[{"intvolume":"        24","abstract":[{"text":"The emergence and radiation of multicellular land plants was driven by crucial innovations to their body plans [1]. The directional transport of the phytohormone auxin represents a key, plant-specific mechanism for polarization and patterning in complex seed plants [2-5]. Here, we show that already in the early diverging land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport by PIN transporters is operational and diversified into ER-localized and plasma membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates crucial developmental transitions in tip-growing filaments and waves of polarization and differentiation in leaf-like structures. Plasma membrane PIN proteins localize in a polar manner to the tips of moss filaments, revealing an unexpected relation between polarization mechanisms in moss tip-growing cells and multicellular tissues of seed plants. Our results trace the origins of polarization and auxin-mediated patterning mechanisms and highlight the crucial role of polarized auxin transport during the evolution of multicellular land plants.","lang":"eng"}],"date_published":"2014-12-01T00:00:00Z","scopus_import":1,"publication":"Current Biology","day":"01","date_updated":"2021-01-12T06:54:34Z","volume":24,"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Landberg, Katarina","last_name":"Landberg","first_name":"Katarina"},{"first_name":"Mattias","full_name":"Thelander, Mattias","last_name":"Thelander"},{"last_name":"Medvecka","full_name":"Medvecka, Eva","first_name":"Eva"},{"full_name":"Pederson, Eric","last_name":"Pederson","first_name":"Eric"},{"last_name":"Feraru","full_name":"Feraru, Elena","first_name":"Elena"},{"first_name":"Endymion","last_name":"Cooper","full_name":"Cooper, Endymion"},{"last_name":"Karimi","full_name":"Karimi, Mansour","first_name":"Mansour"},{"first_name":"Charles","full_name":"Delwiche, Charles","last_name":"Delwiche"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"first_name":"Eva","last_name":"Sundberg","full_name":"Sundberg, Eva"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"doi":"10.1016/j.cub.2014.09.056","type":"journal_article","oa_version":"None","citation":{"ista":"Viaene T, Landberg K, Thelander M, Medvecka E, Pederson E, Feraru E, Cooper E, Karimi M, Delwiche C, Ljung K, Geisler M, Sundberg E, Friml J. 2014. Directional auxin transport mechanisms in early diverging land plants. Current Biology. 24(23), 2786–2791.","short":"T. Viaene, K. Landberg, M. Thelander, E. Medvecka, E. Pederson, E. Feraru, E. Cooper, M. Karimi, C. Delwiche, K. Ljung, M. Geisler, E. Sundberg, J. Friml, Current Biology 24 (2014) 2786–2791.","ieee":"T. Viaene <i>et al.</i>, “Directional auxin transport mechanisms in early diverging land plants,” <i>Current Biology</i>, vol. 24, no. 23. Cell Press, pp. 2786–2791, 2014.","ama":"Viaene T, Landberg K, Thelander M, et al. Directional auxin transport mechanisms in early diverging land plants. <i>Current Biology</i>. 2014;24(23):2786-2791. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">10.1016/j.cub.2014.09.056</a>","chicago":"Viaene, Tom, Katarina Landberg, Mattias Thelander, Eva Medvecka, Eric Pederson, Elena Feraru, Endymion Cooper, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">https://doi.org/10.1016/j.cub.2014.09.056</a>.","apa":"Viaene, T., Landberg, K., Thelander, M., Medvecka, E., Pederson, E., Feraru, E., … Friml, J. (2014). Directional auxin transport mechanisms in early diverging land plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">https://doi.org/10.1016/j.cub.2014.09.056</a>","mla":"Viaene, Tom, et al. “Directional Auxin Transport Mechanisms in Early Diverging Land Plants.” <i>Current Biology</i>, vol. 24, no. 23, Cell Press, 2014, pp. 2786–91, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.09.056\">10.1016/j.cub.2014.09.056</a>."},"date_created":"2018-12-11T11:55:06Z","publication_status":"published","quality_controlled":"1","issue":"23","_id":"1994","publisher":"Cell Press","department":[{"_id":"JiFr"}],"title":"Directional auxin transport mechanisms in early diverging land plants","publist_id":"5088","page":"2786 - 2791","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"month":"12","year":"2014"},{"quality_controlled":"1","citation":{"mla":"Fratini, Filippo, et al. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” <i>Physical Review Letters</i>, vol. 113, no. 24, 243601, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">10.1103/PhysRevLett.113.243601</a>.","apa":"Fratini, F., Mascarenhas, E., Safari, L., Poizat, J., Valente, D., Auffèves, A., … Santos, M. (2014). Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">https://doi.org/10.1103/PhysRevLett.113.243601</a>","chicago":"Fratini, Filippo, Eduardo Mascarenhas, Laleh Safari, Jean Poizat, Daniel Valente, Alexia Auffèves, Dario Gerace, and Marcelo Santos. “Fabry-Perot Interferometer with Quantum Mirrors: Nonlinear Light Transport and Rectification.” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">https://doi.org/10.1103/PhysRevLett.113.243601</a>.","ama":"Fratini F, Mascarenhas E, Safari L, et al. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. <i>Physical Review Letters</i>. 2014;113(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.243601\">10.1103/PhysRevLett.113.243601</a>","ista":"Fratini F, Mascarenhas E, Safari L, Poizat J, Valente D, Auffèves A, Gerace D, Santos M. 2014. Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification. Physical Review Letters. 113(24), 243601.","ieee":"F. Fratini <i>et al.</i>, “Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification,” <i>Physical Review Letters</i>, vol. 113, no. 24. American Physical Society, 2014.","short":"F. Fratini, E. Mascarenhas, L. Safari, J. Poizat, D. Valente, A. Auffèves, D. Gerace, M. Santos, Physical Review Letters 113 (2014)."},"date_created":"2018-12-11T11:55:06Z","article_number":"243601","oa":1,"title":"Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification","publist_id":"5085","date_published":"2014-12-08T00:00:00Z","intvolume":"       113","volume":113,"publication":"Physical Review Letters","day":"08","ec_funded":1,"doi":"10.1103/PhysRevLett.113.243601","issue":"24","_id":"1995","publication_status":"published","type":"journal_article","oa_version":"Submitted Version","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2014","month":"12","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"Optical transport represents a natural route towards fast communications, and it is currently used in large scale data transfer. The progressive miniaturization of devices for information processing calls for the microscopic tailoring of light transport and confinement at length scales appropriate for upcoming technologies. With this goal in mind, we present a theoretical analysis of a one-dimensional Fabry-Perot interferometer built with two highly saturable nonlinear mirrors: a pair of two-level systems. Our approach captures nonlinear and nonreciprocal effects of light transport that were not reported previously. Remarkably, we show that such an elementary device can operate as a microscopic integrated optical rectifier."}],"main_file_link":[{"url":"http://arxiv.org/abs/1410.5972","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:34Z","author":[{"last_name":"Fratini","full_name":"Fratini, Filippo","first_name":"Filippo"},{"first_name":"Eduardo","full_name":"Mascarenhas, Eduardo","last_name":"Mascarenhas"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"full_name":"Poizat, Jean","last_name":"Poizat","first_name":"Jean"},{"full_name":"Valente, Daniel","last_name":"Valente","first_name":"Daniel"},{"last_name":"Auffèves","full_name":"Auffèves, Alexia","first_name":"Alexia"},{"first_name":"Dario","full_name":"Gerace, Dario","last_name":"Gerace"},{"first_name":"Marcelo","last_name":"Santos","full_name":"Santos, Marcelo"}],"status":"public"},{"abstract":[{"lang":"eng","text":"Auxin polar transport, local maxima, and gradients have become an importantmodel system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels."}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273421/","open_access":"1"}],"intvolume":"       111","scopus_import":1,"date_published":"2014-12-16T00:00:00Z","volume":111,"date_updated":"2021-01-12T06:54:35Z","day":"16","publication":"PNAS","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Hazak, Ora","last_name":"Hazak","first_name":"Ora"},{"full_name":"Obolski, Uri","last_name":"Obolski","first_name":"Uri"},{"last_name":"Prat","full_name":"Prat, Tomas","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lilach","full_name":"Hadany, Lilach","last_name":"Hadany"},{"full_name":"Yalovsky, Shaul","last_name":"Yalovsky","first_name":"Shaul"}],"status":"public","doi":"10.1073/pnas.1413918111","citation":{"ieee":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, and S. Yalovsky, “Bimodal regulation of ICR1 levels generates self-organizing auxin distribution,” <i>PNAS</i>, vol. 111, no. 50. National Academy of Sciences, pp. E5471–E5479, 2014.","ista":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. 2014. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. PNAS. 111(50), E5471–E5479.","short":"O. Hazak, U. Obolski, T. Prat, J. Friml, L. Hadany, S. Yalovsky, PNAS 111 (2014) E5471–E5479.","ama":"Hazak O, Obolski U, Prat T, Friml J, Hadany L, Yalovsky S. Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. <i>PNAS</i>. 2014;111(50):E5471-E5479. doi:<a href=\"https://doi.org/10.1073/pnas.1413918111\">10.1073/pnas.1413918111</a>","chicago":"Hazak, Ora, Uri Obolski, Tomas Prat, Jiří Friml, Lilach Hadany, and Shaul Yalovsky. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1413918111\">https://doi.org/10.1073/pnas.1413918111</a>.","apa":"Hazak, O., Obolski, U., Prat, T., Friml, J., Hadany, L., &#38; Yalovsky, S. (2014). Bimodal regulation of ICR1 levels generates self-organizing auxin distribution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1413918111\">https://doi.org/10.1073/pnas.1413918111</a>","mla":"Hazak, Ora, et al. “Bimodal Regulation of ICR1 Levels Generates Self-Organizing Auxin Distribution.” <i>PNAS</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. E5471–79, doi:<a href=\"https://doi.org/10.1073/pnas.1413918111\">10.1073/pnas.1413918111</a>."},"date_created":"2018-12-11T11:55:07Z","oa_version":"Submitted Version","type":"journal_article","_id":"1996","issue":"50","quality_controlled":"1","publication_status":"published","publisher":"National Academy of Sciences","oa":1,"title":"Bimodal regulation of ICR1 levels generates self-organizing auxin distribution","department":[{"_id":"JiFr"}],"month":"12","year":"2014","page":"E5471 - E5479","publist_id":"5083"},{"department":[{"_id":"SyCr"}],"title":"Individual and social immunisation in insects","publist_id":"5081","page":"471 - 482","month":"10","year":"2014","publication_status":"published","quality_controlled":"1","issue":"10","_id":"1998","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:55:07Z","citation":{"chicago":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” <i>Trends in Immunology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.it.2014.08.005\">https://doi.org/10.1016/j.it.2014.08.005</a>.","apa":"El Masri, L., &#38; Cremer, S. (2014). Individual and social immunisation in insects. <i>Trends in Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.it.2014.08.005\">https://doi.org/10.1016/j.it.2014.08.005</a>","mla":"El Masri, Leila, and Sylvia Cremer. “Individual and Social Immunisation in Insects.” <i>Trends in Immunology</i>, vol. 35, no. 10, Elsevier, 2014, pp. 471–82, doi:<a href=\"https://doi.org/10.1016/j.it.2014.08.005\">10.1016/j.it.2014.08.005</a>.","ista":"El Masri L, Cremer S. 2014. Individual and social immunisation in insects. Trends in Immunology. 35(10), 471–482.","short":"L. El Masri, S. Cremer, Trends in Immunology 35 (2014) 471–482.","ieee":"L. El Masri and S. Cremer, “Individual and social immunisation in insects,” <i>Trends in Immunology</i>, vol. 35, no. 10. Elsevier, pp. 471–482, 2014.","ama":"El Masri L, Cremer S. Individual and social immunisation in insects. <i>Trends in Immunology</i>. 2014;35(10):471-482. doi:<a href=\"https://doi.org/10.1016/j.it.2014.08.005\">10.1016/j.it.2014.08.005</a>"},"publisher":"Elsevier","status":"public","author":[{"last_name":"El Masri","full_name":"El Masri, Leila","id":"349A6E66-F248-11E8-B48F-1D18A9856A87","first_name":"Leila"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"doi":"10.1016/j.it.2014.08.005","date_published":"2014-10-01T00:00:00Z","scopus_import":1,"intvolume":"        35","abstract":[{"text":"Immune systems are able to protect the body against secondary infection with the same parasite. In insect colonies, this protection is not restricted to the level of the individual organism, but also occurs at the societal level. Here, we review recent evidence for and insights into the mechanisms underlying individual and social immunisation in insects. We disentangle general immune-protective effects from specific immune memory (priming), and examine immunisation in the context of the lifetime of an individual and that of a colony, and of transgenerational immunisation that benefits offspring. When appropriate, we discuss parallels with disease defence strategies in human societies. We propose that recurrent parasitic threats have shaped the evolution of both the individual immune systems and colony-level social immunity in insects.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Trends in Immunology","day":"01","acknowledgement":"This work was funded by an ERC Starting Grant by the European Research Council (to S.C.) and the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission; to L.M.).\r\nWe thank Christopher D. Pull, Sophie A.O. Armitage, Hinrich Schulenburg, Line V. Ugelvig, Matthias Konrad, Matthias Fürst, Miriam Stock, Barbara Casillas-Perez and three anonymous referees for comments on the manuscript. ","date_updated":"2021-01-12T06:54:35Z","volume":35},{"type":"journal_article","oa_version":"None","publication_status":"published","issue":"1","_id":"1999","publisher":"Elsevier","department":[{"_id":"SyCr"}],"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"}],"year":"2014","month":"11","related_material":{"record":[{"id":"6383","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6435"}]},"abstract":[{"lang":"eng","text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses."}],"scopus_import":1,"date_updated":"2024-03-25T23:30:04Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:55:08Z","citation":{"ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. 2014;5(1):1-15. doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1. Elsevier, pp. 1–15, 2014.","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>.","apa":"Stroeymeyt, N., Casillas Perez, B. E., &#38; Cremer, S. (2014). Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>","chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>."},"quality_controlled":"1","title":"Organisational immunity in social insects","publist_id":"5080","page":"1 - 15","intvolume":"         5","date_published":"2014-11-01T00:00:00Z","day":"01","publication":"Current Opinion in Insect Science","volume":5,"ec_funded":1,"doi":"10.1016/j.cois.2014.09.001"},{"title":"Bacterial responses to antibiotics and their combinations","page":"545 - 557","publist_id":"5076","quality_controlled":"1","citation":{"apa":"Mitosch, K., &#38; Bollenbach, M. T. (2014). Bacterial responses to antibiotics and their combinations. <i>Environmental Microbiology Reports</i>. Wiley. <a href=\"https://doi.org/10.1111/1758-2229.12190\">https://doi.org/10.1111/1758-2229.12190</a>","chicago":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” <i>Environmental Microbiology Reports</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/1758-2229.12190\">https://doi.org/10.1111/1758-2229.12190</a>.","mla":"Mitosch, Karin, and Mark Tobias Bollenbach. “Bacterial Responses to Antibiotics and Their Combinations.” <i>Environmental Microbiology Reports</i>, vol. 6, no. 6, Wiley, 2014, pp. 545–57, doi:<a href=\"https://doi.org/10.1111/1758-2229.12190\">10.1111/1758-2229.12190</a>.","ama":"Mitosch K, Bollenbach MT. Bacterial responses to antibiotics and their combinations. <i>Environmental Microbiology Reports</i>. 2014;6(6):545-557. doi:<a href=\"https://doi.org/10.1111/1758-2229.12190\">10.1111/1758-2229.12190</a>","short":"K. Mitosch, M.T. Bollenbach, Environmental Microbiology Reports 6 (2014) 545–557.","ista":"Mitosch K, Bollenbach MT. 2014. Bacterial responses to antibiotics and their combinations. Environmental Microbiology Reports. 6(6), 545–557.","ieee":"K. Mitosch and M. T. Bollenbach, “Bacterial responses to antibiotics and their combinations,” <i>Environmental Microbiology Reports</i>, vol. 6, no. 6. Wiley, pp. 545–557, 2014."},"date_created":"2018-12-11T11:55:08Z","ec_funded":1,"doi":"10.1111/1758-2229.12190","date_published":"2014-06-22T00:00:00Z","intvolume":"         6","publication":"Environmental Microbiology Reports","day":"22","volume":6,"department":[{"_id":"ToBo"}],"project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507"}],"year":"2014","month":"06","publication_status":"published","issue":"6","_id":"2001","oa_version":"None","type":"journal_article","publisher":"Wiley","status":"public","author":[{"full_name":"Mitosch, Karin","last_name":"Mitosch","first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"818"}]},"abstract":[{"lang":"eng","text":"Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T12:00:25Z"},{"volume":9,"publication":"PLoS One","day":"19","intvolume":"         9","has_accepted_license":"1","date_published":"2014-11-19T00:00:00Z","doi":"10.1371/journal.pone.0113124","file_date_updated":"2020-07-14T12:45:24Z","ec_funded":1,"tmp":{"short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png"},"article_number":"0113124","oa":1,"citation":{"short":"S. Kim, PLoS One 9 (2014).","ista":"Kim S. 2014. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. PLoS One. 9(11), 0113124.","ieee":"S. Kim, “Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus,” <i>PLoS One</i>, vol. 9, no. 11. Public Library of Science, 2014.","ama":"Kim S. Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. <i>PLoS One</i>. 2014;9(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0113124\">10.1371/journal.pone.0113124</a>","chicago":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0113124\">https://doi.org/10.1371/journal.pone.0113124</a>.","apa":"Kim, S. (2014). Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0113124\">https://doi.org/10.1371/journal.pone.0113124</a>","mla":"Kim, Sooyun. “Action Potential Modulation in CA1 Pyramidal Neuron Axons Facilitates OLM Interneuron Activation in Recurrent Inhibitory Microcircuits of Rat Hippocampus.” <i>PLoS One</i>, vol. 9, no. 11, 0113124, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0113124\">10.1371/journal.pone.0113124</a>."},"date_created":"2018-12-11T11:55:09Z","quality_controlled":"1","publist_id":"5074","title":"Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus","date_updated":"2021-01-12T06:54:39Z","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus play a key role in feedback inhibition and in the control of network activity. However, how these cells are efficiently activated in the network remains unclear. To address this question, I performed recordings from CA1 pyramidal neuron axons, the presynaptic fibers that provide feedback innervation of these interneurons. Two forms of axonal action potential (AP) modulation were identified. First, repetitive stimulation resulted in activity-dependent AP broadening. Broadening showed fast onset, with marked changes in AP shape following a single AP. Second, tonic depolarization in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced broadening summated with activity-dependent broadening. Outsideout patch recordings from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive, inactivating K+ channels, suggesting that K+ channel inactivation mechanistically contributes to AP broadening. To examine the functional consequences of axonal AP modulation for synaptic transmission, I performed paired recordings between synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation during both repetitive stimulation and tonic depolarization of the presynaptic neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they were mediated by K+ channel inactivation. Therefore, axonal AP modulation can greatly facilitate the activation of O-LM interneurons. In conclusion, modulation of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons in recurrent inhibitory microcircuits.","lang":"eng"}],"scopus_import":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","author":[{"last_name":"Kim","full_name":"Kim, Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","first_name":"Sooyun"}],"status":"public","pubrep_id":"434","publisher":"Public Library of Science","ddc":["570"],"oa_version":"Published Version","file":[{"file_id":"5107","creator":"system","relation":"main_file","file_name":"IST-2016-434-v1+1_journal.pone.0113124.pdf","checksum":"85e4f4ea144f827272aaf376b2830564","file_size":5179993,"date_created":"2018-12-12T10:14:52Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:24Z"}],"type":"journal_article","issue":"11","_id":"2002","publication_status":"published","year":"2014","month":"11","project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548"}],"department":[{"_id":"PeJo"}]},{"day":"02","publication":"Neuron","date_updated":"2021-01-12T06:54:39Z","volume":83,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":"        83","abstract":[{"text":"Learning can be facilitated by previous knowledge when it is organized into relational representations forming schemas. In this issue of Neuron, McKenzie et al. (2014) demonstrate that the hippocampus rapidly forms interrelated, hierarchical memory representations to support schema-based learning.","lang":"eng"}],"date_published":"2014-07-02T00:00:00Z","scopus_import":1,"doi":"10.1016/j.neuron.2014.06.013","status":"public","author":[{"last_name":"O'Neill","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"publisher":"Elsevier","oa_version":"None","type":"journal_article","citation":{"chicago":"O’Neill, Joseph, and Jozsef L Csicsvari. “Learning by Example in the Hippocampus.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">https://doi.org/10.1016/j.neuron.2014.06.013</a>.","apa":"O’Neill, J., &#38; Csicsvari, J. L. (2014). Learning by example in the hippocampus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">https://doi.org/10.1016/j.neuron.2014.06.013</a>","mla":"O’Neill, Joseph, and Jozsef L. Csicsvari. “Learning by Example in the Hippocampus.” <i>Neuron</i>, vol. 83, no. 1, Elsevier, 2014, pp. 8–10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">10.1016/j.neuron.2014.06.013</a>.","ista":"O’Neill J, Csicsvari JL. 2014. Learning by example in the hippocampus. Neuron. 83(1), 8–10.","ieee":"J. O’Neill and J. L. Csicsvari, “Learning by example in the hippocampus,” <i>Neuron</i>, vol. 83, no. 1. Elsevier, pp. 8–10, 2014.","short":"J. O’Neill, J.L. Csicsvari, Neuron 83 (2014) 8–10.","ama":"O’Neill J, Csicsvari JL. Learning by example in the hippocampus. <i>Neuron</i>. 2014;83(1):8-10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.06.013\">10.1016/j.neuron.2014.06.013</a>"},"date_created":"2018-12-11T11:55:09Z","quality_controlled":"1","publication_status":"published","_id":"2003","issue":"1","page":"8 - 10","publist_id":"5073","month":"07","year":"2014","department":[{"_id":"JoCs"}],"title":"Learning by example in the hippocampus"},{"day":"14","publication":"PLoS One","volume":9,"intvolume":"         9","has_accepted_license":"1","date_published":"2014-11-14T00:00:00Z","doi":"10.1371/journal.pone.0111430","file_date_updated":"2020-07-14T12:45:24Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"oa":1,"article_number":"e111430","date_created":"2018-12-11T11:55:09Z","citation":{"apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H., Dinnyés, A., &#38; Kovács, K. (2014). Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430\">https://doi.org/10.1371/journal.pone.0111430</a>","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen Byrne, András Dinnyés, and Krisztián Kovács. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430\">https://doi.org/10.1371/journal.pone.0111430</a>.","mla":"Lovrics, Anna, et al. “Boolean Modelling Reveals New Regulatory Connections between Transcription Factors Orchestrating the Development of the Ventral Spinal Cord.” <i>PLoS One</i>, vol. 9, no. 11, e111430, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430\">10.1371/journal.pone.0111430</a>.","ama":"Lovrics A, Gao Y, Juhász B, et al. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. <i>PLoS One</i>. 2014;9(11). doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430\">10.1371/journal.pone.0111430</a>","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H. Byrne, A. Dinnyés, K. Kovács, PLoS One 9 (2014).","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne H, Dinnyés A, Kovács K. 2014. Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord. PLoS One. 9(11), e111430.","ieee":"A. Lovrics <i>et al.</i>, “Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord,” <i>PLoS One</i>, vol. 9, no. 11. Public Library of Science, 2014."},"quality_controlled":"1","publist_id":"5072","title":"Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord","date_updated":"2023-02-23T14:06:14Z","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","status":"public","id":"9722"}]},"abstract":[{"lang":"eng","text":"We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks."}],"scopus_import":1,"status":"public","author":[{"first_name":"Anna","full_name":"Lovrics, Anna","last_name":"Lovrics"},{"full_name":"Gao, Yu","last_name":"Gao","first_name":"Yu"},{"first_name":"Bianka","last_name":"Juhász","full_name":"Juhász, Bianka"},{"first_name":"István","last_name":"Bock","full_name":"Bock, István"},{"first_name":"Helen","last_name":"Byrne","full_name":"Byrne, Helen"},{"first_name":"András","full_name":"Dinnyés, András","last_name":"Dinnyés"},{"last_name":"Kovács","full_name":"Kovács, Krisztián","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Public Library of Science","pubrep_id":"435","oa_version":"Published Version","type":"journal_article","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:24Z","checksum":"a2289b843f7463eb1233f9ce45e6a943","file_size":829363,"date_created":"2018-12-12T10:10:58Z","file_name":"IST-2016-435-v1+1_journal.pone.0111430.pdf","creator":"system","file_id":"4850","relation":"main_file"}],"ddc":["570"],"publication_status":"published","issue":"11","_id":"2004","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"month":"11","year":"2014","department":[{"_id":"JoCs"}]},{"publisher":"Nature Publishing Group","date_created":"2018-12-11T11:55:09Z","citation":{"ama":"Dupret D, Csicsvari JL. Turning heads to remember places. <i>Nature Neuroscience</i>. 2014;17(5):643-644. doi:<a href=\"https://doi.org/10.1038/nn.3700\">10.1038/nn.3700</a>","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 17 (2014) 643–644.","ista":"Dupret D, Csicsvari JL. 2014. Turning heads to remember places. Nature Neuroscience. 17(5), 643–644.","ieee":"D. Dupret and J. L. Csicsvari, “Turning heads to remember places,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 643–644, 2014.","mla":"Dupret, David, and Jozsef L. Csicsvari. “Turning Heads to Remember Places.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 643–44, doi:<a href=\"https://doi.org/10.1038/nn.3700\">10.1038/nn.3700</a>.","apa":"Dupret, D., &#38; Csicsvari, J. L. (2014). Turning heads to remember places. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3700\">https://doi.org/10.1038/nn.3700</a>","chicago":"Dupret, David, and Jozsef L Csicsvari. “Turning Heads to Remember Places.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3700\">https://doi.org/10.1038/nn.3700</a>."},"oa_version":"None","type":"journal_article","_id":"2005","issue":"5","publication_status":"published","quality_controlled":"1","year":"2014","month":"04","publist_id":"5071","page":"643 - 644","title":"Turning heads to remember places","department":[{"_id":"JoCs"}],"date_updated":"2021-01-12T06:54:40Z","volume":17,"publication":"Nature Neuroscience","day":"25","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"By eliciting a natural exploratory behavior in rats, head scanning, a study reveals that hippocampal place cells form new, stable firing fields in those locations where the behavior has just occurred."}],"intvolume":"        17","date_published":"2014-04-25T00:00:00Z","scopus_import":1,"doi":"10.1038/nn.3700","author":[{"full_name":"Dupret, David","last_name":"Dupret","first_name":"David"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"status":"public"},{"main_file_link":[{"open_access":"1","url":"https://CRAN.R-project.org/package=gIPFrm "}],"abstract":[{"lang":"eng","text":"Maximum likelihood estimation under relational models, with or without the overall effect. For more information see the reference manual"}],"date_published":"2014-03-20T00:00:00Z","day":"20","date_updated":"2022-08-26T08:12:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"last_name":"Klimova","full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"first_name":"Tamás","full_name":"Rudas, Tamás","last_name":"Rudas"}],"article_processing_charge":"No","type":"research_data_reference","oa_version":"Published Version","citation":{"apa":"Klimova, A., &#38; Rudas, T. (2014). gIPFrm: Generalized iterative proportional fitting for relational models. The Comprehensive R Archive Network.","chicago":"Klimova, Anna, and Tamás Rudas. “GIPFrm: Generalized Iterative Proportional Fitting for Relational Models.” The Comprehensive R Archive Network, 2014.","mla":"Klimova, Anna, and Tamás Rudas. <i>GIPFrm: Generalized Iterative Proportional Fitting for Relational Models</i>. The Comprehensive R Archive Network, 2014.","ama":"Klimova A, Rudas T. gIPFrm: Generalized iterative proportional fitting for relational models. 2014.","short":"A. Klimova, T. Rudas, (2014).","ieee":"A. Klimova and T. Rudas, “gIPFrm: Generalized iterative proportional fitting for relational models.” The Comprehensive R Archive Network, 2014.","ista":"Klimova A, Rudas T. 2014. gIPFrm: Generalized iterative proportional fitting for relational models, The Comprehensive R Archive Network."},"date_created":"2018-12-11T11:55:10Z","_id":"2007","publisher":"The Comprehensive R Archive Network","oa":1,"department":[{"_id":"CaUh"}],"title":"gIPFrm: Generalized iterative proportional fitting for relational models","publist_id":"5069","month":"03","year":"2014"},{"doi":"10.1016/j.jbi.2014.01.008","author":[{"last_name":"Yu","full_name":"Yu, Fei","first_name":"Fei"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"},{"first_name":"Alexandra","full_name":"Slaković, Alexandra","last_name":"Slaković"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline"}],"status":"public","volume":50,"date_updated":"2021-01-12T06:54:42Z","publication":"Journal of Biomedical Informatics","acknowledgement":"This research was partially supported by NSF Awards EMSW21-RTG and BCS-0941518 to the Department of Statistics at Carnegie Mellon University, and by NSF Grant BCS-0941553 to the Department of Statistics at Pennsylvania State University. This work was also supported in part by the National Center for Research Resources, Grant UL1 RR033184, and is now at the National Center for Advancing Translational Sciences, Grant UL1 TR000127 to Pennsylvania State University. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NSF and NIH.","day":"01","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of “an attack” on GWAS data by Homer et al. (2008). Traditional statistical methods for confidentiality and privacy protection of statistical databases do not scale well to deal with GWAS data, especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach that provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, Uhler et al. (2013) proposed new methods to release aggregate GWAS data without compromising an individual’s privacy. We extend the methods developed in Uhler et al. (2013) for releasing differentially-private χ2χ2-statistics by allowing for arbitrary number of cases and controls, and for releasing differentially-private allelic test statistics. We also provide a new interpretation by assuming the controls’ data are known, which is a realistic assumption because some GWAS use publicly available data as controls. We assess the performance of the proposed methods through a risk-utility analysis on a real data set consisting of DNA samples collected by the Wellcome Trust Case Control Consortium and compare the methods with the differentially-private release mechanism proposed by Johnson and Shmatikov (2013).","lang":"eng"}],"intvolume":"        50","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.5193"}],"scopus_import":1,"date_published":"2014-08-01T00:00:00Z","month":"08","year":"2014","publist_id":"5065","page":"133 - 141","title":"Scalable privacy-preserving data sharing methodology for genome-wide association studies","department":[{"_id":"CaUh"}],"publisher":"Elsevier","oa":1,"date_created":"2018-12-11T11:55:12Z","citation":{"mla":"Yu, Fei, et al. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” <i>Journal of Biomedical Informatics</i>, vol. 50, Elsevier, 2014, pp. 133–41, doi:<a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">10.1016/j.jbi.2014.01.008</a>.","apa":"Yu, F., Fienberg, S., Slaković, A., &#38; Uhler, C. (2014). Scalable privacy-preserving data sharing methodology for genome-wide association studies. <i>Journal of Biomedical Informatics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">https://doi.org/10.1016/j.jbi.2014.01.008</a>","chicago":"Yu, Fei, Stephen Fienberg, Alexandra Slaković, and Caroline Uhler. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.” <i>Journal of Biomedical Informatics</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">https://doi.org/10.1016/j.jbi.2014.01.008</a>.","ama":"Yu F, Fienberg S, Slaković A, Uhler C. Scalable privacy-preserving data sharing methodology for genome-wide association studies. <i>Journal of Biomedical Informatics</i>. 2014;50:133-141. doi:<a href=\"https://doi.org/10.1016/j.jbi.2014.01.008\">10.1016/j.jbi.2014.01.008</a>","ieee":"F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving data sharing methodology for genome-wide association studies,” <i>Journal of Biomedical Informatics</i>, vol. 50. Elsevier, pp. 133–141, 2014.","ista":"Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics. 50, 133–141.","short":"F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics 50 (2014) 133–141."},"oa_version":"Submitted Version","type":"journal_article","_id":"2011","quality_controlled":"1","publication_status":"published"},{"title":"Sphere packing with limited overlap","department":[{"_id":"HeEd"},{"_id":"CaUh"}],"month":"01","year":"2014","publist_id":"5064","citation":{"apa":"Iglesias Ham, M., Kerber, M., &#38; Uhler, C. (n.d.). Sphere packing with limited overlap. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1401.0468\">https://doi.org/10.48550/arXiv.1401.0468</a>","chicago":"Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing with Limited Overlap.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1401.0468\">https://doi.org/10.48550/arXiv.1401.0468</a>.","mla":"Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” <i>ArXiv</i>, 1401.0468, doi:<a href=\"https://doi.org/10.48550/arXiv.1401.0468\">10.48550/arXiv.1401.0468</a>.","ama":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1401.0468\">10.48550/arXiv.1401.0468</a>","ista":"Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv, 1401.0468.","short":"M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).","ieee":"M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,” <i>arXiv</i>. ."},"date_created":"2018-12-11T11:55:12Z","type":"preprint","oa_version":"Submitted Version","_id":"2012","arxiv":1,"external_id":{"arxiv":["1401.0468"]},"publication_status":"submitted","article_number":"1401.0468","oa":1,"author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"},{"orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"}],"article_processing_charge":"No","status":"public","doi":"10.48550/arXiv.1401.0468","abstract":[{"text":"The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://cccg.ca/proceedings/2014/papers/paper23.pdf"}],"date_published":"2014-01-01T00:00:00Z","date_updated":"2023-10-18T08:06:45Z","acknowledgement":"We thank Herbert Edelsbrunner for his valuable discussions and ideas on the topic of this paper.  The second author has been supported by the Max Planck Center for Visual Computing and Communication","publication":"arXiv","day":"01","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2014-10-10T00:00:00Z","intvolume":"        14","day":"10","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020).","publication":"Foundations of Computational Mathematics","volume":14,"doi":"10.1007/s10208-014-9205-0","quality_controlled":"1","date_created":"2018-12-11T11:55:12Z","citation":{"mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” <i>Foundations of Computational Mathematics</i>, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:<a href=\"https://doi.org/10.1007/s10208-014-9205-0\">10.1007/s10208-014-9205-0</a>.","apa":"Lin, S., Uhler, C., Sturmfels, B., &#38; Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9205-0\">https://doi.org/10.1007/s10208-014-9205-0</a>","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” <i>Foundations of Computational Mathematics</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10208-014-9205-0\">https://doi.org/10.1007/s10208-014-9205-0</a>.","ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. <i>Foundations of Computational Mathematics</i>. 2014;14(5):1079-1116. doi:<a href=\"https://doi.org/10.1007/s10208-014-9205-0\">10.1007/s10208-014-9205-0</a>","ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” <i>Foundations of Computational Mathematics</i>, vol. 14, no. 5. Springer, pp. 1079–1116, 2014."},"oa":1,"title":"Hypersurfaces and their singularities in partial correlation testing","publist_id":"5063","page":"1079 - 1116","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0285"}],"abstract":[{"text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:54:43Z","status":"public","author":[{"last_name":"Lin","full_name":"Lin, Shaowei","first_name":"Shaowei"},{"orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sturmfels","full_name":"Sturmfels, Bernd","first_name":"Bernd"},{"last_name":"Bühlmann","full_name":"Bühlmann, Peter","first_name":"Peter"}],"publication_status":"published","issue":"5","_id":"2013","oa_version":"Submitted Version","type":"journal_article","publisher":"Springer","department":[{"_id":"CaUh"}],"year":"2014","month":"10"},{"title":"Netrin-G/NGL complexes encode functional synaptic diversification","page":"15779 - 15792","publist_id":"5054","quality_controlled":"1","date_created":"2018-12-11T11:55:14Z","citation":{"ieee":"H. Matsukawa <i>et al.</i>, “Netrin-G/NGL complexes encode functional synaptic diversification,” <i>Journal of Neuroscience</i>, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792.","ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. 2014;34(47):15779-15792. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">10.1523/JNEUROSCI.1141-14.2014</a>.","chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2014. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>.","apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1141-14.2014\">https://doi.org/10.1523/JNEUROSCI.1141-14.2014</a>"},"oa":1,"article_processing_charge":"No","file_date_updated":"2022-05-24T08:41:41Z","doi":"10.1523/JNEUROSCI.1141-14.2014","date_published":"2014-11-19T00:00:00Z","has_accepted_license":"1","intvolume":"        34","pmid":1,"volume":34,"day":"19","acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","publication":"Journal of Neuroscience","article_type":"original","department":[{"_id":"RySh"}],"year":"2014","month":"11","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"issue":"47","_id":"2018","publication_status":"published","external_id":{"pmid":["25411505"]},"type":"journal_article","oa_version":"Published Version","ddc":["570"],"file":[{"file_name":"2014_JournNeuroscience_Matsukawa.pdf","relation":"main_file","creator":"dernst","file_id":"11410","date_updated":"2022-05-24T08:41:41Z","content_type":"application/pdf","access_level":"open_access","date_created":"2022-05-24T08:41:41Z","checksum":"6913e9bc26e9fc1c0441a739a4199229","success":1,"file_size":3963728}],"publisher":"Society for Neuroscience","author":[{"last_name":"Matsukawa","full_name":"Matsukawa, Hiroshi","first_name":"Hiroshi"},{"first_name":"Sachiko","last_name":"Akiyoshi Nishimura","full_name":"Akiyoshi Nishimura, Sachiko"},{"last_name":"Zhang","full_name":"Zhang, Qi","first_name":"Qi"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"},{"full_name":"Yamaguchi, Kazuhiko","last_name":"Yamaguchi","first_name":"Kazuhiko"},{"full_name":"Goto, Hiromichi","last_name":"Goto","first_name":"Hiromichi"},{"first_name":"Kunio","last_name":"Yaguchi","full_name":"Yaguchi, Kunio"},{"full_name":"Hashikawa, Tsutomu","last_name":"Hashikawa","first_name":"Tsutomu"},{"full_name":"Sano, Chie","last_name":"Sano","first_name":"Chie"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Toshiaki","full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba"},{"first_name":"Shigeyoshi","full_name":"Itohara, Shigeyoshi","last_name":"Itohara"}],"status":"public","scopus_import":"1","abstract":[{"text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2022-05-24T08:54:54Z"},{"title":"Phase transition in the density of states of quantum spin glasses","page":"441 - 464","publist_id":"5053","quality_controlled":"1","citation":{"ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. 2014;17(3-4):441-464. doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>","ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464.","ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","apa":"Erdös, L., &#38; Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>","chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s11040-014-9164-3\">https://doi.org/10.1007/s11040-014-9164-3</a>.","mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:<a href=\"https://doi.org/10.1007/s11040-014-9164-3\">10.1007/s11040-014-9164-3</a>."},"date_created":"2018-12-11T11:55:15Z","oa":1,"ec_funded":1,"doi":"10.1007/s11040-014-9164-3","date_published":"2014-12-17T00:00:00Z","intvolume":"        17","publication":"Mathematical Physics, Analysis and Geometry","day":"17","volume":17,"department":[{"_id":"LaEr"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"year":"2014","month":"12","publication_status":"published","_id":"2019","issue":"3-4","oa_version":"Submitted Version","type":"journal_article","publisher":"Springer","status":"public","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","first_name":"Dominik J"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.1552"}],"abstract":[{"lang":"eng","text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory."}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:54:45Z"},{"publist_id":"5052","page":"8850 - 8855","month":"06","year":"2014","department":[{"_id":"SiHi"}],"title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","publisher":"National Academy of Sciences","quality_controlled":"1","publication_status":"published","issue":"24","_id":"2020","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:55:15Z","citation":{"ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. 2014;111(24):8850-8855. doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” <i>PNAS</i>, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855.","ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., &#38; Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>","chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1408233111\">https://doi.org/10.1073/pnas.1408233111</a>.","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” <i>PNAS</i>, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:<a href=\"https://doi.org/10.1073/pnas.1408233111\">10.1073/pnas.1408233111</a>."},"doi":"10.1073/pnas.1408233111","status":"public","author":[{"last_name":"Ali","full_name":"Ali, Shah","first_name":"Shah"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Saadat","full_name":"Saadat, Lily","first_name":"Lily"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"first_name":"Irving","full_name":"Weissman, Irving","last_name":"Weissman"},{"first_name":"Reza","last_name":"Ardehali","full_name":"Ardehali, Reza"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"PNAS","day":"17","volume":111,"date_updated":"2021-01-12T06:54:46Z","scopus_import":1,"date_published":"2014-06-17T00:00:00Z","intvolume":"       111","abstract":[{"text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis.","lang":"eng"}]},{"author":[{"last_name":"William","full_name":"William, Joo","first_name":"Joo"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"}],"status":"public","doi":"10.1126/science.1258996","abstract":[{"text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development.","lang":"eng"}],"intvolume":"       346","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"scopus_import":1,"date_published":"2014-10-31T00:00:00Z","date_updated":"2021-01-12T06:54:47Z","volume":346,"day":"31","publication":"Science","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","department":[{"_id":"SiHi"}],"year":"2014","month":"10","publist_id":"5051","page":"626 - 629","date_created":"2018-12-11T11:55:15Z","citation":{"chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>.","apa":"William, J., Hippenmeyer, S., &#38; Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1258996\">https://doi.org/10.1126/science.1258996</a>","mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” <i>Science</i>, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>.","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” <i>Science</i>, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. <i>Science</i>. 2014;346(6209):626-629. doi:<a href=\"https://doi.org/10.1126/science.1258996\">10.1126/science.1258996</a>"},"type":"journal_article","oa_version":"Submitted Version","issue":"6209","_id":"2021","publication_status":"published","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1},{"year":"2014","month":"11","project":[{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"}],"department":[{"_id":"SiHi"},{"_id":"Bio"}],"pubrep_id":"423","publisher":"Cell Press","_id":"2022","issue":"4","publication_status":"published","type":"journal_article","file":[{"relation":"main_file","creator":"system","file_id":"4709","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","date_created":"2018-12-12T10:08:47Z","file_size":4435787,"checksum":"6c5de8329bb2ffa71cba9fda750f14ce","date_updated":"2020-07-14T12:45:25Z","content_type":"application/pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["570"],"author":[{"first_name":"Peng","last_name":"Gao","full_name":"Gao, Peng"},{"last_name":"Postiglione","full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Teresa","full_name":"Krieger, Teresa","last_name":"Krieger"},{"full_name":"Hernandez, Luisirene","last_name":"Hernandez","first_name":"Luisirene"},{"last_name":"Wang","full_name":"Wang, Chao","first_name":"Chao"},{"last_name":"Han","full_name":"Han, Zhi","first_name":"Zhi"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","full_name":"Papusheva, Ekaterina","last_name":"Papusheva"},{"first_name":"Ryan","last_name":"Insolera","full_name":"Insolera, Ryan"},{"last_name":"Chugh","full_name":"Chugh, Kritika","first_name":"Kritika"},{"last_name":"Kodish","full_name":"Kodish, Oren","first_name":"Oren"},{"full_name":"Huang, Kun","last_name":"Huang","first_name":"Kun"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"last_name":"Shi","full_name":"Shi, Song","first_name":"Song"}],"status":"public","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:47Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program."}],"publist_id":"5050","page":"775 - 788","title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","oa":1,"quality_controlled":"1","citation":{"ieee":"P. Gao <i>et al.</i>, “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” <i>Cell</i>, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788.","short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788.","ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. 2014;159(4):775-788. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>.","apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">https://doi.org/10.1016/j.cell.2014.10.027</a>","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” <i>Cell</i>, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.10.027\">10.1016/j.cell.2014.10.027</a>."},"date_created":"2018-12-11T11:55:16Z","file_date_updated":"2020-07-14T12:45:25Z","doi":"10.1016/j.cell.2014.10.027","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":159,"day":"06","publication":"Cell","date_published":"2014-11-06T00:00:00Z","intvolume":"       159","has_accepted_license":"1"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"doi":"10.1002/ece3.1289","file_date_updated":"2020-07-14T12:45:25Z","intvolume":"         4","has_accepted_license":"1","date_published":"2014-11-27T00:00:00Z","day":"27","publication":"Ecology and Evolution","volume":4,"title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","page":"4589 - 4597","publist_id":"5049","date_created":"2018-12-11T11:55:16Z","citation":{"short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” <i>Ecology and Evolution</i>, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. 2014;4(24):4589-4597. doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>."},"quality_controlled":"1","oa":1,"status":"public","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1125"}]},"abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"scopus_import":1,"date_updated":"2023-09-07T11:55:53Z","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"year":"2014","month":"11","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:25Z","checksum":"9ab43db1b0fede7bfe560ed77e177b76","file_size":118813,"date_created":"2018-12-12T10:12:28Z","file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","creator":"system","file_id":"4946","relation":"main_file"}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article","publication_status":"published","issue":"24","_id":"2023","publisher":"Wiley-Blackwell","pubrep_id":"462"}]