[{"_id":"9014","quality_controlled":"1","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"citation":{"ieee":"I. Theurkauff, C. Cottin-Bizonne, J. A. Palacci, C. Ybert, and L. Bocquet, “Dynamic clustering in active colloidal suspensions with chemical signaling,” <i>Physical Review Letters</i>, vol. 108, no. 26. American Physical Society , 2012.","ista":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. 2012. Dynamic clustering in active colloidal suspensions with chemical signaling. Physical Review Letters. 108(26), 268303.","short":"I. Theurkauff, C. Cottin-Bizonne, J.A. Palacci, C. Ybert, L. Bocquet, Physical Review Letters 108 (2012).","ama":"Theurkauff I, Cottin-Bizonne C, Palacci JA, Ybert C, Bocquet L. Dynamic clustering in active colloidal suspensions with chemical signaling. <i>Physical Review Letters</i>. 2012;108(26). doi:<a href=\"https://doi.org/10.1103/physrevlett.108.268303\">10.1103/physrevlett.108.268303</a>","chicago":"Theurkauff, I., C. Cottin-Bizonne, Jérémie A Palacci, C. Ybert, and L. Bocquet. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” <i>Physical Review Letters</i>. American Physical Society , 2012. <a href=\"https://doi.org/10.1103/physrevlett.108.268303\">https://doi.org/10.1103/physrevlett.108.268303</a>.","apa":"Theurkauff, I., Cottin-Bizonne, C., Palacci, J. A., Ybert, C., &#38; Bocquet, L. (2012). Dynamic clustering in active colloidal suspensions with chemical signaling. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.108.268303\">https://doi.org/10.1103/physrevlett.108.268303</a>","mla":"Theurkauff, I., et al. “Dynamic Clustering in Active Colloidal Suspensions with Chemical Signaling.” <i>Physical Review Letters</i>, vol. 108, no. 26, 268303, American Physical Society , 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.108.268303\">10.1103/physrevlett.108.268303</a>."},"extern":"1","type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers."}],"publication_status":"published","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Dynamic clustering in active colloidal suspensions with chemical signaling","author":[{"last_name":"Theurkauff","first_name":"I.","full_name":"Theurkauff, I."},{"first_name":"C.","last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, C."},{"last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"},{"first_name":"C.","last_name":"Ybert","full_name":"Ybert, C."},{"first_name":"L.","last_name":"Bocquet","full_name":"Bocquet, L."}],"publisher":"American Physical Society ","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"No","date_created":"2021-01-19T10:26:59Z","status":"public","day":"29","pmid":1,"volume":108,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1202.6264","open_access":"1"}],"doi":"10.1103/physrevlett.108.268303","publication":"Physical Review Letters","date_updated":"2023-02-23T13:46:45Z","issue":"26","oa":1,"month":"06","intvolume":"       108","date_published":"2012-06-29T00:00:00Z","article_number":"268303","year":"2012","external_id":{"arxiv":["1202.6264"],"pmid":["23005020"]}},{"oa_version":"None","publication":"Soft Matter","doi":"10.1039/c1sm06395b","publication_status":"published","status":"public","day":"28","quality_controlled":"1","date_created":"2021-02-01T13:43:10Z","_id":"9049","scopus_import":"1","abstract":[{"text":"Diffusiophoretic motion of colloids and macromolecules under salt gradients exhibits a logarithmic-sensing, i.e. the particle velocity is proportional to the spatial gradient of the logarithm of the salt concentration, as VDP = DDP∇logc. Here we explore experimentally the implications of this log-sensing behavior, on the basis of a hydrogel microfluidic device allowing to build spatially and temporally controlled gradients. We first demonstrate that the non-linearity of the salt-taxis leads to a trapping of particles under concentration gradient oscillations via a rectification of the motion. As an alternative, we make use of the high sensitivity of diffusiophoretic migration to vanishing salt concentration due to the log-sensing: in a counter-intuitive way, a vanishing gradient can lead to measurable velocity provided that the solute concentration is low enough, thus keeping ∇c/c finite. We show that this leads to a strong segregation of particles in osmotic shock configuration, resulting from a step change of the salt concentration at the boundaries. These various phenomena are rationalized on the basis of a theoretical description for the time-dependent Smoluchowski equation for the colloidal density.","lang":"eng"}],"type":"journal_article","volume":8,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"citation":{"mla":"Palacci, Jérémie A., et al. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” <i>Soft Matter</i>, vol. 8, no. 4, Royal Society of Chemistry, 2012, pp. 980–94, doi:<a href=\"https://doi.org/10.1039/c1sm06395b\">10.1039/c1sm06395b</a>.","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2012). Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c1sm06395b\">https://doi.org/10.1039/c1sm06395b</a>","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Osmotic Traps for Colloids and Macromolecules Based on Logarithmic Sensing in Salt Taxis.” <i>Soft Matter</i>. Royal Society of Chemistry, 2012. <a href=\"https://doi.org/10.1039/c1sm06395b\">https://doi.org/10.1039/c1sm06395b</a>.","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2012. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. Soft Matter. 8(4), 980–994.","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Soft Matter 8 (2012) 980–994.","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis,” <i>Soft Matter</i>, vol. 8, no. 4. Royal Society of Chemistry, pp. 980–994, 2012.","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis. <i>Soft Matter</i>. 2012;8(4):980-994. doi:<a href=\"https://doi.org/10.1039/c1sm06395b\">10.1039/c1sm06395b</a>"},"extern":"1","article_type":"original","year":"2012","language":[{"iso":"eng"}],"page":"980-994","article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","title":"Osmotic traps for colloids and macromolecules based on logarithmic sensing in salt taxis","author":[{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"},{"last_name":"Cottin-Bizonne","first_name":"Cécile","full_name":"Cottin-Bizonne, Cécile"},{"full_name":"Ybert, Christophe","last_name":"Ybert","first_name":"Christophe"},{"full_name":"Bocquet, Lydéric","first_name":"Lydéric","last_name":"Bocquet"}],"issue":"4","date_updated":"2023-02-23T13:47:31Z","publisher":"Royal Society of Chemistry","date_published":"2012-01-28T00:00:00Z","month":"01","intvolume":"         8"},{"author":[{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"full_name":"Cole, Jacqueline","first_name":"Jacqueline","last_name":"Cole"},{"first_name":"Martin","last_name":"Blood Forsythe","full_name":"Blood Forsythe, Martin"},{"first_name":"Daniel","last_name":"Hickstein","full_name":"Hickstein, Daniel"}],"title":"Identifying and evaluating organic nonlinear optical materials via molecular moments","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","date_updated":"2021-01-12T08:21:50Z","publisher":"American Institute of Physics","acknowledgement":"This work was supported by The Winston Churchill Foundation of the United States (A.P.H., M.A.B.F., D.D.H.), The Royal Society via a University Research Fellowship (J.M.C.), and the University of New Brunswick via The Vice-Chancellor’s Research Chair (J.M.C.).","article_number":"033512","date_published":"2012-02-07T00:00:00Z","month":"02","intvolume":"       111","year":"2012","language":[{"iso":"eng"}],"publist_id":"7963","status":"public","quality_controlled":"1","day":"07","date_created":"2018-12-11T11:44:35Z","_id":"91","abstract":[{"text":"We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. ","lang":"eng"}],"type":"journal_article","volume":111,"extern":"1","citation":{"chicago":"Higginbotham, Andrew P, Jacqueline Cole, Martin Blood Forsythe, and Daniel Hickstein. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” <i>Journal of Applied Physics</i>. American Institute of Physics, 2012. <a href=\"https://doi.org/10.1063/1.3678593\">https://doi.org/10.1063/1.3678593</a>.","ama":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. Identifying and evaluating organic nonlinear optical materials via molecular moments. <i>Journal of Applied Physics</i>. 2012;111(3). doi:<a href=\"https://doi.org/10.1063/1.3678593\">10.1063/1.3678593</a>","short":"A.P. Higginbotham, J. Cole, M. Blood Forsythe, D. Hickstein, Journal of Applied Physics 111 (2012).","ista":"Higginbotham AP, Cole J, Blood Forsythe M, Hickstein D. 2012. Identifying and evaluating organic nonlinear optical materials via molecular moments. Journal of Applied Physics. 111(3), 033512.","ieee":"A. P. Higginbotham, J. Cole, M. Blood Forsythe, and D. Hickstein, “Identifying and evaluating organic nonlinear optical materials via molecular moments,” <i>Journal of Applied Physics</i>, vol. 111, no. 3. American Institute of Physics, 2012.","mla":"Higginbotham, Andrew P., et al. “Identifying and Evaluating Organic Nonlinear Optical Materials via Molecular Moments.” <i>Journal of Applied Physics</i>, vol. 111, no. 3, 033512, American Institute of Physics, 2012, doi:<a href=\"https://doi.org/10.1063/1.3678593\">10.1063/1.3678593</a>.","apa":"Higginbotham, A. P., Cole, J., Blood Forsythe, M., &#38; Hickstein, D. (2012). Identifying and evaluating organic nonlinear optical materials via molecular moments. <i>Journal of Applied Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3678593\">https://doi.org/10.1063/1.3678593</a>"},"oa_version":"None","publication":"Journal of Applied Physics","doi":"10.1063/1.3678593","publication_status":"published"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/JAS-D-11-0257.1"}],"doi":"10.1175/jas-d-11-0257.1","publication":"Journal of the Atmospheric Sciences","oa_version":"Published Version","volume":69,"status":"public","day":"01","date_created":"2021-02-15T14:39:03Z","page":"2551-2565","year":"2012","intvolume":"        69","month":"08","date_published":"2012-08-01T00:00:00Z","issue":"8","oa":1,"date_updated":"2022-01-24T13:49:41Z","keyword":["Atmospheric Science"],"publication_status":"published","type":"journal_article","abstract":[{"text":"In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model.\r\nThe authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km.\r\nThe sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback.","lang":"eng"}],"extern":"1","citation":{"mla":"Muller, Caroline J., and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” <i>Journal of the Atmospheric Sciences</i>, vol. 69, no. 8, American Meteorological Society, 2012, pp. 2551–65, doi:<a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">10.1175/jas-d-11-0257.1</a>.","apa":"Muller, C. J., &#38; Held, I. M. (2012). Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. <i>Journal of the Atmospheric Sciences</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">https://doi.org/10.1175/jas-d-11-0257.1</a>","chicago":"Muller, Caroline J, and Isaac M. Held. “Detailed Investigation of the Self-Aggregation of Convection in Cloud-Resolving Simulations.” <i>Journal of the Atmospheric Sciences</i>. American Meteorological Society, 2012. <a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">https://doi.org/10.1175/jas-d-11-0257.1</a>.","ieee":"C. J. Muller and I. M. Held, “Detailed investigation of the self-aggregation of convection in cloud-resolving simulations,” <i>Journal of the Atmospheric Sciences</i>, vol. 69, no. 8. American Meteorological Society, pp. 2551–2565, 2012.","ista":"Muller CJ, Held IM. 2012. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. Journal of the Atmospheric Sciences. 69(8), 2551–2565.","short":"C.J. Muller, I.M. Held, Journal of the Atmospheric Sciences 69 (2012) 2551–2565.","ama":"Muller CJ, Held IM. Detailed investigation of the self-aggregation of convection in cloud-resolving simulations. <i>Journal of the Atmospheric Sciences</i>. 2012;69(8):2551-2565. doi:<a href=\"https://doi.org/10.1175/jas-d-11-0257.1\">10.1175/jas-d-11-0257.1</a>"},"publication_identifier":{"issn":["0022-4928","1520-0469"]},"quality_controlled":"1","_id":"9142","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"American Meteorological Society","author":[{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J"},{"full_name":"Held, Isaac M.","first_name":"Isaac M.","last_name":"Held"}],"title":"Detailed investigation of the self-aggregation of convection in cloud-resolving simulations","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"type":"journal_article","abstract":[{"text":"We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.","lang":"eng"}],"arxiv":1,"extern":"1","citation":{"short":"E.B. Hannezo, J. Prost, J. Joanny, Physical Review Letters 109 (2012).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Mechanical instabilities of biological tubes,” <i>Physical Review Letters</i>, vol. 109, no. 1. American Physical Society, 2012.","ista":"Hannezo EB, Prost J, Joanny J. 2012. Mechanical instabilities of biological tubes. Physical Review Letters. 109(1).","ama":"Hannezo EB, Prost J, Joanny J. Mechanical instabilities of biological tubes. <i>Physical Review Letters</i>. 2012;109(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">10.1103/PhysRevLett.109.018101</a>","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Mechanical Instabilities of Biological Tubes.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">https://doi.org/10.1103/PhysRevLett.109.018101</a>.","apa":"Hannezo, E. B., Prost, J., &#38; Joanny, J. (2012). Mechanical instabilities of biological tubes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">https://doi.org/10.1103/PhysRevLett.109.018101</a>","mla":"Hannezo, Edouard B., et al. “Mechanical Instabilities of Biological Tubes.” <i>Physical Review Letters</i>, vol. 109, no. 1, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.109.018101\">10.1103/PhysRevLett.109.018101</a>."},"volume":109,"day":"03","status":"public","_id":"922","date_created":"2018-12-11T11:49:13Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1207.1516"}],"doi":"10.1103/PhysRevLett.109.018101","publication":"Physical Review Letters","oa_version":"Preprint","publisher":"American Physical Society","month":"07","intvolume":"       109","date_published":"2012-07-03T00:00:00Z","issue":"1","title":"Mechanical instabilities of biological tubes","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Prost, Jacques","first_name":"Jacques","last_name":"Prost"},{"full_name":"Joanny, Jean","last_name":"Joanny","first_name":"Jean"}],"date_updated":"2021-01-12T08:21:56Z","publist_id":"6519","external_id":{"arxiv":["1207.1516"]},"article_processing_charge":"No","year":"2012","language":[{"iso":"eng"}]},{"publisher":"American Association for the Advancement of Science","has_accepted_license":"1","author":[{"last_name":"Ibarra","first_name":"Christian A.","full_name":"Ibarra, Christian A."},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng"},{"full_name":"Schoft, Vera K.","first_name":"Vera K.","last_name":"Schoft"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"first_name":"Rie","last_name":"Uzawa","full_name":"Uzawa, Rie"},{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"full_name":"Chumak, Nina","first_name":"Nina","last_name":"Chumak"},{"last_name":"Machlicova","first_name":"Adriana","full_name":"Machlicova, Adriana"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"last_name":"Rojas","first_name":"Denisse","full_name":"Rojas, Denisse"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"first_name":"Hisashi","last_name":"Tamaru","full_name":"Tamaru, Hisashi"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"type":"journal_article","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"extern":"1","citation":{"mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>"},"quality_controlled":"1","_id":"9451","publication_status":"published","date_published":"2012-09-14T00:00:00Z","intvolume":"       337","month":"09","oa":1,"issue":"6100","date_updated":"2021-12-14T08:28:51Z","external_id":{"pmid":["22984074"]},"page":"1360-1364","year":"2012","volume":337,"pmid":1,"status":"public","day":"14","ddc":["580"],"date_created":"2021-06-04T07:51:31Z","publication":"Science","doi":"10.1126/science.1224839","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"oa_version":"Published Version"},{"oa":1,"issue":"10","date_updated":"2021-12-14T08:29:57Z","article_number":"e1002988","date_published":"2012-10-11T00:00:00Z","intvolume":"         8","month":"10","year":"2012","external_id":{"pmid":["23071449"]},"day":"11","status":"public","date_created":"2021-06-07T10:55:27Z","volume":8,"pmid":1,"oa_version":"Published Version","publication":"PLoS Genetics","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"doi":"10.1371/journal.pgen.1002988","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"publisher":"Public Library of Science","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"article_processing_charge":"No","quality_controlled":"1","_id":"9497","abstract":[{"text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.","lang":"eng"}],"scopus_import":"1","type":"journal_article","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"citation":{"ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. 2012;8(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012).","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” <i>PLoS Genetics</i>, vol. 8, no. 10. Public Library of Science, 2012.","chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>."},"extern":"1","publication_status":"published"},{"_id":"9499","quality_controlled":"1","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"citation":{"mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>.","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &#38; Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>","chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>.","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. 2012;8(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>","ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” <i>PLoS Genetics</i>, vol. 8, no. 3. Public Library of Science, 2012."},"extern":"1","type":"journal_article","scopus_import":"1","abstract":[{"text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.","lang":"eng"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Kim, Sang Yeol","last_name":"Kim","first_name":"Sang Yeol"},{"full_name":"Lee, Jungeun","last_name":"Lee","first_name":"Jungeun"},{"full_name":"Eshed-Williams, Leor","first_name":"Leor","last_name":"Eshed-Williams"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Sung, Z. Renee","last_name":"Sung","first_name":"Z. Renee"}],"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","publisher":"Public Library of Science","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"DaZi"}],"date_created":"2021-06-07T11:07:56Z","status":"public","day":"22","pmid":1,"volume":8,"oa_version":"Published Version","doi":"10.1371/journal.pgen.1002512","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002512","open_access":"1"}],"publication":"PLoS Genetics","date_updated":"2021-12-14T08:31:14Z","issue":"3","oa":1,"intvolume":"         8","month":"03","date_published":"2012-03-22T00:00:00Z","article_number":"e1002512","year":"2012","external_id":{"pmid":["22457632"]}},{"publisher":"Elsevier","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"department":[{"_id":"DaZi"}],"article_processing_charge":"No","article_type":"review","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory."}],"scopus_import":"1","publication_identifier":{"issn":["0959-437X"]},"extern":"1","citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>.","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>"},"quality_controlled":"1","_id":"9528","publication_status":"published","intvolume":"        22","month":"04","date_published":"2012-04-01T00:00:00Z","issue":"2","date_updated":"2021-12-14T08:32:38Z","external_id":{"pmid":["22336527"]},"page":"132-138","year":"2012","pmid":1,"volume":22,"status":"public","date_created":"2021-06-08T08:58:52Z","doi":"10.1016/j.gde.2012.01.007","publication":"Current Opinion in Genetics and Development","oa_version":"None"},{"language":[{"iso":"eng"}],"article_type":"review","article_processing_charge":"No","department":[{"_id":"DaZi"}],"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","author":[{"first_name":"D.","last_name":"Coleman-Derr","full_name":"Coleman-Derr, D."},{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Cold Spring Harbor Laboratory Press","publication_status":"published","_id":"9535","quality_controlled":"1","publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"extern":"1","citation":{"mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012."},"abstract":[{"text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies.","lang":"eng"}],"scopus_import":"1","type":"journal_article","year":"2012","page":"147-154","external_id":{"pmid":["23250988"]},"date_updated":"2021-12-14T08:33:09Z","oa":1,"date_published":"2012-12-18T00:00:00Z","month":"12","intvolume":"        77","oa_version":"Published Version","publication":"Cold Spring Harbor Symposia on Quantitative Biology","doi":"10.1101/sqb.2012.77.014944","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"date_created":"2021-06-08T13:01:23Z","day":"18","status":"public","volume":77,"pmid":1},{"month":"12","intvolume":"        86","date_published":"2012-12-13T00:00:00Z","publisher":"American Physical Society","acknowledgement":"We thank Kuang-Ting Chen, Rebecca Flint, Dmitri Ivanov, Z.-X. Liu, Tai-Kai Ng, Lara Thompson, Tamás Tóth, and Fa Wang for helpful discussions. T.S. is supported by NSF DMR 1005434. P.A.L. is supported by NSF DMR 1104498. S.B. acknowledges support from the Swiss National Science Foundation (SNSF).","date_updated":"2021-01-12T08:22:18Z","issue":"22","title":"Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice","oa":1,"author":[{"first_name":"Samuel","last_name":"Bieri","full_name":"Bieri, Samuel"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Maksym Serbyn"},{"first_name":"Todadri","last_name":"Senthil","full_name":"Senthil, Todadri S"},{"full_name":"Lee, Patrick","first_name":"Patrick","last_name":"Lee"}],"publist_id":"6431","year":"2012","citation":{"ama":"Bieri S, Serbyn M, Senthil T, Lee P. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2012;86(22). doi:<a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">10.1103/PhysRevB.86.224409</a>","ista":"Bieri S, Serbyn M, Senthil T, Lee P. 2012. Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 86(22).","short":"S. Bieri, M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 86 (2012).","ieee":"S. Bieri, M. Serbyn, T. Senthil, and P. Lee, “Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 86, no. 22. American Physical Society, 2012.","chicago":"Bieri, Samuel, Maksym Serbyn, Todadri Senthil, and Patrick Lee. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">https://doi.org/10.1103/PhysRevB.86.224409</a>.","apa":"Bieri, S., Serbyn, M., Senthil, T., &#38; Lee, P. (2012). Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">https://doi.org/10.1103/PhysRevB.86.224409</a>","mla":"Bieri, Samuel, et al. “Paired Chiral Spin Liquid with a Fermi Surface in S=1 Model on the Triangular Lattice.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 86, no. 22, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevB.86.224409\">10.1103/PhysRevB.86.224409</a>."},"extern":1,"volume":86,"type":"journal_article","abstract":[{"lang":"eng","text":"Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario."}],"date_created":"2018-12-11T11:49:27Z","_id":"966","day":"13","status":"public","quality_controlled":0,"main_file_link":[{"url":"https://arxiv.org/abs/1208.3231","open_access":"1"}],"publication_status":"published","doi":"10.1103/PhysRevB.86.224409","publication":"Physical Review B - Condensed Matter and Materials Physics"},{"author":[{"orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"title":"Mechanism of membrane tube formation induced by adhesive nanocomponents","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Physical Society","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","_id":"10387","type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process."}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"chicago":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012).","ieee":"A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” <i>Physical Review Letters</i>, vol. 109, no. 18. American Physical Society, 2012.","ista":"Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101.","ama":"Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. 2012;109(18). doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” <i>Physical Review Letters</i>, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.109.188101\">10.1103/physrevlett.109.188101</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.109.188101\">https://doi.org/10.1103/physrevlett.109.188101</a>"},"extern":"1","publication_status":"published","issue":"18","oa":1,"date_updated":"2021-11-29T14:29:25Z","keyword":["general physics and astronomy"],"article_number":"188101","month":"10","intvolume":"       109","date_published":"2012-10-31T00:00:00Z","year":"2012","external_id":{"pmid":["23215334"],"arxiv":["1206.3528"]},"day":"31","status":"public","date_created":"2021-11-29T14:08:00Z","pmid":1,"volume":109,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1206.3528","open_access":"1"}],"doi":"10.1103/physrevlett.109.188101","publication":"Physical Review Letters"},{"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"American Physical Society","author":[{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Cacciuto, Angelo","last_name":"Cacciuto","first_name":"Angelo"}],"title":"Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology."}],"arxiv":1,"citation":{"apa":"Šarić, A., &#38; Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>.","ama":"Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. <i>Physical Review Letters</i>. 2012;108(11). doi:<a href=\"https://doi.org/10.1103/physrevlett.108.118101\">10.1103/physrevlett.108.118101</a>","ieee":"A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” <i>Physical Review Letters</i>, vol. 108, no. 11. American Physical Society, 2012.","ista":"Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101.","short":"A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/physrevlett.108.118101\">https://doi.org/10.1103/physrevlett.108.118101</a>."},"extern":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"quality_controlled":"1","_id":"10388","external_id":{"pmid":["22540513"],"arxiv":["1201.0036"]},"year":"2012","article_number":"118101","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n","month":"03","intvolume":"       108","date_published":"2012-03-14T00:00:00Z","issue":"11","oa":1,"date_updated":"2021-11-29T15:12:13Z","keyword":["general physics and astronomy"],"main_file_link":[{"url":"https://arxiv.org/abs/1201.0036","open_access":"1"}],"doi":"10.1103/physrevlett.108.118101","publication":"Physical Review Letters","oa_version":"Preprint","pmid":1,"volume":108,"status":"public","day":"14","date_created":"2021-11-29T14:30:05Z"},{"volume":380,"extern":"1","citation":{"mla":"Erne, Barbara, et al. “Bulla in the Lung.” <i>The Lancet</i>, vol. 380, no. 9849, Elsevier, 2012, doi:<a href=\"https://doi.org/10.1016/S0140-6736(12)60690-4\">10.1016/S0140-6736(12)60690-4</a>.","apa":"Erne, B., Graff, M., Klemm, W., Danzl, J. G., &#38; Leschber, G. (2012). Bulla in the lung. <i>The Lancet</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0140-6736(12)60690-4\">https://doi.org/10.1016/S0140-6736(12)60690-4</a>","chicago":"Erne, Barbara, Mareike Graff, Wolfram Klemm, Johann G Danzl, and Gunda Leschber. “Bulla in the Lung.” <i>The Lancet</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/S0140-6736(12)60690-4\">https://doi.org/10.1016/S0140-6736(12)60690-4</a>.","ista":"Erne B, Graff M, Klemm W, Danzl JG, Leschber G. 2012. Bulla in the lung. The Lancet. 380(9849).","ieee":"B. Erne, M. Graff, W. Klemm, J. G. Danzl, and G. Leschber, “Bulla in the lung,” <i>The Lancet</i>, vol. 380, no. 9849. Elsevier, 2012.","short":"B. Erne, M. Graff, W. Klemm, J.G. Danzl, G. Leschber, The Lancet 380 (2012).","ama":"Erne B, Graff M, Klemm W, Danzl JG, Leschber G. Bulla in the lung. <i>The Lancet</i>. 2012;380(9849). doi:<a href=\"https://doi.org/10.1016/S0140-6736(12)60690-4\">10.1016/S0140-6736(12)60690-4</a>"},"abstract":[{"lang":"eng","text":"In July, 2011, a 32-year-old man presented with thoracic pain radiating to the left arm and upper dorsum, shortness of breath, and palpitations. He had had upper back tension for 6 months. Medical history was unremarkable apart from moderate nicotine use (two pack-years). Echocardiography, electrocardiography, and laboratory tests were unremarkable, excluding a cardiac event. CT of the chest after chest radiography showed a large bulla of 16 cm diameter in the right hemithorax (figure A). We did not detect radiological evidence of underlying pulmonary disease. The bulla wall was unremarkable and no structures were seen within the bulla."}],"type":"journal_article","date_created":"2018-12-11T11:49:54Z","_id":"1055","day":"01","status":"public","publication":"The Lancet","doi":"10.1016/S0140-6736(12)60690-4","publication_status":"published","oa_version":"None","date_published":"2012-10-01T00:00:00Z","intvolume":"       380","month":"10","acknowledgement":"We thank the interdisciplinary team at the ELK Berlin Chest Hospital.","publisher":"Elsevier","date_updated":"2021-01-12T06:47:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bulla in the lung","author":[{"last_name":"Erne","first_name":"Barbara","full_name":"Erne, Barbara"},{"last_name":"Graff","first_name":"Mareike","full_name":"Graff, Mareike"},{"first_name":"Wolfram","last_name":"Klemm","full_name":"Klemm, Wolfram"},{"orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Leschber, Gunda","first_name":"Gunda","last_name":"Leschber"}],"issue":"9849","article_processing_charge":"No","publist_id":"6333","language":[{"iso":"eng"}],"year":"2012"},{"arxiv":1,"abstract":[{"text":"We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation.","lang":"eng"}],"type":"journal_article","extern":"1","citation":{"chicago":"Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>. American Physical Society, 2012. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>.","short":"M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley, H. Nägerl, Physical Review Letters 108 (2012).","ieee":"M. Mark <i>et al.</i>, “Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions,” <i>Physical Review Letters</i>, vol. 108, no. 21. American Physical Society, 2012.","ista":"Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 108(21).","ama":"Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. 2012;108(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>","mla":"Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” <i>Physical Review Letters</i>, vol. 108, no. 21, American Physical Society, 2012, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">10.1103/PhysRevLett.108.215302</a>.","apa":"Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., … Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.108.215302\">https://doi.org/10.1103/PhysRevLett.108.215302</a>"},"_id":"1056","publication_status":"published","publisher":"American Physical Society","author":[{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"last_name":"Lauber","first_name":"Katharina","full_name":"Lauber, Katharina"},{"full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"first_name":"Alexander","last_name":"Janisch","full_name":"Janisch, Alexander"},{"full_name":"Büchler, Hans","last_name":"Büchler","first_name":"Hans"},{"full_name":"Daley, Andrew","last_name":"Daley","first_name":"Andrew"},{"full_name":"Nägerl, Hanns","first_name":"Hanns","last_name":"Nägerl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions","publist_id":"6334","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":108,"status":"public","day":"25","date_created":"2018-12-11T11:49:55Z","publication":"Physical Review Letters","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.1008"}],"doi":"10.1103/PhysRevLett.108.215302","oa_version":"Preprint","acknowledgement":"We are indebted to R. Grimm for generous support. We thank J. von Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417.","date_published":"2012-05-25T00:00:00Z","intvolume":"       108","month":"05","oa":1,"issue":"21","date_updated":"2021-01-12T06:47:58Z","external_id":{"arxiv":["1201.1008"]},"year":"2012"},{"publication_status":"published","_id":"11963","quality_controlled":"1","extern":"1","citation":{"ama":"Kumar GS, Pieber B, Reddy KR, Kappe CO. Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. <i>Chemistry - A European Journal</i>. 2012;18(20):6124-6128. doi:<a href=\"https://doi.org/10.1002/chem.201200815\">10.1002/chem.201200815</a>","ista":"Kumar GS, Pieber B, Reddy KR, Kappe CO. 2012. Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. Chemistry - A European Journal. 18(20), 6124–6128.","ieee":"G. S. Kumar, B. Pieber, K. R. Reddy, and C. O. Kappe, “Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats,” <i>Chemistry - A European Journal</i>, vol. 18, no. 20. Wiley, pp. 6124–6128, 2012.","short":"G.S. Kumar, B. Pieber, K.R. Reddy, C.O. Kappe, Chemistry - A European Journal 18 (2012) 6124–6128.","chicago":"Kumar, G. Sathish, Bartholomäus Pieber, K. Rajender Reddy, and C. Oliver Kappe. “Copper-Catalyzed Formation of C-O Bonds by Direct α-C-H Bond Activation of Ethers Using Stoichiometric Amounts of Peroxide in Batch and Continuous-Flow Formats.” <i>Chemistry - A European Journal</i>. Wiley, 2012. <a href=\"https://doi.org/10.1002/chem.201200815\">https://doi.org/10.1002/chem.201200815</a>.","apa":"Kumar, G. S., Pieber, B., Reddy, K. R., &#38; Kappe, C. O. (2012). Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. <i>Chemistry - A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.201200815\">https://doi.org/10.1002/chem.201200815</a>","mla":"Kumar, G. Sathish, et al. “Copper-Catalyzed Formation of C-O Bonds by Direct α-C-H Bond Activation of Ethers Using Stoichiometric Amounts of Peroxide in Batch and Continuous-Flow Formats.” <i>Chemistry - A European Journal</i>, vol. 18, no. 20, Wiley, 2012, pp. 6124–28, doi:<a href=\"https://doi.org/10.1002/chem.201200815\">10.1002/chem.201200815</a>."},"publication_identifier":{"issn":["0947-6539"],"eissn":["1521-3765"]},"type":"journal_article","abstract":[{"text":"Peroxides and ethers in flow: 2-Carbonyl-substituted phenols and β-ketoesters react safely with ethers in a microreactor environment using a copper catalyst and an organic peroxide (TBHP). This protocol results in unsymmetrical acetal scaffolds not easily available otherwise (see scheme).","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kumar, G. Sathish","last_name":"Kumar","first_name":"G. Sathish"},{"id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"full_name":"Reddy, K. Rajender","last_name":"Reddy","first_name":"K. Rajender"},{"first_name":"C. Oliver","last_name":"Kappe","full_name":"Kappe, C. Oliver"}],"title":"Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats","publisher":"Wiley","oa_version":"None","doi":"10.1002/chem.201200815","publication":"Chemistry - A European Journal","date_created":"2022-08-24T12:33:05Z","status":"public","day":"14","pmid":1,"volume":18,"year":"2012","external_id":{"pmid":["22492535"]},"page":"6124-6128","date_updated":"2023-02-21T10:09:33Z","issue":"20","intvolume":"        18","month":"05","date_published":"2012-05-14T00:00:00Z"},{"publisher":"Wiley","title":"Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Pieber","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus"},{"first_name":"David","last_name":"Cantillo","full_name":"Cantillo, David"},{"full_name":"Kappe, C. Oliver","last_name":"Kappe","first_name":"C. Oliver"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","citation":{"ista":"Pieber B, Cantillo D, Kappe CO. 2012. Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. Chemistry – A European Journal. 18(16), 5047–5055.","ieee":"B. Pieber, D. Cantillo, and C. O. Kappe, “Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry,” <i>Chemistry – A European Journal</i>, vol. 18, no. 16. Wiley, pp. 5047–5055, 2012.","short":"B. Pieber, D. Cantillo, C.O. Kappe, Chemistry – A European Journal 18 (2012) 5047–5055.","ama":"Pieber B, Cantillo D, Kappe CO. Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. <i>Chemistry – A European Journal</i>. 2012;18(16):5047-5055. doi:<a href=\"https://doi.org/10.1002/chem.201103748\">10.1002/chem.201103748</a>","chicago":"Pieber, Bartholomäus, David Cantillo, and C. Oliver Kappe. “Direct Arylation of Benzene with Aryl Bromides Using High‐temperature/High‐pressure Process Windows: Expanding the Scope of C-H Activation Chemistry.” <i>Chemistry – A European Journal</i>. Wiley, 2012. <a href=\"https://doi.org/10.1002/chem.201103748\">https://doi.org/10.1002/chem.201103748</a>.","apa":"Pieber, B., Cantillo, D., &#38; Kappe, C. O. (2012). Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. <i>Chemistry – A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.201103748\">https://doi.org/10.1002/chem.201103748</a>","mla":"Pieber, Bartholomäus, et al. “Direct Arylation of Benzene with Aryl Bromides Using High‐temperature/High‐pressure Process Windows: Expanding the Scope of C-H Activation Chemistry.” <i>Chemistry – A European Journal</i>, vol. 18, no. 16, Wiley, 2012, pp. 5047–55, doi:<a href=\"https://doi.org/10.1002/chem.201103748\">10.1002/chem.201103748</a>."},"extern":"1","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"A detailed investigation on the direct arylation of benzene with aryl bromides by using first-row transition metals under high-temperature/high-pressure (high-T/p) conditions is described. By employing a parallel reactor platform for rapid reaction screening and discovery at elevated temperatures, various metal/ligand/base combinations were evaluated for their ability to enable biaryl formation through C-H activation. The combination of cobalt(III) acetylacetonate and lithium bis(trimethylsilyl)amide was subjected to further process intensification at 200 °C (15 bar), allowing a significant reduction of the catalyst/base loading and a dramatic increase in catalytic efficiency (turnover frequency) by a factor of 1000 compared to traditional protocols. The high-throughput screening additionally identified novel nickel- and copper-based metal/ligand combinations that favored an amination pathway competing with C-H activation, with the addition of ligands, such as 1,10-phenanthroline, having a profound influence on the selectivity. In addition to metal-based catalysts, high-T/p process windows were also successfully applied to transition-metal-free systems, utilizing 1,10-phenanthroline as organocatalyst."}],"_id":"11964","quality_controlled":"1","publication_status":"published","intvolume":"        18","month":"04","date_published":"2012-04-16T00:00:00Z","date_updated":"2023-02-21T10:09:35Z","issue":"16","external_id":{"pmid":["22396386"]},"page":"5047-5055","year":"2012","pmid":1,"volume":18,"date_created":"2022-08-24T12:48:28Z","day":"16","status":"public","doi":"10.1002/chem.201103748","publication":"Chemistry – A European Journal","oa_version":"None"},{"volume":337,"pmid":1,"status":"public","day":"14","date_created":"2023-01-16T09:21:24Z","publication":"Science","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/"}],"doi":"10.1126/science.1224839","oa_version":"Published Version","acknowledgement":"We thank S. Harmer for assistance with the analysis of histone modifications, the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415) to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).","date_published":"2012-09-14T00:00:00Z","month":"09","intvolume":"       337","oa":1,"issue":"6100","keyword":["Multidisciplinary"],"date_updated":"2023-10-16T09:27:26Z","external_id":{"pmid":["22984074"]},"page":"1360-1364","year":"2012","scopus_import":"1","abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"type":"journal_article","citation":{"chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>"},"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"quality_controlled":"1","_id":"12198","publication_status":"published","publisher":"American Association for the Advancement of Science","title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ibarra, Christian A.","first_name":"Christian A.","last_name":"Ibarra"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"last_name":"Uzawa","first_name":"Rie","full_name":"Uzawa, Rie"},{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"last_name":"Machlicova","first_name":"Adriana","full_name":"Machlicova, Adriana"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"last_name":"Rojas","first_name":"Denisse","full_name":"Rojas, Denisse"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","first_name":"Hisashi","full_name":"Tamaru, Hisashi"},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"department":[{"_id":"XiFe"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"publication":"Water Resources Research","doi":"10.1029/2011wr010559","main_file_link":[{"url":"https://doi.org/10.1029/2011WR010559","open_access":"1"}],"oa_version":"Published Version","volume":48,"day":"01","status":"public","date_created":"2023-02-20T08:17:39Z","year":"2012","article_number":"W03509","date_published":"2012-03-01T00:00:00Z","intvolume":"        48","month":"03","oa":1,"issue":"3","date_updated":"2023-02-21T09:38:36Z","publication_status":"published","scopus_import":"1","abstract":[{"lang":"eng","text":"In the Dry Andes of central Chile, summer water resources originate mostly from snowmelt and ice melt. We use the physically based, spatially distributed hydrological model TOPKAPI to study the exchange between glaciers and climate in the upper Aconcagua River Basin during the summer season and identify the model parameters that are robust and transferable and those that are more dependent on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature index approach for snow and ice melting. We suggest a calibration procedure that allows calibration of parameters in three steps by separating parameters governing distinct processes. We evaluate the parameters' transferability in time and in space by applying the model at two spatial scales. TOPKAPI's ability to simulate the relevant processes is tested against meteorological, ablation, and glacier runoff data measured on Juncal Norte Glacier during two glacier ablation seasons. The model was applied successfully to the climatic setting of the Dry Andes once its parameters were recalibrated. We found a clear distinction between parameters that are stable in time and those that need recalibration. The parameters of the melt model are transferable from one season to the other, while the parameters governing the extrapolation of meteorological input data and the routing of glacier meltwater need recalibration from one season to the other. Sensitivity analysis revealed that the model is most sensitive to the temperature lapse rate governing the extrapolation of air temperature from point measurements to the glacier scale and to the melt parameter that multiplies the shortwave radiation balance."}],"type":"journal_article","publication_identifier":{"issn":["0043-1397"]},"citation":{"ama":"Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. <i>Water Resources Research</i>. 2012;48(3). doi:<a href=\"https://doi.org/10.1029/2011wr010559\">10.1029/2011wr010559</a>","ieee":"S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters,” <i>Water Resources Research</i>, vol. 48, no. 3. American Geophysical Union, 2012.","ista":"Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. Water Resources Research. 48(3), W03509.","short":"S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012).","chicago":"Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” <i>Water Resources Research</i>. American Geophysical Union, 2012. <a href=\"https://doi.org/10.1029/2011wr010559\">https://doi.org/10.1029/2011wr010559</a>.","apa":"Ragettli, S., &#38; Pellicciotti, F. (2012). Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2011wr010559\">https://doi.org/10.1029/2011wr010559</a>","mla":"Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” <i>Water Resources Research</i>, vol. 48, no. 3, W03509, American Geophysical Union, 2012, doi:<a href=\"https://doi.org/10.1029/2011wr010559\">10.1029/2011wr010559</a>."},"extern":"1","quality_controlled":"1","_id":"12644","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"American Geophysical Union","title":"Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ragettli, S.","last_name":"Ragettli","first_name":"S."},{"last_name":"Pellicciotti","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca"}]},{"date_published":"2012-02-01T00:00:00Z","month":"02","intvolume":"        32","date_updated":"2023-02-21T09:31:54Z","oa":1,"issue":"1","page":"39-50","year":"2012","volume":32,"date_created":"2023-02-20T08:17:47Z","status":"public","day":"01","publication":"Mountain Research and Development","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1"}],"doi":"10.1659/mrd-journal-d-11-00092.1","oa_version":"Published Version","publisher":"International Mountain Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies","author":[{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"full_name":"Buergi, Cyrill","first_name":"Cyrill","last_name":"Buergi"},{"last_name":"Immerzeel","first_name":"Walter Willem","full_name":"Immerzeel, Walter Willem"},{"first_name":"Markus","last_name":"Konz","full_name":"Konz, Markus"},{"first_name":"Arun B.","last_name":"Shrestha","full_name":"Shrestha, Arun B."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","citation":{"ieee":"F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha, “Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies,” <i>Mountain Research and Development</i>, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012.","short":"F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain Research and Development 32 (2012) 39–50.","ista":"Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. Mountain Research and Development. 32(1), 39–50.","ama":"Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. <i>Mountain Research and Development</i>. 2012;32(1):39-50. doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">10.1659/mrd-journal-d-11-00092.1</a>","chicago":"Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” <i>Mountain Research and Development</i>. International Mountain Society, 2012. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">https://doi.org/10.1659/mrd-journal-d-11-00092.1</a>.","apa":"Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., &#38; Shrestha, A. B. (2012). Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. <i>Mountain Research and Development</i>. International Mountain Society. <a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">https://doi.org/10.1659/mrd-journal-d-11-00092.1</a>","mla":"Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” <i>Mountain Research and Development</i>, vol. 32, no. 1, International Mountain Society, 2012, pp. 39–50, doi:<a href=\"https://doi.org/10.1659/mrd-journal-d-11-00092.1\">10.1659/mrd-journal-d-11-00092.1</a>."},"extern":"1","publication_identifier":{"eissn":["1994-7151"],"issn":["0276-4741"]},"abstract":[{"text":"Assessment of water resources from remote mountainous catchments plays a crucial role for the development of rural areas in or in the vicinity of mountain ranges. The scarcity of data, however, prevents the application of standard approaches that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain range is a crucial area in terms of water resources, but our understanding of the response of its high-elevation catchments to a changing climate is hindered by lack of hydro-meteorological and cryospheric data. Hydrological modeling is challenging here because internal inconsistencies—such as an underestimation of precipitation input that can be compensated for by an overestimation of meltwater—might be hidden due to the complexity of feedback mechanisms that govern melt and runoff generation in such basins. Data scarcity adds to this difficulty by preventing the application of systematic calibration procedures that would allow identification of the parameter set that could guarantee internal consistency in the simulation of the single hydrological components. In this work, we use simulations from the Hunza River Basin in the Karakoram region obtained with the hydrological model TOPKAPI to quantify the predictive power of discharge and snow-cover data sets, as well as the combination of both. We also show that short-term measurements of meteorological variables such as radiative fluxes, wind speed, relative humidity, and air temperature from glacio-meteorological experiments are crucial for a correct parameterization of surface melt processes. They enable detailed simulations of the energy fluxes governing glacier–atmosphere interaction and the resulting ablation through energy-balance modeling. These simulations are used to derive calibrated parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate that such parameters are stable in space and time in similar climatic regions, thus reducing the number of parameters requiring calibration.","lang":"eng"}],"scopus_import":"1","type":"journal_article","_id":"12646","quality_controlled":"1","publication_status":"published"}]