"Toward Computational Information Topology","grant_number":"M62909-18-1-2038","_id":"265683E4-B435-11E9-9278-68D0E5697425"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019.","short":"P. Pranav, R.J. Adler, T. Buchert, H. Edelsbrunner, B.J.T. Jones, A. Schwartzman, H. Wagner, R. Van De Weygaert, Astronomy and Astrophysics 627 (2019).","apa":"Pranav, P., Adler, R. J., Buchert, T., Edelsbrunner, H., Jones, B. J. T., Schwartzman, A., … Van De Weygaert, R. (2019). Unexpected topology of the temperature fluctuations in the cosmic microwave background. 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","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.","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.","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."},"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","author":[{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"first_name":"Robert J.","full_name":"Adler, Robert J.","last_name":"Adler"},{"last_name":"Buchert","full_name":"Buchert, Thomas","first_name":"Thomas"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernard J.T.","last_name":"Jones","full_name":"Jones, Bernard J.T."},{"last_name":"Schwartzman","full_name":"Schwartzman, Armin","first_name":"Armin"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"},{"first_name":"Rien","last_name":"Van De Weygaert","full_name":"Van De Weygaert, Rien"}],"external_id":{"arxiv":["1812.07678"],"isi":["000475839300003"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.","lang":"eng"}],"month":"07","intvolume":" 627","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6766","checksum":"83b9209ed9eefbdcefd89019c5a97805","creator":"dernst","file_size":14420451,"date_updated":"2020-07-14T12:47:39Z","file_name":"2019_AstronomyAstrophysics_Pranav.pdf","date_created":"2019-08-05T08:08:59Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00046361"],"eissn":["14320746"]},"publication_status":"published","volume":627,"_id":"6756","status":"public","article_type":"original","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)"},"ddc":["520","530"],"date_updated":"2023-08-29T07:01:48Z","file_date_updated":"2020-07-14T12:47:39Z","department":[{"_id":"HeEd"}]},{"date_published":"2019-07-01T00:00:00Z","doi":"10.1093/gbe/evz133","date_created":"2019-08-04T21:59:18Z","page":"1909-1922","day":"01","publication":"Genome biology and evolution","has_accepted_license":"1","isi":1,"year":"2019","publisher":"Oxford Academic Press","quality_controlled":"1","oa":1,"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","last_name":"Picard"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"last_name":"Roquis","full_name":"Roquis, David","first_name":"David"},{"last_name":"Bulla","full_name":"Bulla, Ingo","first_name":"Ingo"},{"first_name":"Ronaldo C.","last_name":"Augusto","full_name":"Augusto, Ronaldo C."},{"first_name":"Nathalie","last_name":"Arancibia","full_name":"Arancibia, Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"first_name":"Jérôme","last_name":"Boissier","full_name":"Boissier, Jérôme"},{"last_name":"Cosseau","full_name":"Cosseau, Céline","first_name":"Céline"}],"external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford Academic Press, 2019. https://doi.org/10.1093/gbe/evz133.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford Academic Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford Academic Press. https://doi.org/10.1093/gbe/evz133","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133","ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford Academic Press, pp. 1909–1922, 2019.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922."},"issue":"7","volume":11,"file":[{"file_name":"2019_GenomeBiology_Picard.pdf","date_created":"2019-08-05T07:55:02Z","file_size":580205,"date_updated":"2020-07-14T12:47:39Z","creator":"dernst","file_id":"6765","checksum":"f9e8f6863a406dcc5a36b2be001c138c","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","month":"07","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"CampIT"}],"abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:39Z","ddc":["570"],"date_updated":"2023-08-29T06:53:58Z","status":"public","article_type":"original","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)"},"_id":"6755"},{"intvolume":" 66","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01433"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players."}],"issue":"4","volume":66,"related_material":{"record":[{"id":"950","status":"public","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00045411"],"eissn":["1557735X"]},"status":"public","type":"journal_article","_id":"6752","department":[{"_id":"ToHe"}],"date_updated":"2023-08-29T07:02:13Z","oa":1,"quality_controlled":"1","publisher":"ACM","date_created":"2019-08-04T21:59:16Z","date_published":"2019-07-16T00:00:00Z","doi":"10.1145/3340295","publication":"Journal of the ACM","day":"16","year":"2019","isi":1,"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory"}],"article_number":"31","title":"Infinite-duration bidding games","external_id":{"arxiv":["1705.01433"],"isi":["000487714900008"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","full_name":"Chonev, Ventsislav K"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019.","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31."}},{"_id":"7010","status":"public","conference":{"start_date":"2019-06-26","end_date":"2019-06-27","location":"Munich, Germany","name":"European Conferences on Biomedical Optics"},"type":"conference","date_updated":"2023-08-29T06:54:38Z","department":[{"_id":"MaLo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines."}],"intvolume":" 11076","month":"07","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1605-7422"],"isbn":["9781510628458"]},"volume":11076,"article_number":"110760V","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V.","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.","ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019.","ieee":"H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076."},"title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","external_id":{"isi":["000535353000023"]},"article_processing_charge":"No","author":[{"first_name":"Heather S.","last_name":"Davies","full_name":"Davies, Heather S."},{"last_name":"Baranova","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"first_name":"Nouha","full_name":"El Amri, Nouha","last_name":"El Amri"},{"first_name":"Liliane","full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente"},{"first_name":"Claude","full_name":"Verdier, Claude","last_name":"Verdier"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"last_name":"Richter","full_name":"Richter, Ralf P.","first_name":"Ralf P."},{"first_name":"Delphine","full_name":"Débarre, Delphine","last_name":"Débarre"}],"oa":1,"publisher":"SPIE","quality_controlled":"1","publication":"Advances in Microscopic Imaging II","day":"22","year":"2019","isi":1,"date_created":"2019-11-12T15:10:18Z","date_published":"2019-07-22T00:00:00Z","doi":"10.1117/12.2527058"},{"year":"2019","isi":1,"publication":"Soft Matter","day":"15","page":"5804-5809","date_created":"2019-08-04T21:59:21Z","date_published":"2019-07-15T00:00:00Z","doi":"10.1039/c9sm00756c","publisher":"Royal Society of Chemistry","quality_controlled":"1","citation":{"ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019.","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","apa":"Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c9sm00756c","ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c","mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:10.1039/c9sm00756c.","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"pmid":["31305853"],"isi":["000476909200002"]},"author":[{"first_name":"Hamza K.","full_name":"Khattak, Hamza K.","last_name":"Khattak"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"},{"first_name":"Aaron D.","full_name":"Slepkov, Aaron D.","last_name":"Slepkov"}],"title":"Microwave induced mechanical activation of hydrogel dimers","publication_status":"published","publication_identifier":{"eissn":["17446848"],"issn":["1744683X"]},"language":[{"iso":"eng"}],"volume":15,"issue":"29","abstract":[{"lang":"eng","text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics."}],"pmid":1,"oa_version":"None","scopus_import":"1","intvolume":" 15","month":"07","date_updated":"2023-08-29T06:53:34Z","department":[{"_id":"ScWa"}],"_id":"6763","article_type":"original","type":"journal_article","status":"public"},{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"day":"02","publication":"PLoS Computational Biology","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-07-02T00:00:00Z","doi":"10.1371/journal.pcbi.1007168","date_created":"2019-08-11T21:59:19Z","article_number":"e1007168","project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210"},{"grant_number":"RGY0079/2011","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168."},"title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","author":[{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","last_name":"Ruess"},{"last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"external_id":{"isi":["000481577700032"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems."}],"month":"07","intvolume":" 15","scopus_import":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":2200003,"date_created":"2019-08-12T12:27:26Z","file_name":"2019_PlosComputBiology_Ruess.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7ded4721b41c2a0fc66a1c634540416a","file_id":"6803"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"publication_status":"published","issue":"7","volume":15,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9786"}]},"_id":"6784","status":"public","article_type":"original","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)"},"ddc":["570"],"date_updated":"2023-08-29T07:10:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:40Z"},{"status":"public","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","article_type":"original","_id":"6778","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:40Z","ddc":["580"],"date_updated":"2023-08-29T07:02:44Z","intvolume":" 10","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land."}],"ec_funded":1,"volume":10,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/","relation":"press_release"}]},"language":[{"iso":"eng"}],"file":[{"file_size":6406141,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_name":"2019_NatureComm_Zhang.pdf","date_created":"2019-08-12T07:09:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"d2c654fdb97f33078f606fe0c298bf6e","file_id":"6798"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"3480","title":"Evolution of fast root gravitropism in seed plants","article_processing_charge":"No","external_id":{"isi":["000478576500012"],"pmid":["31375675"]},"author":[{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"},{"last_name":"Wang","full_name":"Wang, X","first_name":"X"},{"last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8.","ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8.","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution of fast root gravitropism in seed plants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11471-8","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8"},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2019-08-09T08:46:26Z","date_published":"2019-08-02T00:00:00Z","doi":"10.1038/s41467-019-11471-8","publication":"Nature Communications","day":"02","year":"2019","isi":1,"has_accepted_license":"1"},{"page":"1447-1460","date_created":"2019-08-18T22:00:41Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1111/1755-0998.13062","year":"2019","isi":1,"publication":"Molecular Ecology Resources","day":"01","oa":1,"publisher":"Wiley","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["31325910"],"isi":["000480196800001"]},"author":[{"full_name":"Yourick, Miranda R.","last_name":"Yourick","first_name":"Miranda R."},{"first_name":"Benjamin A.","full_name":"Sandkam, Benjamin A.","last_name":"Sandkam"},{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger","first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","full_name":"Escobar-Camacho, Daniel","last_name":"Escobar-Camacho"},{"full_name":"Nandamuri, Sri Pratima","last_name":"Nandamuri","first_name":"Sri Pratima"},{"full_name":"Clark, Frances E.","last_name":"Clark","first_name":"Frances E."},{"first_name":"Brendan","last_name":"Joyce","full_name":"Joyce, Brendan"},{"first_name":"Matthew A.","full_name":"Conte, Matthew A.","last_name":"Conte"},{"full_name":"Kocher, Thomas D.","last_name":"Kocher","first_name":"Thomas D."},{"first_name":"Karen L.","full_name":"Carleton, Karen L.","last_name":"Carleton"}],"title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","citation":{"chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources. Wiley, 2019. https://doi.org/10.1111/1755-0998.13062.","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” Molecular Ecology Resources, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:10.1111/1755-0998.13062.","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460.","ieee":"M. R. Yourick et al., “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” Molecular Ecology Resources, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019.","apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13062","ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 2019;19(6):1447-1460. doi:10.1111/1755-0998.13062"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":19,"issue":"6","publication_status":"published","publication_identifier":{"eissn":["1755-0998"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727"}],"scopus_import":"1","intvolume":" 19","month":"11","abstract":[{"text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"BeVi"}],"date_updated":"2023-08-29T07:10:44Z","type":"journal_article","article_type":"original","status":"public","_id":"6821"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Leopold NK, Petrat SP. 2019. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 20(10), 3471–3508.","chicago":"Leopold, Nikolai K, and Sören P Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare. Springer Nature, 2019. https://doi.org/10.1007/s00023-019-00828-w.","short":"N.K. Leopold, S.P. Petrat, Annales Henri Poincare 20 (2019) 3471–3508.","ieee":"N. K. Leopold and S. P. Petrat, “Mean-field dynamics for the Nelson model with fermions,” Annales Henri Poincare, vol. 20, no. 10. Springer Nature, pp. 3471–3508, 2019.","ama":"Leopold NK, Petrat SP. Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. 2019;20(10):3471–3508. doi:10.1007/s00023-019-00828-w","apa":"Leopold, N. K., & Petrat, S. P. (2019). Mean-field dynamics for the Nelson model with fermions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-019-00828-w","mla":"Leopold, Nikolai K., and Sören P. Petrat. “Mean-Field Dynamics for the Nelson Model with Fermions.” Annales Henri Poincare, vol. 20, no. 10, Springer Nature, 2019, pp. 3471–3508, doi:10.1007/s00023-019-00828-w."},"title":"Mean-field dynamics for the Nelson model with fermions","author":[{"last_name":"Leopold","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","last_name":"Petrat","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1807.06781"],"isi":["000487036900008"]},"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"day":"01","publication":"Annales Henri Poincare","isi":1,"has_accepted_license":"1","year":"2019","doi":"10.1007/s00023-019-00828-w","date_published":"2019-10-01T00:00:00Z","date_created":"2019-08-11T21:59:21Z","page":"3471–3508","publisher":"Springer Nature","quality_controlled":"1","oa":1,"ddc":["510"],"date_updated":"2023-08-29T07:09:06Z","file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"RoSe"}],"_id":"6788","status":"public","type":"journal_article","article_type":"original","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)"},"file":[{"file_name":"2019_AnnalesHenriPoincare_Leopold.pdf","date_created":"2019-08-12T12:05:58Z","creator":"dernst","file_size":681139,"date_updated":"2020-07-14T12:47:40Z","checksum":"b6dbf0d837d809293d449adf77138904","file_id":"6801","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1424-0661"],"issn":["1424-0637"]},"publication_status":"published","volume":20,"issue":"10","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations."}],"month":"10","intvolume":" 20","scopus_import":"1"},{"_id":"6795","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","date_updated":"2023-08-29T07:03:10Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:40Z","abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"09","publication_status":"published","publication_identifier":{"eissn":["20457758"]},"language":[{"iso":"eng"}],"file":[{"checksum":"adcb70af4901977d95b8747eeee01bd7","file_id":"6799","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_EcologyEvolution_Trubenova.pdf","date_created":"2019-08-12T07:30:30Z","creator":"dernst","file_size":2839636,"date_updated":"2020-07-14T12:47:40Z"}],"ec_funded":1,"issue":"17","volume":9,"project":[{"grant_number":"704172","name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000479973400001"]},"article_processing_charge":"No","author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"title":"Green beards in the light of indirect genetic effects","oa":1,"quality_controlled":"1","publisher":"Wiley","year":"2019","isi":1,"has_accepted_license":"1","publication":"Ecology and Evolution","day":"01","page":"9597-9608","date_created":"2019-08-11T21:59:24Z","doi":"10.1002/ece3.5484","date_published":"2019-09-01T00:00:00Z"},{"department":[{"_id":"HeEd"}],"date_updated":"2023-08-29T07:08:34Z","type":"journal_article","article_type":"original","status":"public","_id":"6793","ec_funded":1,"volume":51,"issue":"5","publication_status":"published","publication_identifier":{"issn":["00246093"],"eissn":["14692120"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.04929"}],"scopus_import":"1","intvolume":" 51","month":"10","abstract":[{"text":"The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","external_id":{"isi":["000478560200001"],"arxiv":["1903.04929"]},"author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Izmestiev","full_name":"Izmestiev, Ivan","first_name":"Ivan"}],"title":"The Regge symmetry, confocal conics, and the Schläfli formula","citation":{"ieee":"A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775.","ama":"Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775. doi:10.1112/blms.12276","apa":"Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12276","mla":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276.","ista":"Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.","chicago":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society. London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"page":"765-775","date_created":"2019-08-11T21:59:23Z","doi":"10.1112/blms.12276","date_published":"2019-10-01T00:00:00Z","year":"2019","isi":1,"publication":"Bulletin of the London Mathematical Society","day":"01","oa":1,"publisher":"London Mathematical Society","quality_controlled":"1"},{"title":"Supporting text and results","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Ruess, Jakob, et al. Supporting Text and Results. Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.” Public Library of Science, 2019.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public Library of Science, 10.1371/journal.pcbi.1007168.s001."},"date_updated":"2023-08-29T07:10:05Z","status":"public","type":"research_data_reference","_id":"9786","date_published":"2019-07-02T00:00:00Z","doi":"10.1371/journal.pcbi.1007168.s001","related_material":{"record":[{"relation":"used_in_publication","id":"6784","status":"public"}]},"date_created":"2021-08-06T08:23:43Z","day":"02","year":"2019","month":"07","publisher":"Public Library of Science","oa_version":"Published Version"},{"_id":"6831","status":"public","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","ddc":["570"],"date_updated":"2023-08-29T07:17:07Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:42Z","oa_version":"Published Version","abstract":[{"text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle.","lang":"eng"}],"intvolume":" 224","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6370e7567d96b7b562e77d8b89653f80","file_id":"6833","creator":"apreinsp","file_size":2314016,"date_updated":"2020-07-14T12:47:42Z","file_name":"2019_NewPhytologist_Puixeu.pdf","date_created":"2019-08-27T12:44:54Z"}],"publication_status":"published","publication_identifier":{"eissn":["1469-8137"]},"ec_funded":1,"volume":224,"related_material":{"record":[{"status":"public","id":"9803","relation":"research_data"},{"relation":"dissertation_contains","id":"14058","status":"public"}]},"issue":"3","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050."},"title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","external_id":{"isi":["000481376500001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David"},{"first_name":"Spencer C.H.","last_name":"Barrett","full_name":"Barrett, Spencer C.H."}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"New Phytologist","day":"01","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-08-25T22:00:51Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1111/nph.16050","page":"1108-1120"}]