[{"publist_id":"6903","doi":"10.1007/978-3-642-10631-6_95","publisher":"Springer","alternative_title":["LNCS"],"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Gilbert, Seth","last_name":"Gilbert","first_name":"Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"full_name":"Travers, Corentin","first_name":"Corentin","last_name":"Travers"}],"publication_status":"published","extern":"1","article_processing_charge":"No","_id":"752","acknowledgement":"Corentin Travers was supposrted in part by a Sam & Cecilia Neaman Fellowship","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. The complexity of set agreement in synchronous networks has also been a significant research challenge. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. In this paper, we analyze the complexity of set agreement in a "partially synchronous" setting, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone messagepassing system in which some fragments appear synchronous to some processes. We use this technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. We also present an asymptotically matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. By relating environments with differing degrees of synchrony, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of [12], and to re-derive the combinatorial topology lower bound of [13] in an algorithmic way.","lang":"eng"}],"day":"01","page":"943 - 953","title":"Of choices, failures and asynchrony: the many faces of set agreement","conference":{"name":"ISAAC: International Symposium on Algorithms and Computation"},"date_updated":"2023-02-23T13:10:05Z","status":"public","date_created":"2018-12-11T11:48:19Z","date_published":"2009-01-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., & Travers, C. (2009). Of choices, failures and asynchrony: the many faces of set agreement (Vol. 5878 LNCS, pp. 943–953). Presented at the ISAAC: International Symposium on Algorithms and Computation, Springer. https://doi.org/10.1007/978-3-642-10631-6_95","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. Of choices, failures and asynchrony: the many faces of set agreement. In: Vol 5878 LNCS. Springer; 2009:943-953. doi:10.1007/978-3-642-10631-6_95","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and C. Travers, “Of choices, failures and asynchrony: the many faces of set agreement,” presented at the ISAAC: International Symposium on Algorithms and Computation, 2009, vol. 5878 LNCS, pp. 943–953.","mla":"Alistarh, Dan-Adrian, et al. Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement. Vol. 5878 LNCS, Springer, 2009, pp. 943–53, doi:10.1007/978-3-642-10631-6_95.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, C. Travers, in:, Springer, 2009, pp. 943–953.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Travers C. 2009. Of choices, failures and asynchrony: the many faces of set agreement. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 5878 LNCS, 943–953.","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Corentin Travers. “Of Choices, Failures and Asynchrony: The Many Faces of Set Agreement,” 5878 LNCS:943–53. Springer, 2009. https://doi.org/10.1007/978-3-642-10631-6_95."},"oa_version":"None","year":"2009","volume":"5878 LNCS","month":"01","type":"conference"},{"date_updated":"2021-01-12T08:15:17Z","status":"public","date_published":"2009-04-01T00:00:00Z","date_created":"2020-04-30T11:01:57Z","issue":"4","day":"01","abstract":[{"lang":"eng","text":"This work demonstrates that environmental conditions experienced by individuals can shape their development and affect the stability of genetic associations. The implication of this observation is that the environmental response may influence the evolution of traits in the wild. Here, we examined how the genetic architecture of a suite of sexually dimorphic traits changed as a function of environmental conditions in an unmanaged population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, northwest Scotland. We examined the stability of phenotypic, genetic, and environmental (residual) covariance in males during the first year of life between horn length, body weight, and parasite load in environments of different quality. We then examined the same covariance structures across environments within and between the adult sexes. We found significant genotype-by-environment interactions for lamb male body weight and parasite load, leading to a change in the genetic correlation among environments. Horn length was genetically correlated with body weight in males but not females and the genetic correlation among traits within and between the sexes was dependent upon the environmental conditions experienced during adulthood. Genetic correlations were smaller in more favorable environmental conditions, suggesting that in good environments, loci are expressed that have sex-specific effects. The reduction in genetic correlation between the sexes may allow independent evolutionary trajectories for each sex. This study demonstrates that the genetic architecture of traits is not stable under temporally varying environments and highlights the fact that evolutionary processes may depend largely upon ecological conditions.\r\nENVIRONMENTAL heterogeneity has long been recognized as an important factor influencing the evolution of fitness-related traits in the wild (Roff 2002). The evolution of a trait depends upon the selection upon it, underlying genetic variation, and to a large degree the genetic relationships with other traits (Lynch and Walsh 1998). There is evidence that selection can vary considerably from year to year (Price et al. 1984; Robinson et al. 2008) and genetic variability in quantitative traits can change in response to environmental conditions (Hoffmann and Merilä 1999; Charmantier and Garant 2005). However, we know surprisingly little about the influence of environmental conditions on genetic correlations between traits in wild populations. Laboratory evidence suggests that the environment may influence genetic relationships between traits (Sgrò and Hoffmann 2004), but estimates obtained in a controlled or in an arbitrary range of conditions show a lack of concordance with those obtained in wild habitats (Conner et al. 2003). As a result, laboratory and environment-specific estimates of genetic correlations can make predictions for a trait's evolution, but these are valid only for the environment in which they were measured. Therefore, at present, it is difficult to generalize about the evolution of a trait that is expressed in populations that experience variable environmental conditions (Steppan et al. 2002).\r\nThe influence of changing environmental conditions on the G matrix (the matrix of additive genetic variance and covariances corresponding to a set of traits) has been the focus of theoretical quantitative genetic studies (e.g., Jones et al. 2003). There is evidence of genotype-by-environment interaction for many traits expressed in wild populations (Charmantier and Garant 2005) and thus we may also expect that associations between traits may depend upon the environmental conditions encountered by an individual. Genetic correlations among traits may arise from pleiotropy, where a given locus affects more than one trait (Cheverud 1988; Lynch and Walsh 1998), which may limit the potential for those traits to evolve independently. There has recently been much interest in assessing genetic correlations between the sexes (Rice and Chippindale 2001; Foerster et al. 2007; Poissant et al. 2008), but all of these predictions have also been made in average environmental conditions. For sexually dimorphic traits, expectations of between-sex genetic correlations are unclear (Lande 1980; Badyaev 2002). We might expect that the genetic determination of a trait and the patterns of genetic covariance between traits may differ both within and between the sexes, producing the differences in trait growth that are commonly observed (Lande 1980; Badyaev 2002; Roff 2002), but so far evidence suggests that genetic expression in both sexes is influenced by the same developmental pathway (Roff 2002; Jensen et al. 2003; Parker and Garant 2005). However, to our knowledge, no study has yet determined whether genetic correlations, both within and between the sexes, vary across gradients of the environmental conditions encountered by individuals in the wild (Garant et al. 2008).\r\nThis study aims to assess the stability of phenotypic, genetic, and environmental (residual) associations between traits, within and between the sexes, across a range of environmental conditions experienced by a wild population. We focus on the traits of horn length, body weight, and parasite load in a feral population of Soay sheep (Ovis aries) from the island of Hirta, St. Kilda, United Kingdom. Weather conditions, population density, and consequently resource availability fluctuate from year to year, providing substantial differences between individuals in the environments they experience and thus their survival rates (Clutton-Brock and Pemberton 2004). These varying conditions, combined with a large pedigree and extensive repeated morphological measures, provide an excellent opportunity to assess the potential effects of environmental heterogeneity on genetic architecture of traits. Previous studies on this population have shown additive genetic variance for many morphological traits (Milner et al. 2000; Coltman et al. 2001; Wilson et al. 2005), genetic correlations between traits (Coltman et al. 2001), and genotype-by-environment interactions for birth weight (Wilson et al. 2006). Here we apply a random regression animal model approach to assess the extent to which quantitative genetic parameters of a range of morphological traits measured during life vary as a function of environmental conditions. We then extend this methodology to the multivariate case, testing whether the phenotypic covariance structure, and the underlying G matrix, depends on the environmental conditions experienced. Since the traits considered here are known to be sexually dimorphic and there are differences in trait growth and survival across ages, we look at sex-specific traits in lambs and then across all ages."}],"publication":"Genetics","title":"The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep","page":"1639-1648","volume":181,"year":"2009","type":"journal_article","article_type":"original","publication_identifier":{"issn":["0016-6731","1943-2631"]},"month":"04","language":[{"iso":"eng"}],"citation":{"ista":"Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. 2009. The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. Genetics. 181(4), 1639–1648.","chicago":"Robinson, Matthew Richard, Alastair J. Wilson, Jill G. Pilkington, Tim H. Clutton-Brock, Josephine M. Pemberton, and Loeske E. B. Kruuk. “The Impact of Environmental Heterogeneity on Genetic Architecture in a Wild Population of Soay Sheep.” Genetics. Genetics Society of America, 2009. https://doi.org/10.1534/genetics.108.086801.","ama":"Robinson MR, Wilson AJ, Pilkington JG, Clutton-Brock TH, Pemberton JM, Kruuk LEB. The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. Genetics. 2009;181(4):1639-1648. doi:10.1534/genetics.108.086801","apa":"Robinson, M. R., Wilson, A. J., Pilkington, J. G., Clutton-Brock, T. H., Pemberton, J. M., & Kruuk, L. E. B. (2009). The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.108.086801","ieee":"M. R. Robinson, A. J. Wilson, J. G. Pilkington, T. H. Clutton-Brock, J. M. Pemberton, and L. E. B. Kruuk, “The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep,” Genetics, vol. 181, no. 4. Genetics Society of America, pp. 1639–1648, 2009.","mla":"Robinson, Matthew Richard, et al. “The Impact of Environmental Heterogeneity on Genetic Architecture in a Wild Population of Soay Sheep.” Genetics, vol. 181, no. 4, Genetics Society of America, 2009, pp. 1639–48, doi:10.1534/genetics.108.086801.","short":"M.R. Robinson, A.J. Wilson, J.G. Pilkington, T.H. Clutton-Brock, J.M. Pemberton, L.E.B. Kruuk, Genetics 181 (2009) 1639–1648."},"oa_version":"None","publication_status":"published","author":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard"},{"first_name":"Alastair J.","last_name":"Wilson","full_name":"Wilson, Alastair J."},{"first_name":"Jill G.","last_name":"Pilkington","full_name":"Pilkington, Jill G."},{"full_name":"Clutton-Brock, Tim H.","first_name":"Tim H.","last_name":"Clutton-Brock"},{"first_name":"Josephine M.","last_name":"Pemberton","full_name":"Pemberton, Josephine M."},{"first_name":"Loeske E. B.","last_name":"Kruuk","full_name":"Kruuk, Loeske E. B."}],"doi":"10.1534/genetics.108.086801","publisher":"Genetics Society of America","intvolume":" 181","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","_id":"7751","article_processing_charge":"No"},{"date_updated":"2021-01-12T08:16:36Z","issue":"4","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2693069/"}],"date_published":"2009-04-01T00:00:00Z","abstract":[{"text":"Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals.","lang":"eng"}],"title":"Gating multiple signals through detailed balance of excitation and inhibition in spiking networks","volume":12,"year":"2009","publication_identifier":{"issn":["1097-6256","1546-1726"]},"type":"journal_article","oa_version":"Submitted Version","citation":{"ista":"Vogels TP, Abbott LF. 2009. Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. Nature Neuroscience. 12(4), 483–491.","chicago":"Vogels, Tim P, and L F Abbott. “Gating Multiple Signals through Detailed Balance of Excitation and Inhibition in Spiking Networks.” Nature Neuroscience. Springer Nature, 2009. https://doi.org/10.1038/nn.2276.","apa":"Vogels, T. P., & Abbott, L. F. (2009). Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn.2276","ama":"Vogels TP, Abbott LF. Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. Nature Neuroscience. 2009;12(4):483-491. doi:10.1038/nn.2276","ieee":"T. P. Vogels and L. F. Abbott, “Gating multiple signals through detailed balance of excitation and inhibition in spiking networks,” Nature Neuroscience, vol. 12, no. 4. Springer Nature, pp. 483–491, 2009.","mla":"Vogels, Tim P., and L. F. Abbott. “Gating Multiple Signals through Detailed Balance of Excitation and Inhibition in Spiking Networks.” Nature Neuroscience, vol. 12, no. 4, Springer Nature, 2009, pp. 483–91, doi:10.1038/nn.2276.","short":"T.P. Vogels, L.F. Abbott, Nature Neuroscience 12 (2009) 483–491."},"author":[{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P"},{"first_name":"L F","last_name":"Abbott","full_name":"Abbott, L F"}],"publication_status":"published","doi":"10.1038/nn.2276","publisher":"Springer Nature","pmid":1,"extern":"1","_id":"8026","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","date_created":"2020-06-25T13:10:55Z","day":"01","page":"483-491","publication":"Nature Neuroscience","article_type":"original","month":"04","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["19305402"]},"intvolume":" 12","quality_controlled":"1","article_processing_charge":"No"},{"abstract":[{"text":"Let g be a cubic polynomial with integer coefficients and n>9 variables, and assume that the congruence g=0 modulo p^k is soluble for all prime powers p^k. We show that the equation g=0 has infinitely many integer solutions when the cubic part of g defines a projective hypersurface with singular locus of dimension <n-10. The proof is based on the Hardy-Littlewood circle method.","lang":"eng"}],"day":"31","page":"75 - 90","publication":"Analytic Number Theory: Essays in honour of Klaus Roth","title":"Integral points on cubic hypersurfaces","status":"public","date_updated":"2021-01-12T06:52:11Z","date_created":"2018-12-11T11:44:58Z","date_published":"2009-01-31T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/math/0611086"}],"language":[{"iso":"eng"}],"citation":{"apa":"Browning, T. D., & Heath Brown, R. (2009). Integral points on cubic hypersurfaces. In Analytic Number Theory: Essays in honour of Klaus Roth (pp. 75–90). Cambridge University Press.","ama":"Browning TD, Heath Brown R. Integral points on cubic hypersurfaces. In: Analytic Number Theory: Essays in Honour of Klaus Roth. Cambridge University Press; 2009:75-90.","short":"T.D. Browning, R. Heath Brown, in:, Analytic Number Theory: Essays in Honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.","mla":"Browning, Timothy D., and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” Analytic Number Theory: Essays in Honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.","ieee":"T. D. Browning and R. Heath Brown, “Integral points on cubic hypersurfaces,” in Analytic Number Theory: Essays in honour of Klaus Roth, Cambridge University Press, 2009, pp. 75–90.","ista":"Browning TD, Heath Brown R. 2009.Integral points on cubic hypersurfaces. In: Analytic Number Theory: Essays in honour of Klaus Roth. , 75–90.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Integral Points on Cubic Hypersurfaces.” In Analytic Number Theory: Essays in Honour of Klaus Roth, 75–90. Cambridge University Press, 2009."},"oa_version":"Preprint","year":"2009","month":"01","type":"book_chapter","publist_id":"7757","publisher":"Cambridge University Press","external_id":{"arxiv":["0611086"]},"arxiv":1,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Heath Brown, Roger","first_name":"Roger","last_name":"Heath Brown"}],"oa":1,"publication_status":"published","extern":"1","_id":"164","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2018-12-11T11:44:58Z","date_published":"2009-08-24T00:00:00Z","editor":[{"first_name":"Takashi","last_name":"Aoki","full_name":"Aoki, Takashi"},{"first_name":"Shigeru","last_name":"Kanemitsu","full_name":"Kanemitsu, Shigeru"},{"last_name":"Liu","first_name":"Jianya","full_name":"Liu, Jianya"}],"status":"public","date_updated":"2021-01-12T06:52:15Z","page":"1 - 18","title":"Resent progress on the quantitative arithmetic of del Pezzo surfaces","conference":{"name":"Number Theory: Dreaming in dreams"},"abstract":[{"text":"We survey the state of affairs for the distribution of ℚ-rational points on non-singular del Pezzo surfaces of low degree, highlighting the recent resolution of Manin's conjecture for a non-singular del Pezzo surface of degree 4 by la Bretèche and Browning.","lang":"eng"}],"day":"24","month":"08","type":"conference","volume":6,"year":"2009","citation":{"apa":"Browning, T. D. (2009). Resent progress on the quantitative arithmetic of del Pezzo surfaces. In T. Aoki, S. Kanemitsu, & J. Liu (Eds.) (Vol. 6, pp. 1–18). Presented at the Number Theory: Dreaming in dreams, World Scientific Publishing. https://doi.org/10.1142/9789814289924_0001","ama":"Browning TD. Resent progress on the quantitative arithmetic of del Pezzo surfaces. In: Aoki T, Kanemitsu S, Liu J, eds. Vol 6. World Scientific Publishing; 2009:1-18. doi:https://doi.org/10.1142/9789814289924_0001","mla":"Browning, Timothy D. Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces. Edited by Takashi Aoki et al., vol. 6, World Scientific Publishing, 2009, pp. 1–18, doi:https://doi.org/10.1142/9789814289924_0001.","ieee":"T. D. Browning, “Resent progress on the quantitative arithmetic of del Pezzo surfaces,” presented at the Number Theory: Dreaming in dreams, 2009, vol. 6, pp. 1–18.","short":"T.D. Browning, in:, T. Aoki, S. Kanemitsu, J. Liu (Eds.), World Scientific Publishing, 2009, pp. 1–18.","ista":"Browning TD. 2009. Resent progress on the quantitative arithmetic of del Pezzo surfaces. Number Theory: Dreaming in dreams, Series on number theory and its application, vol. 6, 1–18.","chicago":"Browning, Timothy D. “Resent Progress on the Quantitative Arithmetic of Del Pezzo Surfaces.” edited by Takashi Aoki, Shigeru Kanemitsu, and Jianya Liu, 6:1–18. World Scientific Publishing, 2009. https://doi.org/10.1142/9789814289924_0001."},"publication_status":"published","author":[{"first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"publisher":"World Scientific Publishing","alternative_title":["Series on number theory and its application"],"publist_id":"7756","doi":"https://doi.org/10.1142/9789814289924_0001","_id":"165","quality_controlled":0,"acknowledgement":"Proceedings of the 5th China-Japan Seminar","extern":1,"intvolume":" 6"},{"publication_status":"published","author":[{"first_name":"Timothy D","last_name":"Browning","full_name":"Timothy Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dietmann, Rainer","last_name":"Dietmann","first_name":"Rainer"}],"alternative_title":["Contemporary Mathematics"],"publisher":"American Mathematical Society","doi":"http://dx.doi.org/10.1090/conm/493","publist_id":"7753","quality_controlled":0,"_id":"168","intvolume":" 493","extern":1,"date_published":"2009-01-01T00:00:00Z","main_file_link":[{"open_access":"0","url":"https://arxiv.org/abs/0805.3354"}],"date_created":"2018-12-11T11:44:59Z","status":"public","date_updated":"2021-01-12T06:52:29Z","title":"Solubility of Fermat equations","publication":"Quadratic Forms - algebra, arithmetic and geometry","page":"99 - 106","day":"01","abstract":[{"lang":"eng","text":"The arithmetic of ternary diagonal equation is considered for degree d >1, with the outcome that the set of coefficients for which the equation admits a non-zero integer solution is shown to have density zero."}],"type":"book_chapter","month":"01","year":"2009","volume":493,"citation":{"mla":"Browning, Timothy D., and Rainer Dietmann. “Solubility of Fermat Equations.” Quadratic Forms - Algebra, Arithmetic and Geometry, vol. 493, American Mathematical Society, 2009, pp. 99–106, doi:http://dx.doi.org/10.1090/conm/493.","ieee":"T. D. Browning and R. Dietmann, “Solubility of Fermat equations,” in Quadratic Forms - algebra, arithmetic and geometry, vol. 493, American Mathematical Society, 2009, pp. 99–106.","short":"T.D. Browning, R. Dietmann, in:, Quadratic Forms - Algebra, Arithmetic and Geometry, American Mathematical Society, 2009, pp. 99–106.","apa":"Browning, T. D., & Dietmann, R. (2009). Solubility of Fermat equations. In Quadratic Forms - algebra, arithmetic and geometry (Vol. 493, pp. 99–106). American Mathematical Society. http://dx.doi.org/10.1090/conm/493","ama":"Browning TD, Dietmann R. Solubility of Fermat equations. In: Quadratic Forms - Algebra, Arithmetic and Geometry. Vol 493. American Mathematical Society; 2009:99-106. doi:http://dx.doi.org/10.1090/conm/493","chicago":"Browning, Timothy D, and Rainer Dietmann. “Solubility of Fermat Equations.” In Quadratic Forms - Algebra, Arithmetic and Geometry, 493:99–106. American Mathematical Society, 2009. http://dx.doi.org/10.1090/conm/493.","ista":"Browning TD, Dietmann R. 2009.Solubility of Fermat equations. In: Quadratic Forms - algebra, arithmetic and geometry. Contemporary Mathematics, vol. 493, 99–106."}},{"_id":"1718","quality_controlled":0,"acknowledgement":"EK is supported by an EMBO LTF, AK by a FEBS fellowship, and JB by MRC (UK) and the Wellcome Trust","extern":1,"intvolume":" 19","author":[{"last_name":"Kutějová","first_name":"Eva","full_name":"Kutějová, Eva"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Anna Kicheva"}],"publication_status":"published","publisher":"Elsevier","publist_id":"5410","doi":"10.1016/j.gde.2009.05.004","month":"08","type":"journal_article","year":"2009","volume":19,"citation":{"short":"E. Kutějová, J. Briscoe, A. Kicheva, Current Opinion in Genetics & Development 19 (2009) 315–322.","ieee":"E. Kutějová, J. Briscoe, and A. Kicheva, “Temporal dynamics of patterning by morphogen gradients,” Current Opinion in Genetics & Development, vol. 19, no. 4. Elsevier, pp. 315–322, 2009.","mla":"Kutějová, Eva, et al. “Temporal Dynamics of Patterning by Morphogen Gradients.” Current Opinion in Genetics & Development, vol. 19, no. 4, Elsevier, 2009, pp. 315–22, doi:10.1016/j.gde.2009.05.004.","apa":"Kutějová, E., Briscoe, J., & Kicheva, A. (2009). Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2009.05.004","ama":"Kutějová E, Briscoe J, Kicheva A. Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. 2009;19(4):315-322. doi:10.1016/j.gde.2009.05.004","chicago":"Kutějová, Eva, James Briscoe, and Anna Kicheva. “Temporal Dynamics of Patterning by Morphogen Gradients.” Current Opinion in Genetics & Development. Elsevier, 2009. https://doi.org/10.1016/j.gde.2009.05.004.","ista":"Kutějová E, Briscoe J, Kicheva A. 2009. Temporal dynamics of patterning by morphogen gradients. Current Opinion in Genetics & Development. 19(4), 315–322."},"issue":"4","date_created":"2018-12-11T11:53:38Z","date_published":"2009-08-01T00:00:00Z","status":"public","date_updated":"2021-01-12T06:52:44Z","page":"315 - 322","publication":"Current Opinion in Genetics & Development","title":"Temporal dynamics of patterning by morphogen gradients","abstract":[{"lang":"eng","text":"Morphogens act as graded positional cues to control cell fate specification in many developing tissues. This concept, in which a signaling gradient regulates differential gene expression in a concentration-dependent manner, has received considerable experimental support. Nevertheless, several recent studies have challenged the straightforward model of morphogen activity. In particular, the observation that pattern formation is a dynamic process has raised questions about the influence of time on morphogen activity. Here we propose that the spatiotemporal dynamics of the cellular response to a morphogen gradient depend on a combination of temporal alterations to the morphogen gradient itself, the dynamics of its signal transduction and downstream interactions between target genes."}],"day":"01"},{"date_updated":"2021-01-12T06:52:45Z","status":"public","date_published":"2009-09-01T00:00:00Z","date_created":"2018-12-11T11:53:39Z","issue":"3","day":"01","abstract":[{"text":"How morphogen gradients are formed in target tissues is a key question for understanding the mechanisms of morphological patterning. Here, we review different mechanisms of morphogen gradient formation from theoretical and experimental points of view. First, a simple, comprehensive overview of the underlying biophysical principles of several mechanisms of gradient formation is provided. We then discuss the advantages and limitations of different experimental approaches to gradient formation analysis.","lang":"eng"}],"publication":"Cold Spring Harbor perspectives in biology","title":"Morphogen gradient formation ","volume":1,"year":"2009","type":"journal_article","month":"09","citation":{"chicago":"Wartlick, Ortrud, Anna Kicheva, and Marcos González Gaitán. “Morphogen Gradient Formation .” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2009. https://doi.org/10.1101/cshperspect.a001255.","ista":"Wartlick O, Kicheva A, González Gaitán M. 2009. Morphogen gradient formation . Cold Spring Harbor perspectives in biology. 1(3).","mla":"Wartlick, Ortrud, et al. “Morphogen Gradient Formation .” Cold Spring Harbor Perspectives in Biology, vol. 1, no. 3, Cold Spring Harbor Laboratory Press, 2009, doi:10.1101/cshperspect.a001255.","ieee":"O. Wartlick, A. Kicheva, and M. González Gaitán, “Morphogen gradient formation ,” Cold Spring Harbor perspectives in biology, vol. 1, no. 3. Cold Spring Harbor Laboratory Press, 2009.","short":"O. Wartlick, A. Kicheva, M. González Gaitán, Cold Spring Harbor Perspectives in Biology 1 (2009).","ama":"Wartlick O, Kicheva A, González Gaitán M. Morphogen gradient formation . Cold Spring Harbor perspectives in biology. 2009;1(3). doi:10.1101/cshperspect.a001255","apa":"Wartlick, O., Kicheva, A., & González Gaitán, M. (2009). Morphogen gradient formation . Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a001255"},"author":[{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","orcid":"0000-0003-4509-4998"},{"full_name":"González-Gaitán, Marcos A","first_name":"Marcos","last_name":"González Gaitán"}],"publication_status":"published","doi":"10.1101/cshperspect.a001255","publist_id":"5409","publisher":"Cold Spring Harbor Laboratory Press","intvolume":" 1","extern":1,"quality_controlled":0,"_id":"1720"},{"date_created":"2018-12-11T11:53:54Z","issue":"18","date_published":"2009-05-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/0812.2678","open_access":"1"}],"status":"public","date_updated":"2021-01-12T06:53:04Z","title":"Using sideband transitions for two-qubit operations in superconducting circuits","publication":"Physical Review B - Condensed Matter and Materials Physics","abstract":[{"text":"We demonstrate the time-resolved driving of two-photon blue sideband transitions between superconducting qubits and a transmission line resonator. As an example of using these sideband transitions for a two-qubit operation, we implement a pulse sequence that first entangles one qubit with the resonator and subsequently distributes the entanglement between two qubits. We show the generation of 75% fidelity Bell states by this method. The full density matrix of the two-qubit system is extracted using joint measurement and quantum state tomography and shows close agreement with numerical simulation.","lang":"eng"}],"day":"01","month":"05","type":"journal_article","year":"2009","volume":79,"citation":{"ista":"Leek P, Filipp S, Maurer P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Wallraff A. 2009. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 79(18).","chicago":"Leek, Peter, Stefan Filipp, Patrick Maurer, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, and Andreas Wallraff. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevB.79.180511.","apa":"Leek, P., Filipp, S., Maurer, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.79.180511","ama":"Leek P, Filipp S, Maurer P, et al. Using sideband transitions for two-qubit operations in superconducting circuits. Physical Review B - Condensed Matter and Materials Physics. 2009;79(18). doi:10.1103/PhysRevB.79.180511","short":"P. Leek, S. Filipp, P. Maurer, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, A. Wallraff, Physical Review B - Condensed Matter and Materials Physics 79 (2009).","ieee":"P. Leek et al., “Using sideband transitions for two-qubit operations in superconducting circuits,” Physical Review B - Condensed Matter and Materials Physics, vol. 79, no. 18. American Physical Society, 2009.","mla":"Leek, Peter, et al. “Using Sideband Transitions for Two-Qubit Operations in Superconducting Circuits.” Physical Review B - Condensed Matter and Materials Physics, vol. 79, no. 18, American Physical Society, 2009, doi:10.1103/PhysRevB.79.180511."},"oa":1,"publication_status":"published","author":[{"full_name":"Leek, Peter J","first_name":"Peter","last_name":"Leek"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"full_name":"Maurer, Patrick","first_name":"Patrick","last_name":"Maurer"},{"full_name":"Baur, Matthias P","last_name":"Baur","first_name":"Matthias"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"publisher":"American Physical Society","publist_id":"5354","doi":"10.1103/PhysRevB.79.180511","_id":"1766","quality_controlled":0,"acknowledgement":"This work was supported by ETH Zurich, the Swiss National Science Foundation, and by the EC via the EuroSQIP project and the Marie-Curie program (P. J. L.)","extern":1,"intvolume":" 79"},{"issue":"24","date_created":"2018-12-11T11:53:54Z","main_file_link":[{"url":"http://arxiv.org/abs/0812.4384","open_access":"1"}],"date_published":"2009-06-19T00:00:00Z","date_updated":"2021-01-12T06:53:04Z","status":"public","title":"Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit","publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We present spectroscopic measurements of the Autler-Townes doublet and the sidebands of the Mollow triplet in a driven superconducting qubit. The ground to first excited state transition of the qubit is strongly pumped while the resulting dressed qubit spectrum is probed with a weak tone. The corresponding transitions are detected using dispersive readout of the qubit coupled off resonantly to a microwave transmission line resonator. The observed frequencies of the Autler-Townes and Mollow spectral lines are in good agreement with a dispersive Jaynes-Cummings model taking into account higher excited qubit states and dispersive level shifts due to off-resonant drives."}],"day":"19","month":"06","type":"journal_article","year":"2009","volume":102,"citation":{"chicago":"Baur, Matthias, Stefan Filipp, R Bianchetti, Johannes M Fink, M Göppl, L. Steffen, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.102.243602.","ista":"Baur M, Filipp S, Bianchetti R, Fink JM, Göppl M, Steffen L, Leek P, Blais A, Wallraff A. 2009. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 102(24).","short":"M. Baur, S. Filipp, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 102 (2009).","mla":"Baur, Matthias, et al. “Measurement of Autler-Townes and Mollow Transitions in a Strongly Driven Superconducting Qubit.” Physical Review Letters, vol. 102, no. 24, American Physical Society, 2009, doi:10.1103/PhysRevLett.102.243602.","ieee":"M. Baur et al., “Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit,” Physical Review Letters, vol. 102, no. 24. American Physical Society, 2009.","apa":"Baur, M., Filipp, S., Bianchetti, R., Fink, J. M., Göppl, M., Steffen, L., … Wallraff, A. (2009). Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.102.243602","ama":"Baur M, Filipp S, Bianchetti R, et al. Measurement of autler-townes and mollow transitions in a strongly driven superconducting qubit. Physical Review Letters. 2009;102(24). doi:10.1103/PhysRevLett.102.243602"},"author":[{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"last_name":"Filipp","first_name":"Stefan","full_name":"Filipp, Stefan"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Göppl, M","first_name":"M","last_name":"Göppl"},{"last_name":"Steffen","first_name":"L.","full_name":"Steffen, L. Kraig"},{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"full_name":"Blais, Alexandre","first_name":"Alexandre","last_name":"Blais"},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}],"publication_status":"published","oa":1,"publisher":"American Physical Society","publist_id":"5352","doi":"10.1103/PhysRevLett.102.243602","_id":"1767","quality_controlled":0,"acknowledgement":"This work was supported by the Swiss National Science Foundation and by ETH Zürich. P. J. L. acknowledges support from the EC via an Intra-European Marie-Curie Fellowship. A. B. was supported by NSERC, CIFAR, FQRNT, and Alfred P. Sloan Foundation","extern":1,"intvolume":" 102"},{"volume":102,"year":"2009","type":"journal_article","month":"05","citation":{"apa":"Filipp, S., Maurer, P., Leek, P., Baur, M., Bianchetti, R., Fink, J. M., … Wallraff, A. (2009). Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.102.200402","ama":"Filipp S, Maurer P, Leek P, et al. Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. 2009;102(20). doi:10.1103/PhysRevLett.102.200402","short":"S. Filipp, P. Maurer, P. Leek, M. Baur, R. Bianchetti, J.M. Fink, M. Göppl, L. Steffen, J. Gambetta, A. Blais, A. Wallraff, Physical Review Letters 102 (2009).","ieee":"S. Filipp et al., “Two-qubit state tomography using a joint dispersive readout,” Physical Review Letters, vol. 102, no. 20. American Physical Society, 2009.","mla":"Filipp, Stefan, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” Physical Review Letters, vol. 102, no. 20, American Physical Society, 2009, doi:10.1103/PhysRevLett.102.200402.","ista":"Filipp S, Maurer P, Leek P, Baur M, Bianchetti R, Fink JM, Göppl M, Steffen L, Gambetta J, Blais A, Wallraff A. 2009. Two-qubit state tomography using a joint dispersive readout. Physical Review Letters. 102(20).","chicago":"Filipp, Stefan, Patrick Maurer, Peter Leek, Matthias Baur, R Bianchetti, Johannes M Fink, M Göppl, et al. “Two-Qubit State Tomography Using a Joint Dispersive Readout.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.102.200402."},"date_updated":"2021-01-12T06:53:04Z","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/0812.2485","open_access":"1"}],"date_published":"2009-05-18T00:00:00Z","date_created":"2018-12-11T11:53:54Z","issue":"20","day":"18","abstract":[{"text":"Quantum state tomography is an important tool in quantum information science for complete characterization of multiqubit states and their correlations. Here we report a method to perform a joint simultaneous readout of two superconducting qubits dispersively coupled to the same mode of a microwave transmission line resonator. The nonlinear dependence of the resonator transmission on the qubit state dependent cavity frequency allows us to extract the full two-qubit correlations without the need for single-shot readout of individual qubits. We employ standard tomographic techniques to reconstruct the density matrix of two-qubit quantum states.","lang":"eng"}],"title":"Two-qubit state tomography using a joint dispersive readout","publication":"Physical Review Letters","intvolume":" 102","extern":1,"acknowledgement":"This work was supported by Swiss National Science Foundation (SNF) and ETH Zurich. P. J. L. was supported by the EC with a MC-EIF, J. M. G. by CIFAR, MRI, MITACS, and NSERC, and A. B. by NSERC and CIFAR","quality_controlled":0,"_id":"1768","author":[{"full_name":"Filipp, Stefan","first_name":"Stefan","last_name":"Filipp"},{"full_name":"Maurer, Patrick","last_name":"Maurer","first_name":"Patrick"},{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Johannes M","last_name":"Fink","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M","last_name":"Göppl","full_name":"Göppl, M"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"full_name":"Gambetta, Jay M","last_name":"Gambetta","first_name":"Jay"},{"last_name":"Blais","first_name":"Alexandre","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"publication_status":"published","oa":1,"doi":"10.1103/PhysRevLett.102.200402","publist_id":"5353","publisher":"American Physical Society"},{"status":"public","date_updated":"2021-01-12T06:53:05Z","issue":"8","date_created":"2018-12-11T11:53:55Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0812.2651"}],"date_published":"2009-08-17T00:00:00Z","abstract":[{"text":"We present an ideal realization of the Tavis-Cummings model in the absence of atom number and coupling fluctuations by embedding a discrete number of fully controllable superconducting qubits at fixed positions into a transmission line resonator. Measuring the vacuum Rabi mode splitting with one, two, and three qubits strongly coupled to the cavity field, we explore both bright and dark dressed collective multiqubit states and observe the discrete N scaling of the collective dipole coupling strength. Our experiments demonstrate a novel approach to explore collective states, such as the W state, in a fully globally and locally controllable quantum system. Our scalable approach is interesting for solid-state quantum information processing and for fundamental multiatom quantum optics experiments with fixed atom numbers.","lang":"eng"}],"day":"17","publication":"Physical Review Letters","title":"Dressed collective qubit states and the Tavis-Cummings model in circuit QED","volume":103,"year":"2009","month":"08","type":"journal_article","citation":{"chicago":"Fink, Johannes M, R Bianchetti, Matthias Baur, M Göppl, L. Steffen, Stefan Filipp, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” Physical Review Letters. American Physical Society, 2009. https://doi.org/10.1103/PhysRevLett.103.083601.","ista":"Fink JM, Bianchetti R, Baur M, Göppl M, Steffen L, Filipp S, Leek P, Blais A, Wallraff A. 2009. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. 103(8).","short":"J.M. Fink, R. Bianchetti, M. Baur, M. Göppl, L. Steffen, S. Filipp, P. Leek, A. Blais, A. Wallraff, Physical Review Letters 103 (2009).","mla":"Fink, Johannes M., et al. “Dressed Collective Qubit States and the Tavis-Cummings Model in Circuit QED.” Physical Review Letters, vol. 103, no. 8, American Physical Society, 2009, doi:10.1103/PhysRevLett.103.083601.","ieee":"J. M. Fink et al., “Dressed collective qubit states and the Tavis-Cummings model in circuit QED,” Physical Review Letters, vol. 103, no. 8. American Physical Society, 2009.","apa":"Fink, J. M., Bianchetti, R., Baur, M., Göppl, M., Steffen, L., Filipp, S., … Wallraff, A. (2009). Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.103.083601","ama":"Fink JM, Bianchetti R, Baur M, et al. Dressed collective qubit states and the Tavis-Cummings model in circuit QED. Physical Review Letters. 2009;103(8). doi:10.1103/PhysRevLett.103.083601"},"oa":1,"author":[{"full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Bianchetti, R","first_name":"R","last_name":"Bianchetti"},{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"first_name":"M","last_name":"Göppl","full_name":"Göppl, M"},{"full_name":"Steffen, L. Kraig","first_name":"L.","last_name":"Steffen"},{"full_name":"Filipp, Stefan","first_name":"Stefan","last_name":"Filipp"},{"full_name":"Leek, Peter J","first_name":"Peter","last_name":"Leek"},{"last_name":"Blais","first_name":"Alexandre","full_name":"Blais, Alexandre"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"}],"publication_status":"published","publist_id":"5350","doi":"10.1103/PhysRevLett.103.083601","publisher":"American Physical Society","extern":1,"intvolume":" 103","quality_controlled":0,"_id":"1769","acknowledgement":"This work was supported by SNF Grant No. 200021-111899 and ETHZ. P. J. L. was supported by the EU with a MC-EIF. A. B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation"},{"publication_status":"published","oa":1,"author":[{"full_name":"Bianchetti, R","first_name":"R","last_name":"Bianchetti"},{"full_name":"Filipp, Stefan","last_name":"Filipp","first_name":"Stefan"},{"full_name":"Baur, Matthias P","first_name":"Matthias","last_name":"Baur"},{"orcid":"0000-0001-8112-028X","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"},{"first_name":"M","last_name":"Göppl","full_name":"Göppl, M"},{"last_name":"Leek","first_name":"Peter","full_name":"Leek, Peter J"},{"last_name":"Steffen","first_name":"L.","full_name":"Steffen, L. Kraig"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"publisher":"American Physical Society","publist_id":"5349","doi":"10.1103/PhysRevA.80.043840","_id":"1770","quality_controlled":0,"acknowledgement":"This work was supported by the SNF Project No. 111899 and ETH Zurich. A.B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation","extern":1,"intvolume":" 80","date_created":"2018-12-11T11:53:55Z","issue":"4","date_published":"2009-10-30T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/0907.2549","open_access":"1"}],"status":"public","date_updated":"2021-01-12T06:53:05Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","title":"Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics","abstract":[{"lang":"eng","text":"The quantum state of a superconducting qubit nonresonantly coupled to a transmission line resonator can be determined by measuring the quadrature amplitudes of an electromagnetic field transmitted through the resonator. We present experiments in which we analyze in detail the dynamics of the transmitted field as a function of the measurement frequency for both weak continuous and pulsed measurements. We find excellent agreement between our data and calculations based on a set of Bloch-type differential equations for the cavity field derived from the dispersive Jaynes-Cummings Hamiltonian including dissipation. We show that the measured system response can be used to construct a measurement operator from which the qubit population can be inferred accurately. Such a measurement operator can be used in tomographic methods to reconstruct single and multiqubit states in ensemble-averaged measurements."}],"day":"30","month":"10","type":"journal_article","year":"2009","volume":80,"citation":{"ista":"Bianchetti R, Filipp S, Baur M, Fink JM, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 80(4).","chicago":"Bianchetti, R, Stefan Filipp, Matthias Baur, Johannes M Fink, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2009. https://doi.org/10.1103/PhysRevA.80.043840.","ama":"Bianchetti R, Filipp S, Baur M, et al. Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 2009;80(4). doi:10.1103/PhysRevA.80.043840","apa":"Bianchetti, R., Filipp, S., Baur, M., Fink, J. M., Göppl, M., Leek, P., … Wallraff, A. (2009). Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.80.043840","mla":"Bianchetti, R., et al. “Dynamics of Dispersive Single-Qubit Readout in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 80, no. 4, American Physical Society, 2009, doi:10.1103/PhysRevA.80.043840.","ieee":"R. Bianchetti et al., “Dynamics of dispersive single-qubit readout in circuit quantum electrodynamics,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 80, no. 4. American Physical Society, 2009.","short":"R. Bianchetti, S. Filipp, M. Baur, J.M. Fink, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 80 (2009)."}},{"extern":1,"acknowledgement":"Nobel Foundation","_id":"1771","quality_controlled":0,"doi":"10.1088/0031-8949/2009/T137/014013","publist_id":"5348","publisher":"IOP Publishing Ltd.","publication_status":"published","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"},{"last_name":"Baur","first_name":"Matthias","full_name":"Baur, Matthias P"},{"full_name":"Bianchetti, R","first_name":"R","last_name":"Bianchetti"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"full_name":"Leek, Peter J","last_name":"Leek","first_name":"Peter"},{"full_name":"Steffen, L. Kraig","first_name":"L.","last_name":"Steffen"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"oa":1,"citation":{"ama":"Fink JM, Baur M, Bianchetti R, et al. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. 2009;T137. doi:10.1088/0031-8949/2009/T137/014013","apa":"Fink, J. M., Baur, M., Bianchetti, R., Filipp, S., Göppl, M., Leek, P., … Wallraff, A. (2009). Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. IOP Publishing Ltd. https://doi.org/10.1088/0031-8949/2009/T137/014013","short":"J.M. Fink, M. Baur, R. Bianchetti, S. Filipp, M. Göppl, P. Leek, L. Steffen, A. Blais, A. Wallraff, Physica Scripta T T137 (2009).","mla":"Fink, Johannes M., et al. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” Physica Scripta T, vol. T137, IOP Publishing Ltd., 2009, doi:10.1088/0031-8949/2009/T137/014013.","ieee":"J. M. Fink et al., “Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics,” Physica Scripta T, vol. T137. IOP Publishing Ltd., 2009.","ista":"Fink JM, Baur M, Bianchetti R, Filipp S, Göppl M, Leek P, Steffen L, Blais A, Wallraff A. 2009. Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics. Physica Scripta T. T137.","chicago":"Fink, Johannes M, Matthias Baur, R Bianchetti, Stefan Filipp, M Göppl, Peter Leek, L. Steffen, Alexandre Blais, and Andreas Wallraff. “Thermal Excitation of Multi-Photon Dressed States in Circuit Quantum Electrodynamics.” Physica Scripta T. IOP Publishing Ltd., 2009. https://doi.org/10.1088/0031-8949/2009/T137/014013."},"year":"2009","volume":"T137","type":"journal_article","month":"01","day":"01","abstract":[{"lang":"eng","text":"The exceptionally strong coupling realizable between superconducting qubits and photons stored in an on-chip microwave resonator allows for the detailed study of matter-light interactions in the realm of circuit quantum electrodynamics (QED). Here we investigate the resonant interaction between a single transmon-type multilevel artificial atom and weak thermal and coherent fields. We explore up to three photon dressed states of the coupled system in a linear response heterodyne transmission measurement. The results are in good quantitative agreement with a generalized Jaynes-Cummings model. Our data indicate that the role of thermal fields in resonant cavity QED can be studied in detail using superconducting circuits."}],"publication":"Physica Scripta T","title":"Thermal excitation of multi-photon dressed states in circuit quantum electrodynamics","date_updated":"2021-01-12T06:53:06Z","status":"public","date_published":"2009-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0911.3797"}],"date_created":"2018-12-11T11:53:55Z"},{"year":"2009","volume":12,"type":"journal_article","month":"09","citation":{"ama":"Siegert S, Scherf B, Del Punta K, Didkovsky N, Heintz N, Roska B. Genetic address book for retinal cell types. Nature Neuroscience. 2009;12(9):1197-1204. doi:10.1038/nn.2370","apa":"Siegert, S., Scherf, B., Del Punta, K., Didkovsky, N., Heintz, N., & Roska, B. (2009). Genetic address book for retinal cell types. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2370","mla":"Siegert, Sandra, et al. “Genetic Address Book for Retinal Cell Types.” Nature Neuroscience, vol. 12, no. 9, Nature Publishing Group, 2009, pp. 1197–204, doi:10.1038/nn.2370.","ieee":"S. Siegert, B. Scherf, K. Del Punta, N. Didkovsky, N. Heintz, and B. Roska, “Genetic address book for retinal cell types,” Nature Neuroscience, vol. 12, no. 9. Nature Publishing Group, pp. 1197–1204, 2009.","short":"S. Siegert, B. Scherf, K. Del Punta, N. Didkovsky, N. Heintz, B. Roska, Nature Neuroscience 12 (2009) 1197–1204.","ista":"Siegert S, Scherf B, Del Punta K, Didkovsky N, Heintz N, Roska B. 2009. Genetic address book for retinal cell types. Nature Neuroscience. 12(9), 1197–1204.","chicago":"Siegert, Sandra, Brigitte Scherf, Karina Del Punta, Nick Didkovsky, Nathaniel Heintz, and Botond Roska. “Genetic Address Book for Retinal Cell Types.” Nature Neuroscience. Nature Publishing Group, 2009. https://doi.org/10.1038/nn.2370."},"date_updated":"2021-01-12T06:53:16Z","status":"public","date_published":"2009-09-01T00:00:00Z","date_created":"2018-12-11T11:54:04Z","issue":"9","day":"01","abstract":[{"lang":"eng","text":"The mammalian brain is assembled from thousands of neuronal cell types that are organized in distinct circuits to perform behaviorally relevant computations. Transgenic mouse lines with selectively marked cell types would facilitate our ability to dissect functional components of complex circuits. We carried out a screen for cell type-specific green fluorescent protein expression in the retina using BAC transgenic mice from the GENSAT project. Among others, we identified mouse lines in which the inhibitory cell types of the night vision and directional selective circuit were selectively labeled. We quantified the stratification patterns to predict potential synaptic connectivity between marked cells of different lines and found that some of the lines enabled targeted recordings and imaging of cell types from developing or mature retinal circuits. Our results suggest the potential use of a stratification-based screening approach for characterizing neuronal circuitry in other layered brain structures, such as the neocortex."}],"publication":"Nature Neuroscience","title":"Genetic address book for retinal cell types","page":"1197 - 1204","intvolume":" 12","extern":1,"acknowledgement":"This study was supported by Friedrich Miescher Institute funds, a US Office of Naval Research Naval International Cooperative Opportunities in Science and Technology Program grant, a Marie Curie Excellence grant, a National Center for Competence in Research in Genetics grant and a European Union HEALTH-F2-223156 grant to B.R., and by National Institute of Neurological Disorders and Stroke contracts N01NS02331 and HHSN271200723701C to N.H.","_id":"1798","quality_controlled":0,"publication_status":"published","author":[{"last_name":"Siegert","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877"},{"last_name":"Scherf","first_name":"Brigitte","full_name":"Scherf, Brigitte G"},{"last_name":"Del Punta","first_name":"Karina","full_name":"Del Punta, Karina"},{"full_name":"Didkovsky, Nick","last_name":"Didkovsky","first_name":"Nick"},{"first_name":"Nathaniel","last_name":"Heintz","full_name":"Heintz, Nathaniel M"},{"last_name":"Roska","first_name":"Botond","full_name":"Roska, Botond M"}],"doi":"10.1038/nn.2370","publist_id":"5312","publisher":"Nature Publishing Group"},{"citation":{"chicago":"Münch, Thomas, Ravá Da Silveira, Sandra Siegert, Tim Viney, Gautam Awatramani, and Botond Roska. “Approach Sensitivity in the Retina Processed by a Multifunctional Neural Circuit.” Nature Neuroscience. Nature Publishing Group, 2009. https://doi.org/10.1038/nn.2389.","ista":"Münch T, Da Silveira R, Siegert S, Viney T, Awatramani G, Roska B. 2009. Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. 12(10), 1308–1316.","mla":"Münch, Thomas, et al. “Approach Sensitivity in the Retina Processed by a Multifunctional Neural Circuit.” Nature Neuroscience, vol. 12, no. 10, Nature Publishing Group, 2009, pp. 1308–16, doi:10.1038/nn.2389.","ieee":"T. Münch, R. Da Silveira, S. Siegert, T. Viney, G. Awatramani, and B. Roska, “Approach sensitivity in the retina processed by a multifunctional neural circuit,” Nature Neuroscience, vol. 12, no. 10. Nature Publishing Group, pp. 1308–1316, 2009.","short":"T. Münch, R. Da Silveira, S. Siegert, T. Viney, G. Awatramani, B. Roska, Nature Neuroscience 12 (2009) 1308–1316.","ama":"Münch T, Da Silveira R, Siegert S, Viney T, Awatramani G, Roska B. Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. 2009;12(10):1308-1316. doi:10.1038/nn.2389","apa":"Münch, T., Da Silveira, R., Siegert, S., Viney, T., Awatramani, G., & Roska, B. (2009). Approach sensitivity in the retina processed by a multifunctional neural circuit. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2389"},"volume":12,"year":"2009","type":"journal_article","month":"10","day":"01","abstract":[{"lang":"eng","text":"The detection of approaching objects, such as looming predators, is necessary for survival. Which neurons and circuits mediate this function? We combined genetic labeling of cell types, two-photon microscopy, electrophysiology and theoretical modeling to address this question. We identify an approach-sensitive ganglion cell type in the mouse retina, resolve elements of its afferent neural circuit, and describe how these confer approach sensitivity on the ganglion cell. The circuit's essential building block is a rapid inhibitory pathway: it selectively suppresses responses to non-approaching objects. This rapid inhibitory pathway, which includes AII amacrine cells connected to bipolar cells through electrical synapses, was previously described in the context of night-time vision. In the daytime conditions of our experiments, the same pathway conveys signals in the reverse direction. The dual use of a neural pathway in different physiological conditions illustrates the efficiency with which several functions can be accommodated in a single circuit."}],"publication":"Nature Neuroscience","title":"Approach sensitivity in the retina processed by a multifunctional neural circuit","page":"1308 - 1316","status":"public","date_updated":"2021-01-12T06:53:16Z","date_published":"2009-10-01T00:00:00Z","issue":"10","date_created":"2018-12-11T11:54:04Z","intvolume":" 12","extern":1,"acknowledgement":"The study was supported by Friedrich Miescher Institute funds, a US Office of Naval Research Naval International Cooperative Opportunities in Science and Technology program grant, a Marie Curie Excellence Grant, a Human Frontier Science Program Young Investigator grant, a National Centers of Competence in Research in Genetics grant and a European Union HEALTH-F2-223156 grant to B.R., a Marie Curie Postdoctoral Fellowship to T.A.M., the Centre National de la Recherche Scientifique through the Unité Mixte de Recherche 8550 to R.A.d.S.","quality_controlled":0,"_id":"1799","doi":"10.1038/nn.2389","publist_id":"5311","publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Münch, Thomas A","last_name":"Münch","first_name":"Thomas"},{"full_name":"Da Silveira, Ravá A","first_name":"Ravá","last_name":"Da Silveira"},{"first_name":"Sandra","last_name":"Siegert","full_name":"Sandra Siegert","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Viney, Tim J","first_name":"Tim","last_name":"Viney"},{"full_name":"Awatramani, Gautam B","last_name":"Awatramani","first_name":"Gautam"},{"last_name":"Roska","first_name":"Botond","full_name":"Roska, Botond M"}]},{"citation":{"chicago":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent Inactivation.” PNAS. National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0902146106 .","ista":"Friedlander T, Brenner N. 2009. Adaptive response by state-dependent inactivation. PNAS. 106(52), 22558–22563.","short":"T. Friedlander, N. Brenner, PNAS 106 (2009) 22558–22563.","ieee":"T. Friedlander and N. Brenner, “Adaptive response by state-dependent inactivation,” PNAS, vol. 106, no. 52. National Academy of Sciences, pp. 22558–22563, 2009.","mla":"Friedlander, Tamar, and Naama Brenner. “Adaptive Response by State-Dependent Inactivation.” PNAS, vol. 106, no. 52, National Academy of Sciences, 2009, pp. 22558–63, doi:10.1073/pnas.0902146106 .","apa":"Friedlander, T., & Brenner, N. (2009). Adaptive response by state-dependent inactivation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0902146106 ","ama":"Friedlander T, Brenner N. Adaptive response by state-dependent inactivation. PNAS. 2009;106(52):22558-22563. doi:10.1073/pnas.0902146106 "},"year":"2009","volume":106,"type":"journal_article","month":"12","day":"01","abstract":[{"text":"Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. ","lang":"eng"}],"publication":"PNAS","title":"Adaptive response by state-dependent inactivation","page":"22558 - 22563","status":"public","date_updated":"2021-01-12T06:53:26Z","main_file_link":[{"url":"http://www.pnas.org/content/106/52/22558.full.pdf","open_access":"1"}],"date_published":"2009-12-01T00:00:00Z","date_created":"2018-12-11T11:54:13Z","issue":"52","intvolume":" 106","extern":1,"quality_controlled":0,"_id":"1825","doi":"10.1073/pnas.0902146106 ","publist_id":"5281","publisher":"National Academy of Sciences","publication_status":"published","oa":1,"author":[{"full_name":"Tamar Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander"},{"full_name":"Brenner, Naama","first_name":"Naama","last_name":"Brenner"}]},{"volume":284,"year":"2009","month":"10","type":"journal_article","citation":{"ama":"Berrisford J, Sazanov LA. Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. 2009;284(43):29773-29783. doi:10.1074/jbc.M109.032144","apa":"Berrisford, J., & Sazanov, L. A. (2009). Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M109.032144","mla":"Berrisford, John, and Leonid A. Sazanov. “Structural Basis for the Mechanism of Respiratory Complex I.” Journal of Biological Chemistry, vol. 284, no. 43, American Society for Biochemistry and Molecular Biology, 2009, pp. 29773–83, doi:10.1074/jbc.M109.032144.","ieee":"J. Berrisford and L. A. Sazanov, “Structural basis for the mechanism of respiratory complex I,” Journal of Biological Chemistry, vol. 284, no. 43. American Society for Biochemistry and Molecular Biology, pp. 29773–29783, 2009.","short":"J. Berrisford, L.A. Sazanov, Journal of Biological Chemistry 284 (2009) 29773–29783.","ista":"Berrisford J, Sazanov LA. 2009. Structural basis for the mechanism of respiratory complex I. Journal of Biological Chemistry. 284(43), 29773–29783.","chicago":"Berrisford, John, and Leonid A Sazanov. “Structural Basis for the Mechanism of Respiratory Complex I.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2009. https://doi.org/10.1074/jbc.M109.032144."},"date_updated":"2021-01-12T06:54:26Z","status":"public","issue":"43","date_created":"2018-12-11T11:54:59Z","date_published":"2009-10-23T00:00:00Z","abstract":[{"text":"Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 Å resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several α-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.","lang":"eng"}],"day":"23","page":"29773 - 29783","title":"Structural basis for the mechanism of respiratory complex I","publication":"Journal of Biological Chemistry","extern":1,"intvolume":" 284","quality_controlled":0,"_id":"1971","acknowledgement":"This work was supported by the Medical Research Council. ","author":[{"first_name":"John","last_name":"Berrisford","full_name":"Berrisford, John M"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Leonid Sazanov","last_name":"Sazanov","first_name":"Leonid A"}],"publication_status":"published","publist_id":"5114","doi":"10.1074/jbc.M109.032144","publisher":"American Society for Biochemistry and Molecular Biology"},{"publist_id":"5099","doi":"10.1016/j.jsb.2009.03.016","publisher":"Academic Press","publication_status":"published","author":[{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "}],"extern":1,"intvolume":" 168","quality_controlled":0,"_id":"1983","abstract":[{"lang":"eng","text":"During many cellular processes such as cell division, polarization and motility, the plasma membrane does not only represent a passive physical barrier, but also provides a highly dynamic platform for the interplay between lipids, membrane binding proteins and cytoskeletal elements. Even though many regulators of these interactions are known, their mutual interdependence appears to be highly complex and difficult to study in a living cell. Over the past few years, in vitro studies on membrane-cytoskeleton interactions using biomimetic membranes turned out to be extremely helpful to get better mechanistic insight into the dynamics of these processes. In this review, we discuss some of the recent developments using in vitro assays to dissect the role of the players involved: lipids in the membrane, proteins binding to membranes and proteins binding to membrane proteins. We also summarize advantages and disadvantages of supported lipid bilayers as model membrane."}],"day":"01","page":"143 - 151","title":"Biomimetic membrane systems to study cellular organization","publication":"Journal of Structural Biology","date_updated":"2021-01-12T06:54:30Z","status":"public","issue":"1","date_created":"2018-12-11T11:55:03Z","date_published":"2009-10-01T00:00:00Z","citation":{"short":"M. Loose, P. Schwille, Journal of Structural Biology 168 (2009) 143–151.","mla":"Loose, Martin, and Petra Schwille. “Biomimetic Membrane Systems to Study Cellular Organization.” Journal of Structural Biology, vol. 168, no. 1, Academic Press, 2009, pp. 143–51, doi:10.1016/j.jsb.2009.03.016.","ieee":"M. Loose and P. Schwille, “Biomimetic membrane systems to study cellular organization,” Journal of Structural Biology, vol. 168, no. 1. Academic Press, pp. 143–151, 2009.","apa":"Loose, M., & Schwille, P. (2009). Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2009.03.016","ama":"Loose M, Schwille P. Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. 2009;168(1):143-151. doi:10.1016/j.jsb.2009.03.016","chicago":"Loose, Martin, and Petra Schwille. “Biomimetic Membrane Systems to Study Cellular Organization.” Journal of Structural Biology. Academic Press, 2009. https://doi.org/10.1016/j.jsb.2009.03.016.","ista":"Loose M, Schwille P. 2009. Biomimetic membrane systems to study cellular organization. Journal of Structural Biology. 168(1), 143–151."},"volume":168,"year":"2009","month":"10","type":"journal_article"},{"citation":{"apa":"Dinarina, A., Pugieux, C., Corral, M., Loose, M., Spatz, J., Karsenti, É., & Nédélec, F. (2009). Chromatin shapes the mitotic spindle. Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.05.027","ama":"Dinarina A, Pugieux C, Corral M, et al. Chromatin shapes the mitotic spindle. Cell. 2009;138(3):502-513. doi:10.1016/j.cell.2009.05.027","mla":"Dinarina, Ana, et al. “Chromatin Shapes the Mitotic Spindle.” Cell, vol. 138, no. 3, Cell Press, 2009, pp. 502–13, doi:10.1016/j.cell.2009.05.027.","ieee":"A. Dinarina et al., “Chromatin shapes the mitotic spindle,” Cell, vol. 138, no. 3. Cell Press, pp. 502–513, 2009.","short":"A. Dinarina, C. Pugieux, M. Corral, M. Loose, J. Spatz, É. Karsenti, F. Nédélec, Cell 138 (2009) 502–513.","ista":"Dinarina A, Pugieux C, Corral M, Loose M, Spatz J, Karsenti É, Nédélec F. 2009. Chromatin shapes the mitotic spindle. Cell. 138(3), 502–513.","chicago":"Dinarina, Ana, Céline Pugieux, Maria Corral, Martin Loose, Joachim Spatz, Éric Karsenti, and François Nédélec. “Chromatin Shapes the Mitotic Spindle.” Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.05.027."},"month":"08","type":"journal_article","year":"2009","volume":138,"page":"502 - 513","title":"Chromatin shapes the mitotic spindle","publication":"Cell","abstract":[{"text":"In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.","lang":"eng"}],"day":"07","date_created":"2018-12-11T11:55:03Z","issue":"3","date_published":"2009-08-07T00:00:00Z","date_updated":"2021-01-12T06:54:30Z","status":"public","quality_controlled":0,"_id":"1984","acknowledgement":"This work was supported by EU contract LSHG-CT-2004-503568 ComBio, the Spanish ministry of education (M.M.C.), and EU-STREP active BioMics (A.D.). Research in the Nedelec lab is funded by the Center for Modeling and Simulation in the Biosciences (http://www.bioms.de), the Volkswagenstiftung, and Human Frontier Science Program grant RGY84.","extern":1,"intvolume":" 138","publisher":"Cell Press","publist_id":"5100","doi":"10.1016/j.cell.2009.05.027","author":[{"first_name":"Ana","last_name":"Dinarina","full_name":"Dinarina, Ana"},{"last_name":"Pugieux","first_name":"Céline","full_name":"Pugieux, Céline"},{"first_name":"Maria","last_name":"Corral","full_name":"Corral, Maria M"},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Spatz","first_name":"Joachim","full_name":"Spatz, Joachim P"},{"first_name":"Éric","last_name":"Karsenti","full_name":"Karsenti, Éric"},{"full_name":"Nédélec, François J","first_name":"François","last_name":"Nédélec"}],"publication_status":"published"}]