[{"oa_version":"Published Version","_id":"6601","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Mechanochemical feedback loops in development and disease","status":"public","intvolume":" 178","abstract":[{"lang":"eng","text":"There is increasing evidence that both mechanical and biochemical signals play important roles in development and disease. The development of complex organisms, in particular, has been proposed to rely on the feedback between mechanical and biochemical patterning events. This feedback occurs at the molecular level via mechanosensation but can also arise as an emergent property of the system at the cellular and tissue level. In recent years, dynamic changes in tissue geometry, flow, rheology, and cell fate specification have emerged as key platforms of mechanochemical feedback loops in multiple processes. Here, we review recent experimental and theoretical advances in understanding how these feedbacks function in development and disease."}],"issue":"1","type":"journal_article","date_published":"2019-07-27T00:00:00Z","publication":"Cell","citation":{"ama":"Hannezo EB, Heisenberg C-PJ. Mechanochemical feedback loops in development and disease. Cell. 2019;178(1):12-25. doi:10.1016/j.cell.2019.05.052","ista":"Hannezo EB, Heisenberg C-PJ. 2019. Mechanochemical feedback loops in development and disease. Cell. 178(1), 12–25.","apa":"Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Mechanochemical feedback loops in development and disease. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.05.052","ieee":"E. B. Hannezo and C.-P. J. Heisenberg, “Mechanochemical feedback loops in development and disease,” Cell, vol. 178, no. 1. Elsevier, pp. 12–25, 2019.","mla":"Hannezo, Edouard B., and Carl-Philipp J. Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell, vol. 178, no. 1, Elsevier, 2019, pp. 12–25, doi:10.1016/j.cell.2019.05.052.","short":"E.B. Hannezo, C.-P.J. Heisenberg, Cell 178 (2019) 12–25.","chicago":"Hannezo, Edouard B, and Carl-Philipp J Heisenberg. “Mechanochemical Feedback Loops in Development and Disease.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.05.052."},"article_type":"review","page":"12-25","day":"27","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2019-06-30T21:59:11Z","date_updated":"2023-08-28T12:25:21Z","volume":178,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"ec_funded":1,"doi":"10.1016/j.cell.2019.05.052","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.05.052","open_access":"1"}],"external_id":{"isi":["000473002700005"],"pmid":["31251912"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF"}],"month":"07","publication_identifier":{"issn":["00928674"]}},{"_id":"6617","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 234","ddc":["500"],"title":"The choice of representative volumes in the approximation of effective properties of random materials","status":"public","file":[{"creator":"kschuh","file_size":1377659,"content_type":"application/pdf","access_level":"open_access","file_name":"Springer_2019_Fischer.pdf","checksum":"4cff75fa6addb0770991ad9c474ab404","date_created":"2019-07-08T15:56:47Z","date_updated":"2020-07-14T12:47:34Z","file_id":"6626","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably."}],"citation":{"short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 234 (2019) 635–726.","mla":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis, vol. 234, no. 2, Springer, 2019, pp. 635–726, doi:10.1007/s00205-019-01400-w.","chicago":"Fischer, Julian L. “The Choice of Representative Volumes in the Approximation of Effective Properties of Random Materials.” Archive for Rational Mechanics and Analysis. Springer, 2019. https://doi.org/10.1007/s00205-019-01400-w.","ama":"Fischer JL. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 2019;234(2):635–726. doi:10.1007/s00205-019-01400-w","apa":"Fischer, J. L. (2019). The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-019-01400-w","ieee":"J. L. Fischer, “The choice of representative volumes in the approximation of effective properties of random materials,” Archive for Rational Mechanics and Analysis, vol. 234, no. 2. Springer, pp. 635–726, 2019.","ista":"Fischer JL. 2019. The choice of representative volumes in the approximation of effective properties of random materials. Archive for Rational Mechanics and Analysis. 234(2), 635–726."},"publication":"Archive for Rational Mechanics and Analysis","page":"635–726","article_type":"original","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","year":"2019","department":[{"_id":"JuFi"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"volume":234,"date_created":"2019-07-07T21:59:23Z","date_updated":"2023-08-28T12:31:21Z","file_date_updated":"2020-07-14T12:47:34Z","license":"https://creativecommons.org/licenses/by/4.0/","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000482386000006"],"arxiv":["1807.00834"]},"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00205-019-01400-w","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"month":"11"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000475301500018"],"pmid":["31181636"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"doi":"10.3390/biom9060222","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"06","year":"2019","pmid":1,"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"author":[{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"date_updated":"2023-08-28T12:30:24Z","date_created":"2019-07-07T21:59:21Z","volume":9,"article_number":"222","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"publication":"Biomolecules","citation":{"short":"M. Glanc, M. Fendrych, J. Friml, Biomolecules 9 (2019).","mla":"Glanc, Matous, et al. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules, vol. 9, no. 6, 222, MDPI, 2019, doi:10.3390/biom9060222.","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “PIN2 Polarity Establishment in Arabidopsis in the Absence of an Intact Cytoskeleton.” Biomolecules. MDPI, 2019. https://doi.org/10.3390/biom9060222.","ama":"Glanc M, Fendrych M, Friml J. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 2019;9(6). doi:10.3390/biom9060222","ieee":"M. Glanc, M. Fendrych, and J. Friml, “PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton,” Biomolecules, vol. 9, no. 6. MDPI, 2019.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2019). PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. MDPI. https://doi.org/10.3390/biom9060222","ista":"Glanc M, Fendrych M, Friml J. 2019. PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton. Biomolecules. 9(6), 222."},"date_published":"2019-06-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","_id":"6611","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton","ddc":["580"],"status":"public","intvolume":" 9","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-08T15:46:32Z","checksum":"1ce1bd36038fe5381057a1bcc6760083","file_id":"6625","relation":"main_file","creator":"kschuh","file_size":1066773,"content_type":"application/pdf","file_name":"biomolecules-2019-Matous.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking."}],"issue":"6"},{"month":"12","publication_identifier":{"issn":["16747283"]},"oa":1,"external_id":{"isi":["000509102200001"],"arxiv":["1709.09476"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09476"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s11425-018-9543-8","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","publisher":"Springer","department":[{"_id":"TiBr"}],"author":[{"full_name":"De La Bretèche, Régis","last_name":"De La Bretèche","first_name":"Régis"},{"full_name":"Destagnol, Kevin N","first_name":"Kevin N","last_name":"Destagnol","id":"44DDECBC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Liu","first_name":"Jianya","full_name":"Liu, Jianya"},{"first_name":"Jie","last_name":"Wu","full_name":"Wu, Jie"},{"full_name":"Zhao, Yongqiang","first_name":"Yongqiang","last_name":"Zhao"}],"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-08-28T12:32:20Z","volume":62,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Science China Mathematics","citation":{"short":"R. De La Bretèche, K.N. Destagnol, J. Liu, J. Wu, Y. Zhao, Science China Mathematics 62 (2019) 2435–2446.","mla":"De La Bretèche, Régis, et al. “On a Certain Non-Split Cubic Surface.” Science China Mathematics, vol. 62, no. 12, Springer, 2019, pp. 2435–2446, doi:10.1007/s11425-018-9543-8.","chicago":"De La Bretèche, Régis, Kevin N Destagnol, Jianya Liu, Jie Wu, and Yongqiang Zhao. “On a Certain Non-Split Cubic Surface.” Science China Mathematics. Springer, 2019. https://doi.org/10.1007/s11425-018-9543-8.","ama":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. On a certain non-split cubic surface. Science China Mathematics. 2019;62(12):2435–2446. doi:10.1007/s11425-018-9543-8","ieee":"R. De La Bretèche, K. N. Destagnol, J. Liu, J. Wu, and Y. Zhao, “On a certain non-split cubic surface,” Science China Mathematics, vol. 62, no. 12. Springer, pp. 2435–2446, 2019.","apa":"De La Bretèche, R., Destagnol, K. N., Liu, J., Wu, J., & Zhao, Y. (2019). On a certain non-split cubic surface. Science China Mathematics. Springer. https://doi.org/10.1007/s11425-018-9543-8","ista":"De La Bretèche R, Destagnol KN, Liu J, Wu J, Zhao Y. 2019. On a certain non-split cubic surface. Science China Mathematics. 62(12), 2435–2446."},"article_type":"original","page":"2435–2446","date_published":"2019-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures.\r\n","lang":"eng"}],"issue":"12","_id":"6620","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"On a certain non-split cubic surface","intvolume":" 62","oa_version":"Preprint"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"date_updated":"2023-08-29T06:31:14Z","date_created":"2019-07-14T21:59:20Z","volume":73,"author":[{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krejca, Martin ","last_name":"Krejca","first_name":"Martin "},{"full_name":"Lehre, Per Kristian","last_name":"Lehre","first_name":"Per Kristian"},{"full_name":"Kötzing, Timo","first_name":"Timo","last_name":"Kötzing"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","year":"2019","month":"07","language":[{"iso":"eng"}],"doi":"10.1111/evo.13784","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000474031600001"]},"abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-16T06:08:31Z","checksum":"9831ca65def2d62498c7b08338b6d237","relation":"main_file","file_id":"6643","content_type":"application/pdf","file_size":815416,"creator":"apreinsp","file_name":"2019_Evolution_TrubenovaBarbora.pdf","access_level":"open_access"}],"title":"Surfing on the seascape: Adaptation in a changing environment","ddc":["576"],"status":"public","intvolume":" 73","_id":"6637","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","article_type":"original","page":"1356-1374","publication":"Evolution","citation":{"chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784"}},{"month":"06","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000472541600004"],"arxiv":["1612.06926"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1612.06926","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.12775/TMNA.2019.008","ec_funded":1,"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Akademicka Platforma Czasopism","year":"2019","date_updated":"2023-08-29T06:32:48Z","date_created":"2019-07-14T21:59:19Z","volume":53,"author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Hubard, Alfredo","last_name":"Hubard","first_name":"Alfredo"},{"full_name":"Karasev, Roman","first_name":"Roman","last_name":"Karasev"}],"scopus_import":"1","day":"01","article_processing_charge":"No","page":"457-490","publication":"Topological Methods in Nonlinear Analysis","citation":{"ista":"Akopyan A, Hubard A, Karasev R. 2019. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 53(2), 457–490.","ieee":"A. Akopyan, A. Hubard, and R. Karasev, “Lower and upper bounds for the waists of different spaces,” Topological Methods in Nonlinear Analysis, vol. 53, no. 2. Akademicka Platforma Czasopism, pp. 457–490, 2019.","apa":"Akopyan, A., Hubard, A., & Karasev, R. (2019). Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism. https://doi.org/10.12775/TMNA.2019.008","ama":"Akopyan A, Hubard A, Karasev R. Lower and upper bounds for the waists of different spaces. Topological Methods in Nonlinear Analysis. 2019;53(2):457-490. doi:10.12775/TMNA.2019.008","chicago":"Akopyan, Arseniy, Alfredo Hubard, and Roman Karasev. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis. Akademicka Platforma Czasopism, 2019. https://doi.org/10.12775/TMNA.2019.008.","mla":"Akopyan, Arseniy, et al. “Lower and Upper Bounds for the Waists of Different Spaces.” Topological Methods in Nonlinear Analysis, vol. 53, no. 2, Akademicka Platforma Czasopism, 2019, pp. 457–90, doi:10.12775/TMNA.2019.008.","short":"A. Akopyan, A. Hubard, R. Karasev, Topological Methods in Nonlinear Analysis 53 (2019) 457–490."},"date_published":"2019-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper we prove several new results around Gromov's waist theorem. We give a simple proof of Vaaler's theorem on sections of the unit cube using the Borsuk-Ulam-Crofton technique, consider waists of real and complex projective spaces, flat tori, convex bodies in Euclidean space; and establish waist-type results in terms of the Hausdorff measure."}],"issue":"2","status":"public","title":"Lower and upper bounds for the waists of different spaces","intvolume":" 53","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6634","oa_version":"Preprint"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Silva, André , Alan M Arroyo Guevara, Bruce Richter, and Orlando Lee. “Graphs with at Most One Crossing.” Discrete Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.disc.2019.06.031.","short":"A. Silva, A.M. Arroyo Guevara, B. Richter, O. Lee, Discrete Mathematics 342 (2019) 3201–3207.","mla":"Silva, André, et al. “Graphs with at Most One Crossing.” Discrete Mathematics, vol. 342, no. 11, Elsevier, 2019, pp. 3201–07, doi:10.1016/j.disc.2019.06.031.","apa":"Silva, A., Arroyo Guevara, A. M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031","ieee":"A. Silva, A. M. Arroyo Guevara, B. Richter, and O. Lee, “Graphs with at most one crossing,” Discrete Mathematics, vol. 342, no. 11. Elsevier, pp. 3201–3207, 2019.","ista":"Silva A, Arroyo Guevara AM, Richter B, Lee O. 2019. Graphs with at most one crossing. Discrete Mathematics. 342(11), 3201–3207.","ama":"Silva A, Arroyo Guevara AM, Richter B, Lee O. Graphs with at most one crossing. Discrete Mathematics. 2019;342(11):3201-3207. doi:10.1016/j.disc.2019.06.031"},"publication":"Discrete Mathematics","page":"3201-3207","date_published":"2019-11-01T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one.","lang":"eng"}],"_id":"6638","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 342","title":"Graphs with at most one crossing","status":"public","oa_version":"Preprint","publication_identifier":{"issn":["0012-365X"]},"month":"11","oa":1,"external_id":{"arxiv":["1901.09955"],"isi":["000486358100025"]},"main_file_link":[{"url":"https://arxiv.org/abs/1901.09955","open_access":"1"}],"project":[{"_id":"26366136-B435-11E9-9278-68D0E5697425","name":"Reglas de Conectividad funcional en el hipocampo"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.disc.2019.06.031","language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"full_name":"Silva, André ","last_name":"Silva","first_name":"André "},{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","first_name":"Alan M","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M"},{"first_name":"Bruce","last_name":"Richter","full_name":"Richter, Bruce"},{"full_name":"Lee, Orlando","first_name":"Orlando","last_name":"Lee"}],"volume":342,"date_updated":"2023-08-29T06:31:41Z","date_created":"2019-07-14T21:59:20Z"},{"project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design","call_identifier":"H2020"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000475740600085"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3306346.3322992","publication_identifier":{"issn":["0730-0301"]},"month":"07","publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2019","volume":38,"date_updated":"2023-08-29T06:40:49Z","date_created":"2019-07-22T07:22:28Z","author":[{"last_name":"Sumin","first_name":"Denis","full_name":"Sumin, Denis"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"full_name":"Rittig, Tobias","last_name":"Rittig","first_name":"Tobias"},{"full_name":"Babaei, Vahid","last_name":"Babaei","first_name":"Vahid"},{"full_name":"Nindel, Thomas","last_name":"Nindel","first_name":"Thomas"},{"full_name":"Wilkie, Alexander","first_name":"Alexander","last_name":"Wilkie"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"article_number":"111","ec_funded":1,"file_date_updated":"2020-07-14T12:47:36Z","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.","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","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","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","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.","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.","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)."},"publication":"ACM Transactions on Graphics","date_published":"2019-07-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","intvolume":" 38","status":"public","ddc":["000"],"title":"Geometry-aware scattering compensation for 3D printing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6660","oa_version":"Submitted Version","file":[{"checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","date_updated":"2020-07-14T12:47:36Z","date_created":"2019-07-24T07:36:08Z","file_id":"6669","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":10109800,"access_level":"open_access","file_name":"2019_ACM_Sumin_AuthorVersion.pdf"},{"access_level":"open_access","file_name":"sumin19geometry-aware-suppl.zip","creator":"dernst","content_type":"application/zip","file_size":11051245,"file_id":"6938","relation":"supplementary_material","checksum":"f80f365a04e35855fa467ea7ab26b16c","date_created":"2019-10-11T06:51:07Z","date_updated":"2020-07-14T12:47:36Z"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers."}]},{"type":"journal_article","issue":"7","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"}],"intvolume":" 29","status":"public","ddc":["576"],"title":"Haploid selection drives new gene male germline expression","_id":"6658","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2019_GenomeResearch_Raices.pdf","access_level":"open_access","creator":"apreinsp","file_size":2319022,"content_type":"application/pdf","file_id":"6670","relation":"main_file","date_created":"2019-07-24T08:05:56Z","date_updated":"2020-07-14T12:47:35Z","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"1115-1122","citation":{"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","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 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","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.","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."},"publication":"Genome Research","date_published":"2019-07-01T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"BeVi"}],"publisher":"CSH Press","publication_status":"published","year":"2019","volume":29,"date_updated":"2023-08-29T06:35:05Z","date_created":"2019-07-21T21:59:15Z","author":[{"full_name":"Raices, Julia","last_name":"Raices","first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otto, Paulo","first_name":"Paulo","last_name":"Otto"},{"full_name":"Vibranovski, Maria","last_name":"Vibranovski","first_name":"Maria"}],"month":"07","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000473730600007"]},"language":[{"iso":"eng"}],"doi":"10.1101/gr.238824.118"},{"year":"2019","publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published","related_material":{"link":[{"relation":"supplementary_material","description":"YouTube Video","url":"https://youtu.be/SO349S8-x_w"}]},"author":[{"full_name":"Alderighi, Thomas","last_name":"Alderighi","first_name":"Thomas"},{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"first_name":"Daniela","last_name":"Giorgi","full_name":"Giorgi, Daniela"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"volume":38,"date_created":"2019-07-19T06:18:15Z","date_updated":"2023-08-29T06:35:52Z","article_number":"110","ec_funded":1,"file_date_updated":"2020-07-14T12:47:35Z","oa":1,"external_id":{"isi":["000475740600084"]},"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3306346.3322981","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"]},"month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6650","intvolume":" 38","ddc":["000"],"title":"Volume-aware design of composite molds","status":"public","oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","access_level":"open_access","creator":"dernst","file_size":74316182,"content_type":"application/pdf","file_id":"6651","relation":"main_file","date_created":"2019-07-19T06:18:53Z","date_updated":"2020-07-14T12:47:35Z","checksum":"b4562af94672b44d2a501046427412af"}],"type":"journal_article","issue":"4","abstract":[{"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.","lang":"eng"}],"citation":{"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.","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.","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","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.","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.","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"},"publication":"ACM Transactions on Graphics","date_published":"2019-07-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000470131200001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"doi":"10.3389/fmicb.2019.01171","language":[{"iso":"eng"}],"month":"06","year":"2019","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Frontiers","author":[{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","first_name":"Claudia"},{"full_name":"Abedon, Stephen T.","first_name":"Stephen T.","last_name":"Abedon"}],"date_created":"2019-07-28T21:59:18Z","date_updated":"2023-08-29T06:41:20Z","volume":10,"article_number":"1171","file_date_updated":"2020-07-14T12:47:38Z","publication":"Frontiers in Microbiology","citation":{"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.","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","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","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","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.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","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."},"date_published":"2019-06-03T00:00:00Z","scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","_id":"6717","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","ddc":["570"],"status":"public","intvolume":" 10","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_Frontiers_Igler.pdf","creator":"apreinsp","content_type":"application/pdf","file_size":246151,"file_id":"6722","relation":"main_file","checksum":"317a06067e9a8e717bb55f23e0d77ba7","date_created":"2019-07-29T07:51:54Z","date_updated":"2020-07-14T12:47:38Z"}],"type":"journal_article","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."}]},{"related_material":{"record":[{"status":"public","relation":"research_data","id":"9802"}]},"author":[{"last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"}],"volume":73,"date_created":"2019-07-25T09:08:28Z","date_updated":"2023-08-29T06:43:58Z","year":"2019","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:37Z","doi":"10.1111/evo.13812","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481300600001"]},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"09","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_Evolution_Sachdeva.pdf","file_size":937573,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6881","checksum":"772ce7035965153959b946a1033de1ca","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-09-17T10:56:27Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6680","intvolume":" 73","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","ddc":["576"],"status":"public","issue":"9","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"}],"type":"journal_article","date_published":"2019-09-01T00:00:00Z","citation":{"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.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","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.","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.","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 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"},"publication":"Evolution","page":"1729-1745","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1"},{"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2019","volume":123,"date_created":"2019-07-28T21:59:15Z","date_updated":"2023-08-29T06:42:22Z","author":[{"full_name":"Cossard, Guillaume","first_name":"Guillaume","last_name":"Cossard"},{"full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John ","last_name":"Pannell","full_name":"Pannell, John "}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000493043500004"],"pmid":["30289430"]},"main_file_link":[{"url":"https://doi.org/10.1093/aob/mcy183","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/aob/mcy183","publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"month":"06","intvolume":" 123","status":"public","title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6710","oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"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.","lang":"eng"}],"page":"1119-1131","article_type":"original","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.","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","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.","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","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.","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","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."},"publication":"Annals of botany","date_published":"2019-06-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04"},{"type":"research_data_reference","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."}],"year":"2019","_id":"9804","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"last_name":"Castro","first_name":"João Pl","full_name":"Castro, João Pl"},{"last_name":"Yancoskie","first_name":"Michelle N.","full_name":"Yancoskie, Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"last_name":"Beluch","first_name":"William H.","full_name":"Beluch, William H."},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","first_name":"Isabella","full_name":"Skuplik, Isabella"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Rolian, Campbell","first_name":"Campbell","last_name":"Rolian"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]},"date_created":"2021-08-06T11:52:54Z","date_updated":"2023-08-29T06:41:51Z","oa_version":"Published Version","day":"06","month":"06","article_processing_charge":"No","citation":{"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","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","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.","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","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).","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."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"date_published":"2019-06-06T00:00:00Z","doi":"10.5061/dryad.0q2h6tk"},{"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.","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","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","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.","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.","short":"H. Sachdeva, (2019)."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8tp0900","open_access":"1"}],"oa":1,"date_published":"2019-07-16T00:00:00Z","doi":"10.5061/dryad.8tp0900","article_processing_charge":"No","day":"16","month":"07","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","_id":"9802","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","oa_version":"Published Version","date_created":"2021-08-06T11:45:11Z","date_updated":"2023-08-29T06:43:57Z","related_material":{"record":[{"id":"6680","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","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."}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2019-07-17T00:00:00Z","citation":{"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.","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).","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.","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","ieee":"P. Pranav et al., “Unexpected topology of the temperature fluctuations in the cosmic microwave background,” Astronomy and Astrophysics, vol. 627. EDP Sciences, 2019.","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"},"publication":"Astronomy and Astrophysics","article_type":"original","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."}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":14420451,"creator":"dernst","access_level":"open_access","file_name":"2019_AstronomyAstrophysics_Pranav.pdf","checksum":"83b9209ed9eefbdcefd89019c5a97805","date_updated":"2020-07-14T12:47:39Z","date_created":"2019-08-05T08:08:59Z","relation":"main_file","file_id":"6766"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6756","intvolume":" 627","ddc":["520","530"],"title":"Unexpected topology of the temperature fluctuations in the cosmic microwave background","status":"public","publication_identifier":{"eissn":["14320746"],"issn":["00046361"]},"month":"07","doi":"10.1051/0004-6361/201834916","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000475839300003"],"arxiv":["1812.07678"]},"oa":1,"project":[{"name":"Toward Computational Information Topology","grant_number":"M62909-18-1-2038","_id":"265683E4-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:39Z","article_number":"A163","author":[{"first_name":"Pratyush","last_name":"Pranav","full_name":"Pranav, Pratyush"},{"full_name":"Adler, Robert J.","last_name":"Adler","first_name":"Robert J."},{"full_name":"Buchert, Thomas","first_name":"Thomas","last_name":"Buchert"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Bernard J.T.","last_name":"Jones","full_name":"Jones, Bernard J.T."},{"first_name":"Armin","last_name":"Schwartzman","full_name":"Schwartzman, Armin"},{"first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"},{"last_name":"Van De Weygaert","first_name":"Rien","full_name":"Van De Weygaert, Rien"}],"volume":627,"date_created":"2019-08-04T21:59:18Z","date_updated":"2023-08-29T07:01:48Z","year":"2019","department":[{"_id":"HeEd"}],"publisher":"EDP Sciences","publication_status":"published"},{"date_published":"2019-07-01T00:00:00Z","publication":"Genome biology and evolution","citation":{"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.","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.","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","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.","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.","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."},"article_type":"original","page":"1909-1922","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6765","date_created":"2019-08-05T07:55:02Z","date_updated":"2020-07-14T12:47:39Z","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_name":"2019_GenomeBiology_Picard.pdf","access_level":"open_access","file_size":580205,"content_type":"application/pdf","creator":"dernst"}],"_id":"6755","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","ddc":["570"],"intvolume":" 11","abstract":[{"lang":"eng","text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region."}],"issue":"7","type":"journal_article","doi":"10.1093/gbe/evz133","acknowledged_ssus":[{"_id":"CampIT"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["1759-6653"]},"author":[{"last_name":"Picard","first_name":"Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"first_name":"David","last_name":"Roquis","full_name":"Roquis, David"},{"first_name":"Ingo","last_name":"Bulla","full_name":"Bulla, Ingo"},{"full_name":"Augusto, Ronaldo C.","first_name":"Ronaldo C.","last_name":"Augusto"},{"first_name":"Nathalie","last_name":"Arancibia","full_name":"Arancibia, Nathalie"},{"full_name":"Grunau, Christoph","last_name":"Grunau","first_name":"Christoph"},{"full_name":"Boissier, Jérôme","first_name":"Jérôme","last_name":"Boissier"},{"last_name":"Cosseau","first_name":"Céline","full_name":"Cosseau, Céline"}],"date_created":"2019-08-04T21:59:18Z","date_updated":"2023-08-29T06:53:58Z","volume":11,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Oxford Academic Press","file_date_updated":"2020-07-14T12:47:39Z"},{"issue":"4","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."}],"type":"journal_article","oa_version":"Preprint","_id":"6752","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 66","status":"public","title":"Infinite-duration bidding games","article_processing_charge":"No","day":"16","scopus_import":"1","date_published":"2019-07-16T00:00:00Z","citation":{"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","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019.","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295","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.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295."},"publication":"Journal of the ACM","article_number":"31","related_material":{"record":[{"id":"950","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"}],"volume":66,"date_created":"2019-08-04T21:59:16Z","date_updated":"2023-08-29T07:02:13Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","publication_identifier":{"eissn":["1557735X"],"issn":["00045411"]},"month":"07","doi":"10.1145/3340295","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01433"}],"external_id":{"isi":["000487714900008"],"arxiv":["1705.01433"]},"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"isi":1,"quality_controlled":"1"},{"author":[{"first_name":"Heather S.","last_name":"Davies","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","first_name":"Natalia S."},{"last_name":"El Amri","first_name":"Nouha","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","first_name":"Liliane","last_name":"Coche-Guérente"},{"full_name":"Verdier, Claude","last_name":"Verdier","first_name":"Claude"},{"full_name":"Bureau, Lionel","first_name":"Lionel","last_name":"Bureau"},{"full_name":"Richter, Ralf P.","first_name":"Ralf P.","last_name":"Richter"},{"first_name":"Delphine","last_name":"Débarre","full_name":"Débarre, Delphine"}],"volume":11076,"date_updated":"2023-08-29T06:54:38Z","date_created":"2019-11-12T15:10:18Z","year":"2019","publisher":"SPIE","department":[{"_id":"MaLo"}],"publication_status":"published","article_number":"110760V","doi":"10.1117/12.2527058","conference":{"end_date":"2019-06-27","location":"Munich, Germany","start_date":"2019-06-26","name":"European Conferences on Biomedical Optics"},"language":[{"iso":"eng"}],"external_id":{"isi":["000535353000023"]},"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf"}],"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1605-7422"],"isbn":["9781510628458"]},"month":"07","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7010","intvolume":" 11076","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","status":"public","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."}],"type":"conference","date_published":"2019-07-22T00:00:00Z","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"Advances in Microscopic Imaging II","article_processing_charge":"No","day":"22","scopus_import":"1"},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6803","checksum":"7ded4721b41c2a0fc66a1c634540416a","date_created":"2019-08-12T12:27:26Z","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access","file_name":"2019_PlosComputBiology_Ruess.pdf","content_type":"application/pdf","file_size":2200003,"creator":"dernst"}],"_id":"6784","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","intvolume":" 15","abstract":[{"lang":"eng","text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems."}],"issue":"7","type":"journal_article","date_published":"2019-07-02T00:00:00Z","publication":"PLoS Computational Biology","citation":{"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.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).","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.","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","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","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"},"article_type":"original","day":"02","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9786"}]},"date_created":"2019-08-11T21:59:19Z","date_updated":"2023-08-29T07:10:06Z","volume":15,"year":"2019","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:47:40Z","article_number":"e1007168","doi":"10.1371/journal.pcbi.1007168","language":[{"iso":"eng"}],"external_id":{"isi":["000481577700032"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"}],"month":"07","publication_identifier":{"eissn":["1553-7358"]}}]