[{"author":[{"first_name":"Chao","last_name":"Chen","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Freedman, Daniel","last_name":"Freedman","first_name":"Daniel"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"ddc":["000"],"type":"technical_report","pubrep_id":"22","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2011-0002","status":"public","related_material":{"record":[{"status":"public","id":"3336","relation":"later_version"}]},"page":"69","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T20:54:30Z","abstract":[{"text":"We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"alternative_title":["IST Austria Technical Report"],"day":"28","month":"03","oa":1,"citation":{"short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>.","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","ama":"Chen C, Freedman D, Lampert C. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>","ieee":"C. Chen, D. Freedman, and C. Lampert, <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria, 2011.","apa":"Chen, C., Freedman, D., &#38; Lampert, C. (2011). <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>","mla":"Chen, Chao, et al. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>."},"language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"ChLa"}],"publisher":"IST Austria","file":[{"creator":"system","content_type":"application/pdf","file_size":26390601,"relation":"main_file","date_created":"2018-12-12T11:53:34Z","access_level":"open_access","file_name":"IST-2011-0002_IST-2011-0002.pdf","date_updated":"2020-07-14T12:46:41Z","file_id":"5495","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526"}],"year":"2011","file_date_updated":"2020-07-14T12:46:41Z","date_published":"2011-03-28T00:00:00Z","title":"Enforcing topological constraints in random field image segmentation","_id":"5386","date_created":"2018-12-12T11:39:02Z"},{"title":"Energy and mean-payoff parity Markov decision processes","_id":"5387","date_created":"2018-12-12T11:39:02Z","year":"2011","date_published":"2011-02-16T00:00:00Z","file_date_updated":"2020-07-14T12:46:41Z","department":[{"_id":"KrCh"}],"publisher":"IST Austria","file":[{"checksum":"824d6c70e6d3feb3e836b009e0b3cf73","file_id":"5458","date_updated":"2020-07-14T12:46:41Z","file_name":"IST-2011-0001_IST-2011-0001.pdf","access_level":"open_access","date_created":"2018-12-12T11:52:57Z","relation":"main_file","file_size":329976,"content_type":"application/pdf","creator":"system"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011.","ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011."},"has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"day":"16","month":"02","abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"date_updated":"2025-04-15T08:12:14Z","related_material":{"record":[{"status":"public","id":"3345","relation":"later_version"}]},"page":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","doi":"10.15479/AT:IST-2011-0001","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"23","publication_status":"published","type":"technical_report","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"ddc":["000","005"]},{"quality_controlled":0,"doi":"10.1038/474170a","status":"public","page":"170 - 171","author":[{"first_name":"Onur","last_name":"Hosten","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","extern":1,"publication_status":"published","issue":"7350","citation":{"chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>.","ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","short":"O. Hosten, Nature 474 (2011) 170–171.","ieee":"O. Hosten, “Quantum physics: How to catch a wave,” <i>Nature</i>, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>","ama":"Hosten O. Quantum physics: How to catch a wave. <i>Nature</i>. 2011;474(7350):170-171. doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>"},"publication":"Nature","publisher":"Nature Publishing Group","intvolume":"       474","year":"2011","publist_id":"7224","date_published":"2011-06-08T00:00:00Z","_id":"580","title":"Quantum physics: How to catch a wave","date_created":"2018-12-11T11:47:18Z","date_updated":"2021-01-12T08:03:34Z","volume":474,"day":"08","month":"06"},{"status":"public","doi":"10.1364/CLEO_AT.2011.JThB130","quality_controlled":0,"conference":{"name":"QELS: Quantum Electronics and Laser Science"},"author":[{"last_name":"Schmid","first_name":"David","full_name":"Schmid, David"},{"first_name":"Shiraz","last_name":"Hazrat","full_name":"Hazrat, Shiraz"},{"first_name":"Radhika","last_name":"Rangarajan","full_name":"Rangarajan, Radhika"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur"},{"first_name":"Stephan","last_name":"Quint","full_name":"Quint, Stephan"},{"first_name":"Paul","last_name":"Kwiat","full_name":"Kwiat, Paul G"}],"publication_status":"published","type":"conference","extern":1,"publisher":"OSA","citation":{"ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., &#38; Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>","mla":"Schmid, David, et al. <i>Methods towards Achieving Precise Birefringent Focusing</i>. OSA, 2011, doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>.","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011.","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, .","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>."},"date_created":"2018-12-11T11:47:20Z","title":"Methods towards achieving precise birefringent focusing","_id":"585","date_published":"2011-01-01T00:00:00Z","year":"2011","publist_id":"7220","date_updated":"2021-01-12T08:03:44Z","month":"01","day":"01","alternative_title":["Optics InfoBase Conference Papers"],"abstract":[{"text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n","lang":"eng"}]},{"intvolume":"       107","publisher":"American Physical Society","publication":"Physical Review Letters","issue":"6","citation":{"ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. 2011;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>","ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” <i>Physical Review Letters</i>, vol. 107, no. 6. American Physical Society, 2011.","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., &#38; Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>, vol. 107, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>.","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>.","ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6)."},"date_created":"2018-12-11T11:47:20Z","_id":"586","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","date_published":"2011-08-04T00:00:00Z","year":"2011","publist_id":"7223","volume":107,"date_updated":"2021-01-12T08:05:05Z","day":"04","month":"08","abstract":[{"text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research.","lang":"eng"}],"status":"public","doi":"10.1103/PhysRevLett.107.063904","quality_controlled":0,"author":[{"first_name":"Geert","last_name":"Vrijsen","full_name":"Vrijsen, Geert"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur"},{"full_name":"Lee, Jongmin","last_name":"Lee","first_name":"Jongmin"},{"full_name":"Bernon, Simon","last_name":"Bernon","first_name":"Simon"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark A"}],"publication_status":"published","extern":1,"type":"journal_article"},{"status":"public","doi":"10.1371/journal.pbio.1000603","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","author":[{"last_name":"Bernecky","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"last_name":"Grob","first_name":"Patricia","full_name":"Grob, Patricia"},{"last_name":"Ebmeier","first_name":"Christopher","full_name":"Ebmeier, Christopher"},{"last_name":"Nogales","first_name":"Eva","full_name":"Nogales, Eva"},{"last_name":"Taatjes","first_name":"Dylan","full_name":"Taatjes, Dylan"}],"publication_status":"published","article_processing_charge":"No","extern":"1","type":"journal_article","intvolume":"         9","publisher":"Public Library of Science","publication":"PLoS Biology","issue":"3","language":[{"iso":"eng"}],"citation":{"ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. 2011;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., &#38; Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>, vol. 9, no. 3, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>.","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” <i>PLoS Biology</i>, vol. 9, no. 3. Public Library of Science, 2011.","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>."},"date_created":"2018-12-11T11:47:24Z","_id":"597","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","date_published":"2011-03-01T00:00:00Z","publist_id":"7209","year":"2011","date_updated":"2021-01-12T08:05:25Z","volume":9,"day":"01","month":"03","abstract":[{"lang":"eng","text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly."}]},{"publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/"}],"citation":{"apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., &#38; Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>.","ieee":"K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011.","ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(51):20672-20677. doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>","ista":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 108(51), 20672–20677.","chicago":"Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>.","short":"K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings of the National Academy of Sciences 108 (2011) 20672–20677."},"publication":"Proceedings of the National Academy of Sciences","title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","_id":"6137","date_updated":"2021-01-12T08:06:18Z","day":"20","status":"public","quality_controlled":"1","doi":"10.1073/pnas.1106134109","publication_identifier":{"issn":["0027-8424","1091-6490"]},"page":"20672-20677","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","extern":"1","type":"journal_article","intvolume":"       108","language":[{"iso":"eng"}],"issue":"51","oa":1,"date_created":"2019-03-20T14:30:06Z","year":"2011","date_published":"2011-12-20T00:00:00Z","volume":108,"month":"12","abstract":[{"lang":"eng","text":"Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies."}],"author":[{"first_name":"K.","last_name":"Milward","full_name":"Milward, K."},{"full_name":"Busch, K. E.","first_name":"K. E.","last_name":"Busch"},{"full_name":"Murphy, R. J.","last_name":"Murphy","first_name":"R. J."},{"last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"},{"full_name":"Olofsson, B.","first_name":"B.","last_name":"Olofsson"}],"pmid":1,"publication_status":"published","external_id":{"pmid":["22135454"]}},{"title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","_id":"6138","file":[{"checksum":"547cffd123f4c508ae927c9244b8f92a","file_id":"6139","file_name":"2011_Cell_Bretscher.pdf","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-20T15:06:32Z","relation":"main_file","access_level":"open_access","creator":"kschuh","file_size":2448332,"content_type":"application/pdf"}],"publisher":"Elsevier BV","publication":"Neuron","has_accepted_license":"1","citation":{"chicago":"Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>. Elsevier BV, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>.","ista":"Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.","short":"A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P. Laurent, M. de Bono, Neuron 69 (2011) 1099–1113.","ieee":"A. J. Bretscher <i>et al.</i>, “Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior,” <i>Neuron</i>, vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.","mla":"Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>, vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>.","apa":"Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z., Laurent, P., &#38; de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>","ama":"Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. 2011;69(6):1099-1113. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>"},"day":"24","date_updated":"2021-01-12T08:06:18Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","page":"1099-1113","status":"public","doi":"10.1016/j.neuron.2011.02.023","publication_identifier":{"issn":["0896-6273"]},"quality_controlled":"1","extern":"1","type":"journal_article","ddc":["570"],"date_created":"2019-03-20T15:01:41Z","date_published":"2011-03-24T00:00:00Z","file_date_updated":"2020-07-14T12:47:20Z","year":"2011","intvolume":"        69","oa":1,"issue":"6","language":[{"iso":"eng"}],"month":"03","volume":69,"publication_status":"published","pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["21435556"]},"author":[{"last_name":"Bretscher","first_name":"Andrew Jonathan","full_name":"Bretscher, Andrew Jonathan"},{"full_name":"Kodama-Namba, Eiji","first_name":"Eiji","last_name":"Kodama-Namba"},{"full_name":"Busch, Karl Emanuel","last_name":"Busch","first_name":"Karl Emanuel"},{"full_name":"Murphy, Robin Joseph","first_name":"Robin Joseph","last_name":"Murphy"},{"first_name":"Zoltan","last_name":"Soltesz","full_name":"Soltesz, Zoltan"},{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono"}]},{"quality_controlled":"1","publication_identifier":{"issn":["1553-7404"]},"doi":"10.1371/journal.pgen.1001341","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","ddc":["570"],"type":"journal_article","extern":"1","citation":{"apa":"Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse, M., &#38; de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>","mla":"Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>, vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>.","ieee":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse, and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability,” <i>PLoS Genetics</i>, vol. 7, no. 3. Public Library of Science, 2011.","ama":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. 2011;7(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>","ista":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. 7(3), e1001341.","chicago":"Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H. Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>.","short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011)."},"publication":"PLoS Genetics","has_accepted_license":"1","publisher":"Public Library of Science","file":[{"creator":"kschuh","file_size":5625063,"content_type":"application/pdf","relation":"main_file","date_created":"2019-03-20T15:18:11Z","access_level":"open_access","file_name":"2011_PLOS_Arellano-Carbajal.PDF","date_updated":"2020-07-14T12:47:20Z","file_id":"6141","checksum":"c609b2ce616d7dafbb617ec5d022f1ea"}],"title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability","_id":"6140","date_updated":"2021-01-12T08:06:19Z","day":"17","author":[{"first_name":"Fausto","last_name":"Arellano-Carbajal","full_name":"Arellano-Carbajal, Fausto"},{"full_name":"Briseño-Roa, Luis","first_name":"Luis","last_name":"Briseño-Roa"},{"first_name":"Africa","last_name":"Couto","full_name":"Couto, Africa"},{"first_name":"Benny H. H.","last_name":"Cheung","full_name":"Cheung, Benny H. H."},{"first_name":"Michel","last_name":"Labouesse","full_name":"Labouesse, Michel"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"external_id":{"pmid":["21437263"]},"article_number":"e1001341","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication_status":"published","oa":1,"issue":"3","language":[{"iso":"eng"}],"intvolume":"         7","year":"2011","file_date_updated":"2020-07-14T12:47:20Z","date_published":"2011-03-17T00:00:00Z","date_created":"2019-03-20T15:08:23Z","volume":7,"abstract":[{"lang":"eng","text":"Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca2+ transients, at least in some neurons: in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O2, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+ channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators."}],"month":"03"},{"year":"2011","date_published":"2011-07-22T00:00:00Z","_id":"6298","title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers","date_created":"2019-04-11T20:57:43Z","oa":1,"issue":"29","citation":{"short":"N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day, R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.","chicago":"Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs, Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>.","ista":"Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29), 25675–25686.","ama":"Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. 2011;286(29):25675-25686. doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>","ieee":"N. S. Baranova <i>et al.</i>, “The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29. American Society for Biochemistry &#38; Molecular Biology, pp. 25675–25686, 2011.","apa":"Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day, A. J., &#38; Richter, R. P. (2011). The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>","mla":"Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29, American Society for Biochemistry &#38; Molecular Biology, 2011, pp. 25675–86, doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>."},"language":[{"iso":"eng"}],"publication":"Journal of Biological Chemistry","publisher":"American Society for Biochemistry & Molecular Biology","intvolume":"       286","main_file_link":[{"url":"http://www.jbc.org/content/286/29/25675.full.pdf","open_access":"1"}],"abstract":[{"text":"Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding protein that plays important roles ininflammation and ovulation. TSG-6-mediated cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know very little about its impact on HA ultra-structure. Here we used films of polymeric and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced positive cooperativity and demonstrate that it cancross-link HA at physiologically relevant concentrations. Ourdata indicate that cooperative binding of full-length TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module) alone binds withoutpositive cooperativity and weaker than the full-length protein.Both the Link module and full-length TSG-6 condensed andrigidified HA films, and the degree of condensation scaled withthe affinity between the TSG-6 constructs and HA. We proposethat condensation is the result of protein-mediated HA cross-linking. Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and might hence have important implica-tions for the mechanistic understanding of the biological func-tion of TSG-6 (e.g.in inflammation).","lang":"eng"}],"day":"22","month":"07","volume":286,"date_updated":"2021-01-12T08:06:58Z","page":"25675-25686","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_identifier":{"issn":["0021-9258","1083-351X"]},"doi":"10.1074/jbc.m111.247395","status":"public","type":"journal_article","extern":"1","publication_status":"published","author":[{"id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia","last_name":"Baranova","first_name":"Natalia"},{"last_name":"Nilebäck","first_name":"Erik","full_name":"Nilebäck, Erik"},{"first_name":"F. Michael","last_name":"Haller","full_name":"Haller, F. Michael"},{"first_name":"David C.","last_name":"Briggs","full_name":"Briggs, David C."},{"first_name":"Sofia","last_name":"Svedhem","full_name":"Svedhem, Sofia"},{"last_name":"Day","first_name":"Anthony J.","full_name":"Day, Anthony J."},{"full_name":"Richter, Ralf P.","first_name":"Ralf P.","last_name":"Richter"}]},{"volume":18,"date_updated":"2021-01-12T06:54:31Z","month":"05","day":"01","abstract":[{"lang":"eng","text":"\n\nIn Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation."}],"publisher":"Nature Publishing Group","intvolume":"        18","issue":"5","acknowledgement":"This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.).","citation":{"short":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583.","ista":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 18(5), 577–583.","chicago":"Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse, and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>.","ama":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. 2011;18(5):577-583. doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>","apa":"Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., &#38; Schwille, P. (2011). Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>","mla":"Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>.","ieee":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min protein patterns emerge from rapid rebinding and membrane interaction of MinE,” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011."},"publication":"Nature Structural and Molecular Biology","_id":"1985","title":"Min protein patterns emerge from rapid rebinding and membrane interaction of MinE","date_created":"2018-12-11T11:55:03Z","publist_id":"5098","year":"2011","date_published":"2011-05-01T00:00:00Z","author":[{"last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Martin Loose"},{"full_name":"Fischer-Friedrich, Elisabeth","first_name":"Elisabeth","last_name":"Fischer Friedrich"},{"full_name":"Herold, Christoph","last_name":"Herold","first_name":"Christoph"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "}],"publication_status":"published","type":"journal_article","extern":1,"status":"public","quality_controlled":0,"doi":"10.1038/nsmb.2037","page":"577 - 583"},{"month":"06","day":"09","abstract":[{"lang":"eng","text":"One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell."}],"volume":40,"date_updated":"2021-01-12T06:54:31Z","title":"Protein self-organization: Lessons from the min system","_id":"1986","date_created":"2018-12-11T11:55:04Z","publist_id":"5097","year":"2011","date_published":"2011-06-09T00:00:00Z","publisher":"Annual Reviews","intvolume":"        40","issue":"1","citation":{"ieee":"M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” <i>Annual Review of Biophysics</i>, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011.","apa":"Loose, M., Kruse, K., &#38; Schwille, P. (2011). Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>","mla":"Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>.","ama":"Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. 2011;40(1):315-336. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>","chicago":"Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2011. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>.","ista":"Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.","short":"M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336."},"publication":"Annual Review of Biophysics","publication_status":"published","type":"journal_article","extern":1,"author":[{"full_name":"Martin Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "}],"page":"315 - 336","status":"public","quality_controlled":0,"doi":"10.1146/annurev-biophys-042910-155332"},{"month":"02","abstract":[{"lang":"eng","text":"Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation."}],"volume":3,"date_created":"2018-12-11T11:55:33Z","publist_id":"4966","year":"2011","file_date_updated":"2020-07-14T12:45:27Z","date_published":"2011-02-11T00:00:00Z","intvolume":"         3","language":[{"iso":"eng"}],"oa":1,"issue":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"publication_status":"published","author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"day":"11","date_updated":"2021-01-12T06:55:08Z","title":"Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite","_id":"2072","publisher":"Oxford University Press","file":[{"date_updated":"2020-07-14T12:45:27Z","file_name":"2011_GBE_Vicoso.pdf","file_id":"6395","checksum":"7855c134436e4f6a13d63b6606d7e8dd","file_size":212547,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2019-05-10T07:41:28Z","relation":"main_file"}],"citation":{"apa":"Vicoso, B., &#38; Bachtrog, D. (2011). Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>, vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>.","ieee":"B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite,” <i>Genome Biology and Evolution</i>, vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011.","ama":"Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. 2011;3(1):230-235. doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>","ista":"Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1), 230–235.","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>.","short":"B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235."},"has_accepted_license":"1","publication":"Genome Biology and Evolution","extern":"1","type":"journal_article","ddc":["570"],"page":"230 - 235","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","quality_controlled":"1","doi":"10.1093/gbe/evr010"},{"oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"doi":"10.1039/c1sm05773a","quality_controlled":"1","status":"public","extern":"1","type":"journal_article","arxiv":1,"article_processing_charge":"No","_id":"10389","title":"Soft elastic surfaces as a platform for particle self-assembly","publication":"Soft Matter","keyword":["condensed matter physics","general chemistry"],"citation":{"ista":"Šarić A, Cacciuto A. 2011. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 7(18), 8324.","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” <i>Soft Matter</i>. Royal Society of Chemistry, 2011. <a href=\"https://doi.org/10.1039/c1sm05773a\">https://doi.org/10.1039/c1sm05773a</a>.","short":"A. Šarić, A. Cacciuto, Soft Matter 7 (2011).","mla":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” <i>Soft Matter</i>, vol. 7, no. 18, 8324, Royal Society of Chemistry, 2011, doi:<a href=\"https://doi.org/10.1039/c1sm05773a\">10.1039/c1sm05773a</a>.","apa":"Šarić, A., &#38; Cacciuto, A. (2011). Soft elastic surfaces as a platform for particle self-assembly. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c1sm05773a\">https://doi.org/10.1039/c1sm05773a</a>","ieee":"A. Šarić and A. Cacciuto, “Soft elastic surfaces as a platform for particle self-assembly,” <i>Soft Matter</i>, vol. 7, no. 18. Royal Society of Chemistry, 2011.","ama":"Šarić A, Cacciuto A. Soft elastic surfaces as a platform for particle self-assembly. <i>Soft Matter</i>. 2011;7(18). doi:<a href=\"https://doi.org/10.1039/c1sm05773a\">10.1039/c1sm05773a</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1106.2995","open_access":"1"}],"publisher":"Royal Society of Chemistry","day":"08","date_updated":"2021-11-29T15:12:10Z","external_id":{"arxiv":["1106.2995"]},"publication_status":"published","article_number":"8324","author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"date_published":"2011-08-08T00:00:00Z","article_type":"original","year":"2011","date_created":"2021-11-29T14:33:18Z","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies and William L. Miller for helpful discussions.","oa":1,"issue":"18","intvolume":"         7","abstract":[{"text":"We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication.","lang":"eng"}],"month":"08","volume":7},{"status":"public","doi":"10.1088/1742-6596/264/1/012015","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","arxiv":1,"extern":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1011.0179"}],"publisher":"IOP Publishing Ltd.","publication":"Journal of Physics: Conference Series","citation":{"mla":"Nägerl, Hanns, et al. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” <i>Journal of Physics: Conference Series</i>, vol. 264, no. 1, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/1742-6596/264/1/012015\">10.1088/1742-6596/264/1/012015</a>.","apa":"Nägerl, H., Mark, M., Haller, E., Gustavsson, M., Hart, R., &#38; Danzl, J. G. (2011). Ultracold and dense samples of ground-state molecules in lattice potentials. <i>Journal of Physics: Conference Series</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1742-6596/264/1/012015\">https://doi.org/10.1088/1742-6596/264/1/012015</a>","ieee":"H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and J. G. Danzl, “Ultracold and dense samples of ground-state molecules in lattice potentials,” <i>Journal of Physics: Conference Series</i>, vol. 264, no. 1. IOP Publishing Ltd., 2011.","ama":"Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. Ultracold and dense samples of ground-state molecules in lattice potentials. <i>Journal of Physics: Conference Series</i>. 2011;264(1). doi:<a href=\"https://doi.org/10.1088/1742-6596/264/1/012015\">10.1088/1742-6596/264/1/012015</a>","ista":"Nägerl H, Mark M, Haller E, Gustavsson M, Hart R, Danzl JG. 2011. Ultracold and dense samples of ground-state molecules in lattice potentials. Journal of Physics: Conference Series. 264(1).","chicago":"Nägerl, Hanns, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Johann G Danzl. “Ultracold and Dense Samples of Ground-State Molecules in Lattice Potentials.” <i>Journal of Physics: Conference Series</i>. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/1742-6596/264/1/012015\">https://doi.org/10.1088/1742-6596/264/1/012015</a>.","short":"H. Nägerl, M. Mark, E. Haller, M. Gustavsson, R. Hart, J.G. Danzl, Journal of Physics: Conference Series 264 (2011)."},"title":"Ultracold and dense samples of ground-state molecules in lattice potentials","_id":"1048","date_updated":"2021-01-12T06:47:54Z","day":"01","author":[{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"full_name":"Gustavsson, Mattias","first_name":"Mattias","last_name":"Gustavsson"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"}],"publication_status":"published","external_id":{"arxiv":["1011.0179"]},"intvolume":"       264","issue":"1","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank H. Ritsch, N. Bouloufa, O. Dulieu, J. Aldegunde, J. M. Hutson, H. Salami, T. Bergeman,  S. D ̈urr, and K. Bergmann for valuable discussions and H. Telle, H. Schnatz, B. Lipphardt, and J. Alnis for sharing technical expertise. We are indebted to R. Grimm for generous support. We gratefully acknowledge funding by the Austrian Ministry of Science and\r\nResearch (Bundesministerium f ̈ur Wissenschaft und Forschung) and the Austrian Science Fund\r\n(Fonds zur F ̈orderung der wissenschaftlichen Forschung) in the form of a START prize grant\r\nand by the European Science Foundation within the framework of the EuroQUASAR collective\r\nresearch project QuDeGPM (Project I 153-N16) and within the framework of the EuroQUAM\r\ncollective research project QuDipMol (Project I 124-N16).  R.H. was supported by a Marie Curie\r\nInternational Incoming Fellowship within the 7th European Community Framework Programme","date_created":"2018-12-11T11:49:52Z","date_published":"2011-01-01T00:00:00Z","publist_id":"6340","year":"2011","volume":264,"month":"01","abstract":[{"text":"We produce an ultracold and dense sample of rovibronic ground state Cs 2 molecules close to the regime of quantum degeneracy, in a single hyperfine level, in the presence of an optical lattice. The molecules are individually trapped, in the motional ground state of an optical lattice well, with a lifetime of 8 s. For preparation, we start with a zero-temperature atomic Mott-insulator state with optimized double-site occupancy and efficiently associate weakly-bound dimer molecules on a Feshbach resonance. Despite extremely weak Franck-Condon wavefunction overlap, the molecules are subsequently transferred with &gt;50% efficiency to the rovibronic ground state by a stimulated four-photon process. Our results present a crucial step towards the generation of Bose-Einstein condensates of ground-state molecules and, when suitably generalized to polar heteronuclear molecules such as RbCs, the realization of dipolar many-body quantum-gas phases in periodic potentials.","lang":"eng"}]},{"citation":{"mla":"Bai, Jianmei, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 3, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.032514\">10.1103/PhysRevA.83.032514</a>.","apa":"Bai, J., Ahmed, E., Beser, B., Guan, Y., Kotochigova, S., Lyyra, M., … Bergeman, T. (2011). Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.83.032514\">https://doi.org/10.1103/PhysRevA.83.032514</a>","ieee":"J. Bai <i>et al.</i>, “Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 83, no. 3. American Physical Society, 2011.","ama":"Bai J, Ahmed E, Beser B, et al. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2011;83(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.83.032514\">10.1103/PhysRevA.83.032514</a>","ista":"Bai J, Ahmed E, Beser B, Guan Y, Kotochigova S, Lyyra M, Ashman S, Wolfe C, Huennekens J, Xie F, Li D, Li L, Tamanis M, Ferber R, Drozdova A, Pazyuk E, Stolyarov A, Danzl JG, Nägerl H, Bouloufa N, Dulieu O, Amiot C, Salami H, Bergeman T. 2011. Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2.  Physical Review A - Atomic, Molecular, and Optical Physics. 83(3).","chicago":"Bai, Jianmei, Ergin Ahmed, Bediha Beser, Yafei Guan, Svetlana Kotochigova, Marjatta Lyyra, Seth Ashman, et al. “Global Analysis of Data on the Spin-Orbit-Coupled A 1Σu+ and b 3Πu Inf States of Cs2.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevA.83.032514\">https://doi.org/10.1103/PhysRevA.83.032514</a>.","short":"J. Bai, E. Ahmed, B. Beser, Y. Guan, S. Kotochigova, M. Lyyra, S. Ashman, C. Wolfe, J. Huennekens, F. Xie, D. Li, L. Li, M. Tamanis, R. Ferber, A. Drozdova, E. Pazyuk, A. Stolyarov, J.G. Danzl, H. Nägerl, N. Bouloufa, O. Dulieu, C. Amiot, H. Salami, T. Bergeman,  Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011)."},"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1101.5412"}],"_id":"1050","title":"Global analysis of data on the spin-orbit-coupled A 1Σu+ and b 3Πu inf states of Cs2","date_updated":"2021-01-12T06:47:55Z","day":"28","doi":"10.1103/PhysRevA.83.032514","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","extern":"1","arxiv":1,"article_processing_charge":"No","acknowledgement":"The work in Temple University was supported by NSF grant no. PHY-0855502. S.K. acknowledges support from AFOSR and from NSF grant no. PHY-1005453. S.A., C.M., and J.H. were supported by NSF grants no. PHY-0652938 and PHY-0968898. The work at Stony Brook was supported by NSF grants no. PHY-0652459 and PHY-0968905. The work in Tsinghua University was supported by NSFC of China, under grant no. 20773072. The Moscow team thanks the Russian Foundation for Basic Researches by the grant no. 10-03-00195 and MSU Priority Direction 2.3. M.T. and R.F. are grateful to Ilze Klincare, Olga Nikolayeva, and Artis Kruzins for their help in spectra analysis, as well as appreciate the support from the ESF 2009/0223/1DP/1.1.1.2.0/09/APIA/VIAA/008 project.","language":[{"iso":"eng"}],"issue":"3","oa":1,"intvolume":"        83","publist_id":"6339","year":"2011","date_published":"2011-03-28T00:00:00Z","date_created":"2018-12-11T11:49:53Z","volume":83,"abstract":[{"text":"We present experimentally derived potential curves 1?and spin-orbit interaction functions for the strongly perturbed AΣu+ 3?and bΠu states of the cesium dimer. The results are based on data from several sources. Laser-induced fluorescence Fourier transform spectroscopy (LIF FTS) was used some time ago in the Laboratoire Aimé Cotton primarily to study the XΣg+ state. More recent work at Tsinghua University provides information from moderate 3?resolution spectroscopy on the lowest levels of the bΠ0u± state as well as additional high-resolution data. From Innsbruck University, we have precision data obtained with cold Cs2 molecules. Recent data from Temple University was obtained using the optical-optical double resonance polarization spectroscopy technique, and finally, a group at the University of Latvia has added additional LIF FTS data. In the Hamiltonian matrix, we have used analytic potentials (the expanded Morse oscillator form) with both finite-difference (FD) coupled-channel and discrete variable representation (DVR) calculations of the term values. Fitted diagonal and off-diagonal spin-orbit functions are obtained and compared with ab initio results from Temple and Moscow State universities.","lang":"eng"}],"month":"03","author":[{"last_name":"Bai","first_name":"Jianmei","full_name":"Bai, Jianmei"},{"full_name":"Ahmed, Ergin","last_name":"Ahmed","first_name":"Ergin"},{"full_name":"Beser, Bediha","last_name":"Beser","first_name":"Bediha"},{"last_name":"Guan","first_name":"Yafei","full_name":"Guan, Yafei"},{"full_name":"Kotochigova, Svetlana","first_name":"Svetlana","last_name":"Kotochigova"},{"full_name":"Lyyra, Marjatta","first_name":"Marjatta","last_name":"Lyyra"},{"full_name":"Ashman, Seth","last_name":"Ashman","first_name":"Seth"},{"first_name":"Christopher","last_name":"Wolfe","full_name":"Wolfe, Christopher"},{"full_name":"Huennekens, John","last_name":"Huennekens","first_name":"John"},{"full_name":"Xie, Feng","first_name":"Feng","last_name":"Xie"},{"last_name":"Li","first_name":"Dan","full_name":"Li, Dan"},{"first_name":"Li","last_name":"Li","full_name":"Li, Li"},{"first_name":"Maris","last_name":"Tamanis","full_name":"Tamanis, Maris"},{"full_name":"Ferber, Ruvin","last_name":"Ferber","first_name":"Ruvin"},{"last_name":"Drozdova","first_name":"Anastasia","full_name":"Drozdova, Anastasia"},{"first_name":"Elena","last_name":"Pazyuk","full_name":"Pazyuk, Elena"},{"full_name":"Stolyarov, Andrey","last_name":"Stolyarov","first_name":"Andrey"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"full_name":"Nägerl, Hanns","first_name":"Hanns","last_name":"Nägerl"},{"full_name":"Bouloufa, Nadia","first_name":"Nadia","last_name":"Bouloufa"},{"first_name":"Olivier","last_name":"Dulieu","full_name":"Dulieu, Olivier"},{"first_name":"Claude","last_name":"Amiot","full_name":"Amiot, Claude"},{"first_name":"Houssam","last_name":"Salami","full_name":"Salami, Houssam"},{"first_name":"Thomas","last_name":"Bergeman","full_name":"Bergeman, Thomas"}],"external_id":{"arxiv":["1101.5412"]},"publication_status":"published"},{"abstract":[{"lang":"eng","text":"We demonstrate the temporal Talbot effect for trapped matter waves using ultracold atoms in an optical lattice. We investigate the phase evolution of an array of essentially non-interacting matter waves and observe matter-wave collapse and revival in the form of a Talbot interference pattern. By using long expansion times, we image momentum space with sub-recoil resolution, allowing us to observe fractional Talbot fringes up to tenth order."}],"day":"01","month":"08","volume":13,"date_updated":"2021-01-12T06:47:56Z","year":"2011","publist_id":"6338","date_published":"2011-08-01T00:00:00Z","title":"Demonstration of the temporal matter-wave Talbot effect for trapped matter waves","_id":"1051","date_created":"2018-12-11T11:49:53Z","citation":{"ama":"Mark M, Haller E, Danzl JG, Lauber K, Gustavsson M, Nägerl H. Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. <i>New Journal of Physics</i>. 2011;13. doi:<a href=\"https://doi.org/10.1088/1367-2630/13/8/085008\">10.1088/1367-2630/13/8/085008</a>","mla":"Mark, Manfred, et al. “Demonstration of the Temporal Matter-Wave Talbot Effect for Trapped Matter Waves.” <i>New Journal of Physics</i>, vol. 13, IOP Publishing Ltd., 2011, doi:<a href=\"https://doi.org/10.1088/1367-2630/13/8/085008\">10.1088/1367-2630/13/8/085008</a>.","apa":"Mark, M., Haller, E., Danzl, J. G., Lauber, K., Gustavsson, M., &#38; Nägerl, H. (2011). Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/13/8/085008\">https://doi.org/10.1088/1367-2630/13/8/085008</a>","ieee":"M. Mark, E. Haller, J. G. Danzl, K. Lauber, M. Gustavsson, and H. Nägerl, “Demonstration of the temporal matter-wave Talbot effect for trapped matter waves,” <i>New Journal of Physics</i>, vol. 13. IOP Publishing Ltd., 2011.","short":"M. Mark, E. Haller, J.G. Danzl, K. Lauber, M. Gustavsson, H. Nägerl, New Journal of Physics 13 (2011).","ista":"Mark M, Haller E, Danzl JG, Lauber K, Gustavsson M, Nägerl H. 2011. Demonstration of the temporal matter-wave Talbot effect for trapped matter waves. New Journal of Physics. 13.","chicago":"Mark, Manfred, Elmar Haller, Johann G Danzl, Katharina Lauber, Mattias Gustavsson, and Hanns Nägerl. “Demonstration of the Temporal Matter-Wave Talbot Effect for Trapped Matter Waves.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2011. <a href=\"https://doi.org/10.1088/1367-2630/13/8/085008\">https://doi.org/10.1088/1367-2630/13/8/085008</a>."},"language":[{"iso":"eng"}],"acknowledgement":"We are indebted to R Grimm for generous support and we thank A Daley for valuable discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within project I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM.","publication":"New Journal of Physics","publisher":"IOP Publishing Ltd.","intvolume":"        13","extern":"1","type":"journal_article","article_processing_charge":"No","publication_status":"published","author":[{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lauber","first_name":"Katharina","full_name":"Lauber, Katharina"},{"full_name":"Gustavsson, Mattias","first_name":"Mattias","last_name":"Gustavsson"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","doi":"10.1088/1367-2630/13/8/085008","status":"public"},{"intvolume":"        65","issue":"1-2","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank E. Haller for important contributions to the experimental work and R. Grimm for generous support. We acknowledge  funding  by  the  Austrian  Science  Fund  (FWF)  within\r\nproject Quantum Gases  of Ground-State Molecules,  project\r\nnumber P 21555-N20.","date_created":"2018-12-11T11:49:53Z","year":"2011","publist_id":"6336","date_published":"2011-11-01T00:00:00Z","volume":65,"month":"11","abstract":[{"text":"The present paper aims at finding optimal parameters for trapping of Cs 2 molecules in optical lattices, with the perspective of creating a quantum degenerate gas of ground-state molecules. We have calculated dynamic polarizabilities of Cs 2 molecules subject to an oscillating electric field, using accurate potential curves and electronic transition dipole moments. We show that for some particular wavelengths of the optical lattice, called &quot;magic wavelengths&quot;, the polarizability of the ground-state molecules is equal to the one of a Feshbach molecule. As the creation of the sample of ground-state molecules relies on an adiabatic population transfer from weakly-bound molecules created on a Feshbach resonance, such a coincidence ensures that both the initial and final states are favorably trapped by the lattice light, allowing optimized transfer in agreement with the experimental observation.","lang":"eng"}],"author":[{"last_name":"Vexiau","first_name":"Romain","full_name":"Vexiau, Romain"},{"full_name":"Bouloufa, Nadia","last_name":"Bouloufa","first_name":"Nadia"},{"first_name":"Mireille","last_name":"Aymar","full_name":"Aymar, Mireille"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"},{"last_name":"Dulieu","first_name":"Olivier","full_name":"Dulieu, Olivier"}],"publication_status":"published","external_id":{"arxiv":["1102.1793"]},"publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1102.1793","open_access":"1"}],"citation":{"ista":"Vexiau R, Bouloufa N, Aymar M, Danzl JG, Mark M, Nägerl H, Dulieu O. 2011. Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. European Physical Journal D. 65(1–2), 243–250.","chicago":"Vexiau, Romain, Nadia Bouloufa, Mireille Aymar, Johann G Danzl, Manfred Mark, Hanns Nägerl, and Olivier Dulieu. “Optimal Trapping Wavelengths of Cs 2 Molecules in an Optical Lattice.” <i>European Physical Journal D</i>. Springer, 2011. <a href=\"https://doi.org/10.1140/epjd/e2011-20085-4\">https://doi.org/10.1140/epjd/e2011-20085-4</a>.","short":"R. Vexiau, N. Bouloufa, M. Aymar, J.G. Danzl, M. Mark, H. Nägerl, O. Dulieu, European Physical Journal D 65 (2011) 243–250.","mla":"Vexiau, Romain, et al. “Optimal Trapping Wavelengths of Cs 2 Molecules in an Optical Lattice.” <i>European Physical Journal D</i>, vol. 65, no. 1–2, Springer, 2011, pp. 243–50, doi:<a href=\"https://doi.org/10.1140/epjd/e2011-20085-4\">10.1140/epjd/e2011-20085-4</a>.","apa":"Vexiau, R., Bouloufa, N., Aymar, M., Danzl, J. G., Mark, M., Nägerl, H., &#38; Dulieu, O. (2011). Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. <i>European Physical Journal D</i>. Springer. <a href=\"https://doi.org/10.1140/epjd/e2011-20085-4\">https://doi.org/10.1140/epjd/e2011-20085-4</a>","ieee":"R. Vexiau <i>et al.</i>, “Optimal trapping wavelengths of Cs 2 molecules in an optical lattice,” <i>European Physical Journal D</i>, vol. 65, no. 1–2. Springer, pp. 243–250, 2011.","ama":"Vexiau R, Bouloufa N, Aymar M, et al. Optimal trapping wavelengths of Cs 2 molecules in an optical lattice. <i>European Physical Journal D</i>. 2011;65(1-2):243-250. doi:<a href=\"https://doi.org/10.1140/epjd/e2011-20085-4\">10.1140/epjd/e2011-20085-4</a>"},"publication":"European Physical Journal D","title":"Optimal trapping wavelengths of Cs 2 molecules in an optical lattice","_id":"1052","date_updated":"2021-01-12T06:47:56Z","day":"01","status":"public","doi":"10.1140/epjd/e2011-20085-4","page":"243 - 250","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","arxiv":1,"type":"journal_article","extern":"1"},{"month":"10","abstract":[{"lang":"eng","text":"We perform precision measurements on a Mott-insulator quantum state of ultracold atoms with tunable interactions. We probe the dependence of the superfluid-to-Mott-insulator transition on the interaction strength and explore the limits of the standard Bose-Hubbard model description. By tuning the on-site interaction energies to values comparable to the interband separation, we are able to quantitatively measure number-dependent shifts in the excitation spectrum caused by effective multibody interactions."}],"volume":107,"date_created":"2018-12-11T11:49:54Z","publist_id":"6337","year":"2011","date_published":"2011-10-18T00:00:00Z","intvolume":"       107","oa":1,"issue":"17","language":[{"iso":"eng"}],"acknowledgement":"We are indebted to R. Grimm for generous support. We thank D. Boyanovsky, H. Büchler, P. Johnson, W. Niedenzu, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within project I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM.","publication_status":"published","external_id":{"arxiv":["1107.1803"]},"author":[{"full_name":"Mark, Manfred","first_name":"Manfred","last_name":"Mark"},{"full_name":"Haller, Elmar","first_name":"Elmar","last_name":"Haller"},{"full_name":"Lauber, Katharina","first_name":"Katharina","last_name":"Lauber"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Daley, Andrew","last_name":"Daley","first_name":"Andrew"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"day":"18","date_updated":"2021-01-12T06:47:56Z","title":"Precision measurements on a tunable Mott insulator of ultracold atoms","_id":"1053","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1107.1803"}],"citation":{"chicago":"Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Andrew Daley, and Hanns Nägerl. “Precision Measurements on a Tunable Mott Insulator of Ultracold Atoms.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.175301\">https://doi.org/10.1103/PhysRevLett.107.175301</a>.","ista":"Mark M, Haller E, Lauber K, Danzl JG, Daley A, Nägerl H. 2011. Precision measurements on a tunable Mott insulator of ultracold atoms. Physical Review Letters. 107(17).","short":"M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Daley, H. Nägerl, Physical Review Letters 107 (2011).","ieee":"M. Mark, E. Haller, K. Lauber, J. G. Danzl, A. Daley, and H. Nägerl, “Precision measurements on a tunable Mott insulator of ultracold atoms,” <i>Physical Review Letters</i>, vol. 107, no. 17. American Physical Society, 2011.","mla":"Mark, Manfred, et al. “Precision Measurements on a Tunable Mott Insulator of Ultracold Atoms.” <i>Physical Review Letters</i>, vol. 107, no. 17, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.175301\">10.1103/PhysRevLett.107.175301</a>.","apa":"Mark, M., Haller, E., Lauber, K., Danzl, J. G., Daley, A., &#38; Nägerl, H. (2011). Precision measurements on a tunable Mott insulator of ultracold atoms. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.175301\">https://doi.org/10.1103/PhysRevLett.107.175301</a>","ama":"Mark M, Haller E, Lauber K, Danzl JG, Daley A, Nägerl H. Precision measurements on a tunable Mott insulator of ultracold atoms. <i>Physical Review Letters</i>. 2011;107(17). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.175301\">10.1103/PhysRevLett.107.175301</a>"},"publication":"Physical Review Letters","article_processing_charge":"No","arxiv":1,"extern":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","status":"public","doi":"10.1103/PhysRevLett.107.175301"},{"publist_id":"6335","year":"2011","date_published":"2011-12-02T00:00:00Z","date_created":"2018-12-11T11:49:54Z","issue":"23","oa":1,"acknowledgement":"We thank R. Grimm for generous support. 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. G. P. acknowledges funding from the EU through NAME-QUAM and AQUTE.","language":[{"iso":"eng"}],"intvolume":"       107","abstract":[{"lang":"eng","text":"We investigate local three-body correlations for bosonic particles in three dimensions and one dimension as a function of the interaction strength. The three-body correlation function g(3) is determined by measuring the three-body recombination rate in an ultracold gas of Cs atoms. In three dimensions, we measure the dependence of g(3) on the gas parameter in a BEC, finding good agreement with the theoretical prediction accounting for beyond-mean-field effects. In one dimension, we observe a reduction of g( 3) by several orders of magnitude upon increasing interactions from the weakly interacting BEC to the strongly interacting Tonks-Girardeau regime, in good agreement with predictions from the Lieb-Liniger model for all strengths of interaction."}],"month":"12","volume":107,"external_id":{"arxiv":["1107.4516"]},"publication_status":"published","author":[{"full_name":"Haller, Elmar","last_name":"Haller","first_name":"Elmar"},{"full_name":"Rabie, Mahmoud","first_name":"Mahmoud","last_name":"Rabie"},{"last_name":"Mark","first_name":"Manfred","full_name":"Mark, Manfred"},{"first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"full_name":"Lauber, Katharina","first_name":"Katharina","last_name":"Lauber"},{"full_name":"Pupillo, Guido","last_name":"Pupillo","first_name":"Guido"},{"last_name":"Nägerl","first_name":"Hanns","full_name":"Nägerl, Hanns"}],"_id":"1054","title":"Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension","citation":{"ama":"Haller E, Rabie M, Mark M, et al. Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. <i>Physical Review Letters</i>. 2011;107(23). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.230404\">10.1103/PhysRevLett.107.230404</a>","ieee":"E. Haller <i>et al.</i>, “Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension,” <i>Physical Review Letters</i>, vol. 107, no. 23. American Physical Society, 2011.","apa":"Haller, E., Rabie, M., Mark, M., Danzl, J. G., Hart, R., Lauber, K., … Nägerl, H. (2011). Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.230404\">https://doi.org/10.1103/PhysRevLett.107.230404</a>","mla":"Haller, Elmar, et al. “Three-Body Correlation Functions and Recombination Rates for Bosons in Three Dimensions and One Dimension.” <i>Physical Review Letters</i>, vol. 107, no. 23, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.230404\">10.1103/PhysRevLett.107.230404</a>.","short":"E. Haller, M. Rabie, M. Mark, J.G. Danzl, R. Hart, K. Lauber, G. Pupillo, H. Nägerl, Physical Review Letters 107 (2011).","chicago":"Haller, Elmar, Mahmoud Rabie, Manfred Mark, Johann G Danzl, Russell Hart, Katharina Lauber, Guido Pupillo, and Hanns Nägerl. “Three-Body Correlation Functions and Recombination Rates for Bosons in Three Dimensions and One Dimension.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.230404\">https://doi.org/10.1103/PhysRevLett.107.230404</a>.","ista":"Haller E, Rabie M, Mark M, Danzl JG, Hart R, Lauber K, Pupillo G, Nägerl H. 2011. Three-body correlation functions and recombination rates for bosons in three dimensions and one dimension. Physical Review Letters. 107(23)."},"publication":"Physical Review Letters","publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/1107.4516","open_access":"1"}],"day":"02","date_updated":"2021-01-12T06:47:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","doi":"10.1103/PhysRevLett.107.230404","status":"public","type":"journal_article","extern":"1","arxiv":1,"article_processing_charge":"No"}]