[{"citation":{"short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>","mla":"Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>, vol. 112, no. 4, 049801, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. 2014;112(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”. Physical Review Letters. 112(4), 049801.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>.","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact interactions make jammed particulate systems inherently nonharmonic,’” <i>Physical Review Letters</i>, vol. 112, no. 4. American Physical Society, 2014."},"year":"2014","publisher":"American Physical Society","volume":112,"external_id":{"arxiv":["1306.1285"]},"doi":"10.1103/physrevlett.112.049801","date_updated":"2021-01-12T08:15:26Z","issue":"4","publication_identifier":{"issn":["0031-9007","1079-7114"]},"title":"Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”","fulldoi":"https://doi.org/10.1103/physrevlett.112.049801","publication":"Physical Review Letters","author":[{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"article_type":"letter_note","language":[{"iso":"eng"}],"article_number":"049801 ","extern":"1","oa_version":"Preprint","article_processing_charge":"No","date_published":"2014-04-20T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is \"no harmonic regime in the large system limit for all compressions\" and \"at jamming onset for any system size.\" Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. ","lang":"eng"}],"arxiv":1,"intvolume":"       112","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.1285"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:42:39Z","type":"journal_article","_id":"7771","day":"20","oa":1},{"publication_identifier":{"issn":["1539-3755","1550-2376"]},"month":"01","intvolume":"        89","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:43:02Z","issue":"1","fulldoi":"https://doi.org/10.1103/physreve.89.012301","author":[{"first_name":"Tim","full_name":"Still, Tim","last_name":"Still"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Chen, Ke","first_name":"Ke","last_name":"Chen"},{"first_name":"Peter J.","full_name":"Yunker, Peter J.","last_name":"Yunker"},{"last_name":"Schoenholz","full_name":"Schoenholz, Samuel","first_name":"Samuel"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"A. G.","full_name":"Yodh, A. G.","last_name":"Yodh"}],"publication":"Physical Review E","_id":"7772","day":"03","type":"journal_article","title":"Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions","quality_controlled":"1","year":"2014","citation":{"apa":"Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A. J., &#38; Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>","short":"T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G. Yodh, Physical Review E 89 (2014).","mla":"Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>, vol. 89, no. 1, 012301, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>.","ista":"Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. 89(1), 012301.","ama":"Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>","chicago":"Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz, Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>.","ieee":"T. Still <i>et al.</i>, “Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions,” <i>Physical Review E</i>, vol. 89, no. 1. American Physical Society, 2014."},"volume":89,"publisher":"American Physical Society","language":[{"iso":"eng"}],"article_type":"original","article_number":"012301","article_processing_charge":"No","abstract":[{"text":"Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient.","lang":"eng"}],"status":"public","publication_status":"published","date_published":"2014-01-03T00:00:00Z","extern":"1","doi":"10.1103/physreve.89.012301","date_updated":"2021-01-12T08:15:26Z","oa_version":"None"},{"volume":10,"publisher":"Springer Nature","year":"2014","citation":{"mla":"Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>, vol. 10, no. 8, Springer Nature, 2014, pp. 578–81, doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. 2014;10(8):578-581. doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes of order and disorder. Nature Physics. 10(8), 578–581.","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical extremes of order and disorder,” <i>Nature Physics</i>, vol. 10, no. 8. Springer Nature, pp. 578–581, 2014."},"language":[{"iso":"eng"}],"article_type":"original","date_published":"2014-07-06T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder."}],"article_processing_charge":"No","oa_version":"None","extern":"1","doi":"10.1038/nphys3006","date_updated":"2021-01-12T08:15:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:43:29Z","intvolume":"        10","publication_identifier":{"issn":["1745-2473","1745-2481"]},"month":"07","issue":"8","publication":"Nature Physics","author":[{"orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich"},{"first_name":"Andrea J.","full_name":"Liu, Andrea J.","last_name":"Liu"},{"last_name":"Nagel","full_name":"Nagel, Sidney R.","first_name":"Sidney R."}],"fulldoi":"https://doi.org/10.1038/nphys3006","quality_controlled":"1","page":"578-581","title":"Solids between the mechanical extremes of order and disorder","day":"06","_id":"7773","type":"journal_article"},{"year":"2014","citation":{"chicago":"Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>.","ama":"Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(28):E2895-E2904. doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>","ista":"Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 111(28), E2895–E2904.","ieee":"R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine neck changes are correlated with synaptic strength,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28. Proceedings of the National Academy of Sciences, pp. E2895–E2904, 2014.","mla":"Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904, doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>.","short":"R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences 111 (2014) E2895–E2904.","apa":"Araya, R., Vogels, T. P., &#38; Yuste, R. (2014). Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>"},"publisher":"Proceedings of the National Academy of Sciences","volume":111,"external_id":{"pmid":["24982196"]},"pmid":1,"doi":"10.1073/pnas.1321869111","date_updated":"2021-01-12T08:16:34Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"28","fulldoi":"https://doi.org/10.1073/pnas.1321869111","author":[{"first_name":"R.","full_name":"Araya, R.","last_name":"Araya"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"},{"last_name":"Yuste","first_name":"R.","full_name":"Yuste, R."}],"publication":"Proceedings of the National Academy of Sciences","page":"E2895-E2904","title":"Activity-dependent dendritic spine neck changes are correlated with synaptic strength","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","date_published":"2014-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. "}],"publication_status":"published","status":"public","extern":"1","oa_version":"Published Version","intvolume":"       111","month":"07","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2020-06-25T13:06:24Z","oa":1,"day":"15","_id":"8021","type":"journal_article","quality_controlled":"1"},{"author":[{"full_name":"Hennequin, Guillaume","first_name":"Guillaume","last_name":"Hennequin"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Gerstner, Wulfram","first_name":"Wulfram","last_name":"Gerstner"}],"publication":"Neuron","fulldoi":"https://doi.org/10.1016/j.neuron.2014.04.045","page":"1394-1406","title":"Optimal control of transient dynamics in balanced networks supports generation of complex movements","publication_identifier":{"issn":["0896-6273"]},"issue":"6","pmid":1,"external_id":{"pmid":["24945778"]},"doi":"10.1016/j.neuron.2014.04.045","date_updated":"2021-01-12T08:16:35Z","publisher":"Elsevier","volume":82,"year":"2014","citation":{"ista":"Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406.","ama":"Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. 2014;82(6):1394-1406. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>","chicago":"Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>.","ieee":"G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” <i>Neuron</i>, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.","apa":"Hennequin, G., Vogels, T. P., &#38; Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>","mla":"Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>."},"oa":1,"quality_controlled":"1","day":"18","_id":"8022","type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2020-06-25T13:07:37Z","intvolume":"        82","month":"06","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/","open_access":"1"}],"date_published":"2014-06-18T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex."}],"publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","extern":"1","language":[{"iso":"eng"}],"article_type":"original"},{"doi":"10.1152/jn.00629.2013","date_updated":"2021-01-12T08:16:35Z","external_id":{"pmid":["24944218"]},"pmid":1,"year":"2014","citation":{"mla":"Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>, vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>.","apa":"Tomm, C., Avermann, M., Petersen, C., Gerstner, W., &#38; Vogels, T. P. (2014). Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>","short":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology 112 (2014) 1801–1814.","ieee":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific biases make uniform random network models consistent with cortical recordings,” <i>Journal of Neurophysiology</i>, vol. 112, no. 8. American Physiological Society, pp. 1801–1814, 2014.","chicago":"Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>.","ista":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. 112(8), 1801–1814.","ama":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. 2014;112(8):1801-1814. doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>"},"publisher":"American Physiological Society","volume":112,"title":"Connection-type-specific biases make uniform random network models consistent with cortical recordings","page":"1801-1814","file":[{"content_type":"application/pdf","date_updated":"2020-07-16T10:12:13Z","relation":"main_file","file_id":"8122","creator":"cziletti","checksum":"7c06a086da6f924342650de6dc555c3f","success":1,"access_level":"open_access","file_size":1632295,"file_name":"2014_JNeurophysiol_Tomm.pdf","date_created":"2020-07-16T10:12:13Z"}],"fulldoi":"https://doi.org/10.1152/jn.00629.2013","publication":"Journal of Neurophysiology","author":[{"last_name":"Tomm","first_name":"Christian","full_name":"Tomm, Christian"},{"full_name":"Avermann, Michael","first_name":"Michael","last_name":"Avermann"},{"last_name":"Petersen","first_name":"Carl","full_name":"Petersen, Carl"},{"first_name":"Wulfram","full_name":"Gerstner, Wulfram","last_name":"Gerstner"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"issue":"8","license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2020-07-16T10:12:13Z","ddc":["570"],"publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]},"extern":"1","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","status":"public","abstract":[{"text":"Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used.","lang":"eng"}],"has_accepted_license":"1","date_published":"2014-10-15T00:00:00Z","language":[{"iso":"eng"}],"article_type":"original","day":"15","_id":"8023","type":"journal_article","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)"},"month":"10","intvolume":"       112","date_created":"2020-06-25T13:08:30Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"date_updated":"2026-06-18T19:30:06Z","scopus_import":"1","OA_place":"publisher","year":"2014","citation":{"apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014."},"department":[{"_id":"RoSe"}],"publisher":"International Congress of Mathematicians","volume":3,"page":"1175-1194","title":"Structure of the excitation spectrum for many-body quantum systems","conference":{"location":"Seoul, South Korea","start_date":"2014-08-13","end_date":"2014-08-21","name":"ICM: International Congress of Mathematicans"},"author":[{"orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publication":"Proceeding of the International Congress of Mathematicans","ddc":["500"],"publication_identifier":{"isbn":["9788961058063"]},"oa_version":"Published Version","article_processing_charge":"No","date_published":"2014-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system."}],"status":"public","publication_status":"published","language":[{"iso":"eng"}],"_id":"8044","type":"conference","day":"01","quality_controlled":"1","corr_author":"1","oa":1,"OA_type":"free access","intvolume":"         3","main_file_link":[{"url":"http://www.icm2014.org/en/vod/proceedings.html","open_access":"1"}],"month":"08","date_created":"2020-06-29T07:59:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"8244","day":"01","type":"journal_article","page":"1777-1790","quality_controlled":"1","title":"Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients","fulldoi":"https://doi.org/10.1158/1535-7163.mct-13-0288","publication":"Molecular Cancer Therapeutics","author":[{"first_name":"J.","full_name":"Singer, J.","last_name":"Singer"},{"full_name":"Fazekas, Judit","first_name":"Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wang, W.","first_name":"W.","last_name":"Wang"},{"full_name":"Weichselbaumer, M.","first_name":"M.","last_name":"Weichselbaumer"},{"first_name":"M.","full_name":"Matz, M.","last_name":"Matz"},{"last_name":"Mader","full_name":"Mader, A.","first_name":"A."},{"last_name":"Steinfellner","full_name":"Steinfellner, W.","first_name":"W."},{"full_name":"Meitz, S.","first_name":"S.","last_name":"Meitz"},{"last_name":"Mechtcheriakova","first_name":"D.","full_name":"Mechtcheriakova, D."},{"full_name":"Sobanov, Y.","first_name":"Y.","last_name":"Sobanov"},{"first_name":"M.","full_name":"Willmann, M.","last_name":"Willmann"},{"last_name":"Stockner","first_name":"T.","full_name":"Stockner, T."},{"first_name":"E.","full_name":"Spillner, E.","last_name":"Spillner"},{"last_name":"Kunert","full_name":"Kunert, R.","first_name":"R."},{"full_name":"Jensen-Jarolim, E.","first_name":"E.","last_name":"Jensen-Jarolim"}],"issue":"7","intvolume":"        13","month":"07","publication_identifier":{"issn":["1535-7163","1538-8514"]},"date_created":"2020-08-10T11:54:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:17:42Z","doi":"10.1158/1535-7163.mct-13-0288","extern":"1","oa_version":"None","article_processing_charge":"No","date_published":"2014-07-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer."}],"status":"public","article_type":"original","language":[{"iso":"eng"}],"citation":{"mla":"Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” <i>Molecular Cancer Therapeutics</i>, vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:<a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">10.1158/1535-7163.mct-13-0288</a>.","short":"J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner, R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.","apa":"Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A., … Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. <i>Molecular Cancer Therapeutics</i>. American Association for Cancer Research. <a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">https://doi.org/10.1158/1535-7163.mct-13-0288</a>","chicago":"Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” <i>Molecular Cancer Therapeutics</i>. American Association for Cancer Research, 2014. <a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">https://doi.org/10.1158/1535-7163.mct-13-0288</a>.","ista":"Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E, Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 13(7), 1777–1790.","ama":"Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. <i>Molecular Cancer Therapeutics</i>. 2014;13(7):1777-1790. doi:<a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">10.1158/1535-7163.mct-13-0288</a>","ieee":"J. Singer <i>et al.</i>, “Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients,” <i>Molecular Cancer Therapeutics</i>, vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014."},"year":"2014","publisher":"American Association for Cancer Research","volume":13},{"date_created":"2020-09-18T10:07:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"issn":["0002-7863","1520-5126"]},"intvolume":"       136","issue":"51","publication":"Journal of the American Chemical Society","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Sébastien","full_name":"Triboulet, Sébastien","last_name":"Triboulet"},{"last_name":"Laguri","first_name":"Cédric","full_name":"Laguri, Cédric"},{"last_name":"Bougault","full_name":"Bougault, Catherine M.","first_name":"Catherine M."},{"last_name":"Ayala","full_name":"Ayala, Isabel","first_name":"Isabel"},{"full_name":"Callon, Morgane","first_name":"Morgane","last_name":"Callon"},{"last_name":"Arthur","full_name":"Arthur, Michel","first_name":"Michel"},{"full_name":"Simorre, Jean-Pierre","first_name":"Jean-Pierre","last_name":"Simorre"}],"fulldoi":"https://doi.org/10.1021/ja5105987","title":"Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan","page":"17852-17860","quality_controlled":"1","type":"journal_article","_id":"8458","day":"27","publisher":"American Chemical Society","volume":136,"citation":{"ieee":"P. Schanda <i>et al.</i>, “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014.","chicago":"Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>.","ama":"Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. 2014;136(51):17852-17860. doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>","ista":"Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860.","mla":"Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>.","short":"P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860.","apa":"Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>"},"year":"2014","article_type":"original","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis."}],"date_published":"2014-11-27T00:00:00Z","article_processing_charge":"No","oa_version":"None","date_updated":"2021-01-12T08:19:24Z","doi":"10.1021/ja5105987","extern":"1"},{"issue":"15","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioinformatics/btz397"}]},"publication_identifier":{"issn":["1367-4803","1460-2059"]},"page":"2219-2220","title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","author":[{"full_name":"Morin, Sébastien","first_name":"Sébastien","last_name":"Morin"},{"full_name":"Linnet, Troels E","first_name":"Troels E","last_name":"Linnet"},{"full_name":"Lescanne, Mathilde","first_name":"Mathilde","last_name":"Lescanne"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"last_name":"Thompson","full_name":"Thompson, Gary S","first_name":"Gary S"},{"first_name":"Martin","full_name":"Tollinger, Martin","last_name":"Tollinger"},{"last_name":"Teilum","first_name":"Kaare","full_name":"Teilum, Kaare"},{"full_name":"Gagné, Stéphane","first_name":"Stéphane","last_name":"Gagné"},{"last_name":"Marion","full_name":"Marion, Dominique","first_name":"Dominique"},{"last_name":"Griesinger","full_name":"Griesinger, Christian","first_name":"Christian"},{"last_name":"Blackledge","first_name":"Martin","full_name":"Blackledge, Martin"},{"first_name":"Edward J","full_name":"d’Auvergne, Edward J","last_name":"d’Auvergne"}],"publication":"Bioinformatics","fulldoi":"https://doi.org/10.1093/bioinformatics/btu166","publisher":"Oxford University Press","volume":30,"year":"2014","citation":{"ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. 2014;30(15):2219-2220. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>.","ieee":"S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220.","mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>."},"date_updated":"2021-01-12T08:19:25Z","doi":"10.1093/bioinformatics/btu166","keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-18T10:08:07Z","intvolume":"        30","month":"08","quality_controlled":"1","_id":"8459","day":"01","type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","oa_version":"None","extern":"1","date_published":"2014-08-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.","lang":"eng"}],"article_processing_charge":"No"},{"status":"public","abstract":[{"text":"The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states.","lang":"eng"}],"publication_status":"published","date_published":"2014-03-18T00:00:00Z","article_processing_charge":"No","oa_version":"None","doi":"10.1002/anie.201311275","date_updated":"2021-01-12T08:19:25Z","extern":"1","volume":53,"publisher":"Wiley","year":"2014","citation":{"chicago":"Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>.","ama":"Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. 2014;53(17):4312-4317. doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>","ista":"Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317.","ieee":"P. Ma <i>et al.</i>, “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.","mla":"Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>.","apa":"Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>","short":"P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317."},"language":[{"iso":"eng"}],"article_type":"original","author":[{"last_name":"Ma","full_name":"Ma, Peixiang","first_name":"Peixiang"},{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Zajakala","first_name":"Jérémy","full_name":"Zajakala, Jérémy"},{"full_name":"Macek, Pavel","first_name":"Pavel","last_name":"Macek"},{"last_name":"Sivertsen","full_name":"Sivertsen, Astrid C.","first_name":"Astrid C."},{"full_name":"Willbold, Dieter","first_name":"Dieter","last_name":"Willbold"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jérôme","first_name":"Jérôme"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"publication":"Angewandte Chemie International Edition","fulldoi":"https://doi.org/10.1002/anie.201311275","title":"Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy","quality_controlled":"1","page":"4312-4317","_id":"8460","day":"18","type":"journal_article","date_created":"2020-09-18T10:08:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1433-7851"]},"month":"03","intvolume":"        53","issue":"17"},{"oa_version":"None","extern":"1","date_published":"2014-05-01T00:00:00Z","abstract":[{"lang":"eng","text":"The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way."}],"publication_status":"published","status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","quality_controlled":"1","day":"01","_id":"8500","type":"journal_article","keyword":["Applied Mathematics","General Mathematics"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-18T10:47:01Z","intvolume":"        67","month":"05","doi":"10.1002/cpa.21509","date_updated":"2022-08-25T13:58:13Z","volume":67,"publisher":"Wiley","citation":{"mla":"Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>.","short":"V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775.","apa":"Kaloshin, V., Levi, M., &#38; Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>","chicago":"Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>.","ista":"Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775.","ama":"Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. 2014;67(5):748-775. doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>","ieee":"V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5. Wiley, pp. 748–775, 2014."},"year":"2014","page":"748-775","title":"Arnol′d diffusion in a pendulum lattice","author":[{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"},{"full_name":"Saprykina, Maria","first_name":"Maria","last_name":"Saprykina"}],"publication":"Communications on Pure and Applied Mathematics","fulldoi":"https://doi.org/10.1002/cpa.21509","issue":"5","publication_identifier":{"issn":["0010-3640"]}},{"intvolume":"        14","month":"04","keyword":["General Mathematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-18T10:47:09Z","arxiv":1,"_id":"8501","type":"journal_article","day":"01","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","date_published":"2014-04-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation."}],"status":"public","extern":"1","oa_version":"Preprint","publication_identifier":{"issn":["1609-3321","1609-4514"]},"issue":"2","fulldoi":"https://doi.org/10.17323/1609-4514-2014-14-2-181-203","author":[{"last_name":"Bounemoura","first_name":"Abed","full_name":"Bounemoura, Abed"},{"orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin"}],"publication":"Moscow Mathematical Journal","page":"181-203","title":"Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom","year":"2014","citation":{"mla":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>.","short":"A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>","ieee":"A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>.","ista":"Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203.","ama":"Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. 2014;14(2):181-203. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>"},"volume":14,"publisher":"Independent University of Moscow","external_id":{"arxiv":["1304.3050"]},"date_updated":"2021-01-12T08:19:43Z","doi":"10.17323/1609-4514-2014-14-2-181-203"},{"quality_controlled":"1","type":"journal_article","_id":"9050","day":"21","oa":1,"arxiv":1,"keyword":["General Chemistry","Condensed Matter Physics"],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2021-02-01T13:43:31Z","intvolume":"        10","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.5662"}],"oa_version":"Preprint","extern":"1","date_published":"2014-03-21T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter.","lang":"eng"}],"article_processing_charge":"No","article_number":"1784","language":[{"iso":"eng"}],"article_type":"original","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","publication":"Soft Matter","author":[{"last_name":"Takagi","full_name":"Takagi, Daisuke","first_name":"Daisuke"},{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"},{"last_name":"Braunschweig","full_name":"Braunschweig, Adam B.","first_name":"Adam B."},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"first_name":"Jun","full_name":"Zhang, Jun","last_name":"Zhang"}],"fulldoi":"https://doi.org/10.1039/c3sm52815d","issue":"11","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"scopus_import":"1","pmid":1,"external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"date_updated":"2023-02-23T13:47:35Z","doi":"10.1039/c3sm52815d","publisher":"Royal Society of Chemistry ","volume":10,"citation":{"mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>"},"year":"2014"},{"intvolume":"       372","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_created":"2021-02-18T14:31:11Z","arxiv":1,"oa":1,"type":"journal_article","_id":"9166","day":"28","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","article_number":"20130372","article_processing_charge":"No","date_published":"2014-11-28T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.","lang":"eng"}],"extern":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"issue":"2029","fulldoi":"https://doi.org/10.1098/rsta.2013.0372","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","author":[{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"},{"first_name":"S.","full_name":"Sacanna, S.","last_name":"Sacanna"},{"first_name":"S.-H.","full_name":"Kim, S.-H.","last_name":"Kim"},{"full_name":"Yi, G.-R.","first_name":"G.-R.","last_name":"Yi"},{"last_name":"Pine","first_name":"D. J.","full_name":"Pine, D. J."},{"last_name":"Chaikin","first_name":"P. M.","full_name":"Chaikin, P. M."}],"title":"Light-activated self-propelled colloids","citation":{"short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., &#38; Chaikin, P. M. (2014). Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>.","ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2014;372(2029). doi:<a href=\"https://doi.org/10.1098/rsta.2013.0372\">10.1098/rsta.2013.0372</a>","chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rsta.2013.0372\">https://doi.org/10.1098/rsta.2013.0372</a>.","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” <i>Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 372, no. 2029. The Royal Society, 2014."},"year":"2014","publisher":"The Royal Society","volume":372,"pmid":1,"external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"date_updated":"2021-02-22T10:44:16Z","doi":"10.1098/rsta.2013.0372","scopus_import":"1"},{"language":[{"iso":"eng"}],"article_type":"original","extern":"1","oa_version":"Published Version","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"publication_status":"published","status":"public","date_published":"2014-03-13T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"month":"03","intvolume":"       156","date_created":"2021-06-04T12:00:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"13","_id":"9458","type":"journal_article","quality_controlled":"1","oa":1,"department":[{"_id":"DaZi"}],"year":"2014","citation":{"ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>."},"volume":156,"publisher":"Elsevier","date_updated":"2021-12-14T08:22:36Z","doi":"10.1016/j.cell.2014.01.029","external_id":{"pmid":["24630728"]},"pmid":1,"scopus_import":"1","issue":"6","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","page":"1286-1297","fulldoi":"https://doi.org/10.1016/j.cell.2014.01.029","publication":"Cell","author":[{"last_name":"Huff","full_name":"Huff, Jason T.","first_name":"Jason T."},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"}]},{"department":[{"_id":"DaZi"}],"year":"2014","citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>"},"publisher":"National Academy of Sciences","volume":111,"date_updated":"2021-12-14T08:23:26Z","doi":"10.1073/pnas.1418564111","external_id":{"pmid":["25344531"]},"pmid":1,"scopus_import":"1","issue":"45","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","page":"16166-16171","fulldoi":"https://doi.org/10.1073/pnas.1418564111","author":[{"full_name":"Mérai, Zsuzsanna","first_name":"Zsuzsanna","last_name":"Mérai"},{"last_name":"Chumak","first_name":"Nina","full_name":"Chumak, Nina"},{"full_name":"García-Aguilar, Marcelina","first_name":"Marcelina","last_name":"García-Aguilar"},{"first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh"},{"last_name":"Nishimura","full_name":"Nishimura, Toshiro","first_name":"Toshiro"},{"last_name":"Schoft","full_name":"Schoft, Vera K.","first_name":"Vera K."},{"last_name":"Bindics","full_name":"Bindics, János","first_name":"János"},{"first_name":"Lucyna","full_name":"Ślusarz, Lucyna","last_name":"Ślusarz"},{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"full_name":"Opravil, Susanne","first_name":"Susanne","last_name":"Opravil"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"first_name":"Hisashi","full_name":"Tamaru, Hisashi","last_name":"Tamaru"}],"publication":"Proceedings of the National Academy of Sciences","article_type":"original","language":[{"iso":"eng"}],"extern":"1","oa_version":"Published Version","article_processing_charge":"No","status":"public","publication_status":"published","abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"date_published":"2014-11-11T00:00:00Z","month":"11","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"intvolume":"       111","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-06-07T07:23:43Z","day":"11","_id":"9479","type":"journal_article","quality_controlled":"1","oa":1},{"year":"2014","citation":{"ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>"},"department":[{"_id":"DaZi"}],"volume":19,"publisher":"Elsevier","external_id":{"pmid":["24618094 "]},"pmid":1,"date_updated":"2021-12-14T08:24:48Z","doi":"10.1016/j.tplants.2014.01.014","scopus_import":"1","issue":"5","publication_identifier":{"eissn":["1878-4372"],"issn":["1360-1385"]},"page":"320-326","title":"DNA methylation as a system of plant genomic immunity","fulldoi":"https://doi.org/10.1016/j.tplants.2014.01.014","publication":"Trends in Plant Science","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"language":[{"iso":"eng"}],"article_type":"review","extern":"1","oa_version":"None","article_processing_charge":"No","date_published":"2014-05-04T00:00:00Z","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"intvolume":"        19","month":"05","date_created":"2021-06-07T14:38:09Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9519","day":"04","type":"journal_article","quality_controlled":"1"},{"arxiv":1,"intvolume":"        21","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.37236/3752"}],"date_created":"2021-06-23T06:29:35Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9594","day":"28","type":"journal_article","quality_controlled":"1","oa":1,"article_type":"original","language":[{"iso":"eng"}],"article_number":"P1.45","extern":"1","oa_version":"Published Version","article_processing_charge":"No","date_published":"2014-02-28T00:00:00Z","abstract":[{"lang":"eng","text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture."}],"status":"public","publication_status":"published","issue":"1","publication_identifier":{"eissn":["1077-8926"]},"title":"On the number of spanning trees in random regular graphs","fulldoi":"https://doi.org/10.37236/3752","author":[{"full_name":"Greenhill, Catherine","first_name":"Catherine","last_name":"Greenhill"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"first_name":"David","full_name":"Wind, David","last_name":"Wind"}],"publication":"The Electronic Journal of Combinatorics","year":"2014","citation":{"apa":"Greenhill, C., Kwan, M. A., &#38; Wind, D. (2014). On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>.","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. 2014;21(1). doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>","ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2014. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>.","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014."},"volume":21,"publisher":"The Electronic Journal of Combinatorics","external_id":{"arxiv":["1309.6710"]},"doi":"10.37236/3752","date_updated":"2023-02-23T14:02:12Z","scopus_import":"1"},{"year":"2014","citation":{"mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., &#38; Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. American Physiological Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>","short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2. American Physiological Society, 2014.","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>.","ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. 2014;112(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>","ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801."},"publisher":"American Physiological Society","volume":112,"doi":"10.1103/PhysRevLett.112.026801","date_updated":"2021-01-12T08:22:14Z","external_id":{"arxiv":["1306.2720"]},"issue":"2","acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","fulldoi":"https://doi.org/10.1103/PhysRevLett.112.026801","publication":"APS Physics, Physical Review Letters","author":[{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"},{"first_name":"Micah","full_name":"Hanson, Micah","last_name":"Hanson"},{"last_name":"Gossard","first_name":"Arthur","full_name":"Gossard, Arthur"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"title":"Coherent operations and screening in multielectron spin qubits","publist_id":"7958","language":[{"iso":"eng"}],"article_number":"026801","abstract":[{"lang":"eng","text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (&gt;1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range."}],"publication_status":"published","status":"public","date_published":"2014-01-14T00:00:00Z","extern":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.2720"}],"month":"01","intvolume":"       112","date_created":"2018-12-11T11:44:36Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa":1,"_id":"96","type":"journal_article","day":"14","quality_controlled":"1"}]