[{"date_created":"2018-12-11T11:52:10Z","doi":"10.1073/pnas.0601337103","intvolume":"       103","month":"04","title":"Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform","issue":"16","day":"18","date_updated":"2021-01-12T06:50:55Z","publist_id":"5734","status":"public","type":"journal_article","publication_status":"published","volume":103,"author":[{"full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas"}],"citation":{"short":"T. Hausel, PNAS 103 (2006) 6120–6124.","ista":"Hausel T. 2006. Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform. PNAS. 103(16), 6120–6124.","chicago":"Hausel, Tamás. “Betti Numbers of Holomorphic Symplectic Quotients via Arithmetic Fourier Transform.” <i>PNAS</i>. National Academy of Sciences, 2006. <a href=\"https://doi.org/10.1073/pnas.0601337103\">https://doi.org/10.1073/pnas.0601337103</a>.","ama":"Hausel T. Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform. <i>PNAS</i>. 2006;103(16):6120-6124. doi:<a href=\"https://doi.org/10.1073/pnas.0601337103\">10.1073/pnas.0601337103</a>","ieee":"T. Hausel, “Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform,” <i>PNAS</i>, vol. 103, no. 16. National Academy of Sciences, pp. 6120–6124, 2006.","apa":"Hausel, T. (2006). Betti numbers of holomorphic symplectic quotients via arithmetic Fourier transform. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0601337103\">https://doi.org/10.1073/pnas.0601337103</a>","mla":"Hausel, Tamás. “Betti Numbers of Holomorphic Symplectic Quotients via Arithmetic Fourier Transform.” <i>PNAS</i>, vol. 103, no. 16, National Academy of Sciences, 2006, pp. 6120–24, doi:<a href=\"https://doi.org/10.1073/pnas.0601337103\">10.1073/pnas.0601337103</a>."},"_id":"1462","quality_controlled":0,"date_published":"2006-04-18T00:00:00Z","publication":"PNAS","publisher":"National Academy of Sciences","acknowledgement":"This work was supported by a Royal Society University Research Fellowship, National Science Foundation Grant DMS-0305505, an Alfred P. Sloan Research Fellowship, and a Summer Research Assignment of the University of Texas at Austin.","extern":1,"page":"6120 - 6124","abstract":[{"text":"A Fourier transform technique is introduced for counting the number of solutions of holomorphic moment map equations over a finite field. This technique in turn gives information on Betti numbers of holomorphic symplectic quotients. As a consequence, simple unified proofs are obtained for formulas of Poincaré polynomials of toric hyperkähler varieties (recovering results of Bielawski-Dancer and Hausel-Sturmfels), Poincaré polynomials of Hubert schemes of points and twisted Atiyah-Drinfeld-Hitchin-Manin (ADHM) spaces of instantons on ℂ2 (recovering results of Nakajima-Yoshioka), and Poincaré polynomials of all Nakajima quiver varieties. As an application, a proof of a conjecture of Kac on the number of absolutely indecomposable representations of a quiver is announced.","lang":"eng"}],"year":"2006","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0511163"}]},{"extern":"1","year":"2006","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"American Chemical Society","publication":"Journal of the American Chemical Society","quality_controlled":"1","_id":"13428","citation":{"apa":"Kalsin, A. M., Kowalczyk, B., Smoukov, S. K., Klajn, R., &#38; Grzybowski, B. A. (2006). Ionic-like behavior of oppositely charged nanoparticles. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja0642966\">https://doi.org/10.1021/ja0642966</a>","mla":"Kalsin, Alexander M., et al. “Ionic-like Behavior of Oppositely Charged Nanoparticles.” <i>Journal of the American Chemical Society</i>, vol. 128, no. 47, American Chemical Society, 2006, pp. 15046–47, doi:<a href=\"https://doi.org/10.1021/ja0642966\">10.1021/ja0642966</a>.","ama":"Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. Ionic-like behavior of oppositely charged nanoparticles. <i>Journal of the American Chemical Society</i>. 2006;128(47):15046-15047. doi:<a href=\"https://doi.org/10.1021/ja0642966\">10.1021/ja0642966</a>","ieee":"A. M. Kalsin, B. Kowalczyk, S. K. Smoukov, R. Klajn, and B. A. Grzybowski, “Ionic-like behavior of oppositely charged nanoparticles,” <i>Journal of the American Chemical Society</i>, vol. 128, no. 47. American Chemical Society, pp. 15046–15047, 2006.","chicago":"Kalsin, Alexander M., Bartlomiej Kowalczyk, Stoyan K. Smoukov, Rafal Klajn, and Bartosz A. Grzybowski. “Ionic-like Behavior of Oppositely Charged Nanoparticles.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2006. <a href=\"https://doi.org/10.1021/ja0642966\">https://doi.org/10.1021/ja0642966</a>.","ista":"Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. 2006. Ionic-like behavior of oppositely charged nanoparticles. Journal of the American Chemical Society. 128(47), 15046–15047.","short":"A.M. Kalsin, B. Kowalczyk, S.K. Smoukov, R. Klajn, B.A. Grzybowski, Journal of the American Chemical Society 128 (2006) 15046–15047."},"type":"journal_article","date_updated":"2023-08-08T11:30:06Z","pmid":1,"day":"29","title":"Ionic-like behavior of oppositely charged nanoparticles","issue":"47","month":"11","intvolume":"       128","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"page":"15046-15047","abstract":[{"text":"Mixtures of oppositely charged nanoparticles of various sizes and charge ratios precipitate only at the point of electroneutrality. This phenomenonspecific to the nanoscale and reminiscent of threshold precipitation of ionsis a consequence of the formation of core-and-shell nanoparticle aggregates, in which the shells are composed of like-charged particles and are stabilized by efficient electrostatic screening.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2006-11-29T00:00:00Z","oa_version":"None","author":[{"full_name":"Kalsin, Alexander M.","first_name":"Alexander M.","last_name":"Kalsin"},{"last_name":"Kowalczyk","first_name":"Bartlomiej","full_name":"Kowalczyk, Bartlomiej"},{"last_name":"Smoukov","first_name":"Stoyan K.","full_name":"Smoukov, Stoyan K."},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"scopus_import":"1","publication_status":"published","volume":128,"external_id":{"pmid":["17117829"]},"status":"public","article_type":"original","doi":"10.1021/ja0642966","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"date_created":"2023-08-01T10:36:27Z"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Wiley","extern":"1","year":"2006","citation":{"chicago":"Bishop, Kyle J. M., Rafal Klajn, and Bartosz A. Grzybowski. “The Core and Most Useful Molecules in Organic Chemistry.” <i>Angewandte Chemie International Edition</i>. Wiley, 2006. <a href=\"https://doi.org/10.1002/anie.200600881\">https://doi.org/10.1002/anie.200600881</a>.","short":"K.J.M. Bishop, R. Klajn, B.A. Grzybowski, Angewandte Chemie International Edition 45 (2006) 5348–5354.","ista":"Bishop KJM, Klajn R, Grzybowski BA. 2006. The core and most useful molecules in organic chemistry. Angewandte Chemie International Edition. 45(32), 5348–5354.","apa":"Bishop, K. J. M., Klajn, R., &#38; Grzybowski, B. A. (2006). The core and most useful molecules in organic chemistry. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.200600881\">https://doi.org/10.1002/anie.200600881</a>","mla":"Bishop, Kyle J. M., et al. “The Core and Most Useful Molecules in Organic Chemistry.” <i>Angewandte Chemie International Edition</i>, vol. 45, no. 32, Wiley, 2006, pp. 5348–54, doi:<a href=\"https://doi.org/10.1002/anie.200600881\">10.1002/anie.200600881</a>.","ieee":"K. J. M. Bishop, R. Klajn, and B. A. Grzybowski, “The core and most useful molecules in organic chemistry,” <i>Angewandte Chemie International Edition</i>, vol. 45, no. 32. Wiley, pp. 5348–5354, 2006.","ama":"Bishop KJM, Klajn R, Grzybowski BA. The core and most useful molecules in organic chemistry. <i>Angewandte Chemie International Edition</i>. 2006;45(32):5348-5354. doi:<a href=\"https://doi.org/10.1002/anie.200600881\">10.1002/anie.200600881</a>"},"publication":"Angewandte Chemie International Edition","quality_controlled":"1","_id":"13429","date_updated":"2023-08-08T11:31:27Z","type":"journal_article","keyword":["General Chemistry","Catalysis"],"month":"08","intvolume":"        45","day":"11","pmid":1,"issue":"32","title":"The core and most useful molecules in organic chemistry","page":"5348-5354","abstract":[{"text":"The fruitful core: Organic syntheses reported in the literature from 1850 to 2004 are analyzed with mathematical tools from network theory and statistical physics. There is a set of substances (the core) from which the majority of other organic compounds can be made (see picture; red: core, blue: periphery, green: islands). Search algorithms are used to identify small optimal sets of maximally useful chemicals.","lang":"eng"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2006-08-11T00:00:00Z","status":"public","external_id":{"pmid":["16835857"]},"author":[{"last_name":"Bishop","first_name":"Kyle J. M.","full_name":"Bishop, Kyle J. M."},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"publication_status":"published","scopus_import":"1","volume":45,"doi":"10.1002/anie.200600881","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"date_created":"2023-08-01T10:37:16Z","article_type":"original"},{"month":"01","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"intvolume":"       110","title":"Principles and implementations of dissipative (dynamic) self-assembly","issue":"6","day":"25","pmid":1,"date_updated":"2023-08-08T11:33:08Z","type":"journal_article","citation":{"ama":"Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA. Principles and implementations of dissipative (dynamic) self-assembly. <i>The Journal of Physical Chemistry B</i>. 2006;110(6):2482-2496. doi:<a href=\"https://doi.org/10.1021/jp054153q\">10.1021/jp054153q</a>","ieee":"M. Fialkowski, K. J. M. Bishop, R. Klajn, S. K. Smoukov, C. J. Campbell, and B. A. Grzybowski, “Principles and implementations of dissipative (dynamic) self-assembly,” <i>The Journal of Physical Chemistry B</i>, vol. 110, no. 6. American Chemical Society, pp. 2482–2496, 2006.","apa":"Fialkowski, M., Bishop, K. J. M., Klajn, R., Smoukov, S. K., Campbell, C. J., &#38; Grzybowski, B. A. (2006). Principles and implementations of dissipative (dynamic) self-assembly. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jp054153q\">https://doi.org/10.1021/jp054153q</a>","mla":"Fialkowski, Marcin, et al. “Principles and Implementations of Dissipative (Dynamic) Self-Assembly.” <i>The Journal of Physical Chemistry B</i>, vol. 110, no. 6, American Chemical Society, 2006, pp. 2482–96, doi:<a href=\"https://doi.org/10.1021/jp054153q\">10.1021/jp054153q</a>.","ista":"Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA. 2006. Principles and implementations of dissipative (dynamic) self-assembly. The Journal of Physical Chemistry B. 110(6), 2482–2496.","short":"M. Fialkowski, K.J.M. Bishop, R. Klajn, S.K. Smoukov, C.J. Campbell, B.A. Grzybowski, The Journal of Physical Chemistry B 110 (2006) 2482–2496.","chicago":"Fialkowski, Marcin, Kyle J. M. Bishop, Rafal Klajn, Stoyan K. Smoukov, Christopher J. Campbell, and Bartosz A. Grzybowski. “Principles and Implementations of Dissipative (Dynamic) Self-Assembly.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2006. <a href=\"https://doi.org/10.1021/jp054153q\">https://doi.org/10.1021/jp054153q</a>."},"_id":"13430","quality_controlled":"1","publication":"The Journal of Physical Chemistry B","language":[{"iso":"eng"}],"publisher":"American Chemical Society","article_processing_charge":"No","extern":"1","year":"2006","date_created":"2023-08-01T10:37:35Z","doi":"10.1021/jp054153q","publication_identifier":{"issn":["1520-6106","1520-5207"]},"article_type":"original","status":"public","external_id":{"pmid":["16471845"]},"publication_status":"published","scopus_import":"1","volume":110,"author":[{"last_name":"Fialkowski","first_name":"Marcin","full_name":"Fialkowski, Marcin"},{"last_name":"Bishop","first_name":"Kyle J. M.","full_name":"Bishop, Kyle J. M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn"},{"first_name":"Stoyan K.","last_name":"Smoukov","full_name":"Smoukov, Stoyan K."},{"first_name":"Christopher J.","last_name":"Campbell","full_name":"Campbell, Christopher J."},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"oa_version":"None","date_published":"2006-01-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2482-2496","abstract":[{"text":"Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.","lang":"eng"}]},{"title":"Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis","day":"09","date_created":"2018-12-11T11:49:07Z","month":"02","doi":"10.1186/1471-2407-6-36","intvolume":"         6","publication_status":"published","type":"journal_article","volume":6,"author":[{"last_name":"Babenko","first_name":"Vladimir","full_name":"Babenko, Vladimir N"},{"full_name":"Basu, Malay K","last_name":"Basu","first_name":"Malay"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Rogozin","first_name":"Igor","full_name":"Rogozin, Igor B"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene V"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"6744","date_updated":"2021-01-12T08:21:47Z","status":"public","_id":"903","date_published":"2006-02-09T00:00:00Z","quality_controlled":0,"publication":"BMC Cancer","citation":{"short":"V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).","ista":"Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 6.","chicago":"Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” <i>BMC Cancer</i>. BioMed Central, 2006. <a href=\"https://doi.org/10.1186/1471-2407-6-36\">https://doi.org/10.1186/1471-2407-6-36</a>.","ieee":"V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis,” <i>BMC Cancer</i>, vol. 6. BioMed Central, 2006.","ama":"Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. <i>BMC Cancer</i>. 2006;6. doi:<a href=\"https://doi.org/10.1186/1471-2407-6-36\">10.1186/1471-2407-6-36</a>","mla":"Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” <i>BMC Cancer</i>, vol. 6, BioMed Central, 2006, doi:<a href=\"https://doi.org/10.1186/1471-2407-6-36\">10.1186/1471-2407-6-36</a>.","apa":"Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., &#38; Koonin, E. (2006). Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. <i>BMC Cancer</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2407-6-36\">https://doi.org/10.1186/1471-2407-6-36</a>"},"extern":1,"abstract":[{"text":"Background: Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods: A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. Results: We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion: The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.","lang":"eng"}],"year":"2006","publisher":"BioMed Central","acknowledgement":"This work was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health/DHHS. FAK is an NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions."},{"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"article_processing_charge":"No","extern":"1","year":"2006","citation":{"ama":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>","ieee":"D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.","apa":"Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>","mla":"Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>.","ista":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69.","short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.","chicago":"Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>."},"_id":"9505","quality_controlled":"1","publication":"Nature Genetics","date_updated":"2021-12-14T09:02:51Z","department":[{"_id":"DaZi"}],"type":"journal_article","month":"11","intvolume":"        39","title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","issue":"1","day":"26","pmid":1,"page":"61-69","abstract":[{"text":"Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.","lang":"eng"}],"oa_version":"None","date_published":"2006-11-26T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["17128275"]},"status":"public","publication_status":"published","scopus_import":"1","volume":39,"author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman"},{"first_name":"Mary","last_name":"Gehring","full_name":"Gehring, Mary"},{"last_name":"Tran","first_name":"Robert K.","full_name":"Tran, Robert K."},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"date_created":"2021-06-07T12:19:31Z","doi":"10.1038/ng1929","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"article_type":"original"},{"day":"16","issue":"7082","title":"Evidence for Efimov quantum states in an ultracold gas of caesium atoms","doi":"10.1038/nature04626","month":"03","intvolume":"       440","date_created":"2018-12-11T11:49:47Z","author":[{"last_name":"Kraemer","first_name":"Tobias","full_name":"Kraemer, Tobias"},{"last_name":"Mark","first_name":"Michael","full_name":"Mark, Michael"},{"full_name":"Waldburger, Philipp","last_name":"Waldburger","first_name":"Philipp"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"},{"full_name":"Chin, Cheng","first_name":"Cheng","last_name":"Chin"},{"first_name":"Bastian","last_name":"Engeser","full_name":"Engeser, Bastian"},{"first_name":"Adam","last_name":"Lange","full_name":"Lange, Adam"},{"full_name":"Pilch, Karl","first_name":"Karl","last_name":"Pilch"},{"last_name":"Jaakkola","first_name":"Antti","full_name":"Jaakkola, Antti"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"},{"full_name":"Grimm, Rudolf","first_name":"Rudolf","last_name":"Grimm"}],"type":"journal_article","publication_status":"published","volume":440,"status":"public","publist_id":"6356","date_updated":"2021-01-12T06:47:48Z","publication":"Nature","date_published":"2006-03-16T00:00:00Z","_id":"1033","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kraemer, Tobias, et al. “Evidence for Efimov Quantum States in an Ultracold Gas of Caesium Atoms.” <i>Nature</i>, vol. 440, no. 7082, Nature Publishing Group, 2006, pp. 315–18, doi:<a href=\"https://doi.org/10.1038/nature04626\">10.1038/nature04626</a>.","apa":"Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Chin, C., Engeser, B., … Grimm, R. (2006). Evidence for Efimov quantum states in an ultracold gas of caesium atoms. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature04626\">https://doi.org/10.1038/nature04626</a>","ama":"Kraemer T, Mark M, Waldburger P, et al. Evidence for Efimov quantum states in an ultracold gas of caesium atoms. <i>Nature</i>. 2006;440(7082):315-318. doi:<a href=\"https://doi.org/10.1038/nature04626\">10.1038/nature04626</a>","ieee":"T. Kraemer <i>et al.</i>, “Evidence for Efimov quantum states in an ultracold gas of caesium atoms,” <i>Nature</i>, vol. 440, no. 7082. Nature Publishing Group, pp. 315–318, 2006.","chicago":"Kraemer, Tobias, Michael Mark, Philipp Waldburger, Johann G Danzl, Cheng Chin, Bastian Engeser, Adam Lange, et al. “Evidence for Efimov Quantum States in an Ultracold Gas of Caesium Atoms.” <i>Nature</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nature04626\">https://doi.org/10.1038/nature04626</a>.","short":"T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, C. Chin, B. Engeser, A. Lange, K. Pilch, A. Jaakkola, H. Nägerl, R. Grimm, Nature 440 (2006) 315–318.","ista":"Kraemer T, Mark M, Waldburger P, Danzl JG, Chin C, Engeser B, Lange A, Pilch K, Jaakkola A, Nägerl H, Grimm R. 2006. Evidence for Efimov quantum states in an ultracold gas of caesium atoms. Nature. 440(7082), 315–318."},"oa_version":"None","main_file_link":[{"url":"https://arxiv.org/abs/cond-mat/0512394","open_access":"1"}],"oa":1,"page":"315 - 318","extern":"1","year":"2006","abstract":[{"text":"Systems of three interacting particles are notorious for their complex physical behaviour. A landmark theoretical result in few-body quantum physics is Efimov\\'s prediction1,2 of a universal set of bound trimer states appearing for three identical bosons with a resonant two-body interaction. Counterintuitively, these states even exist in the absence of a corresponding two-body bound state. Since the formulation of Efimov\\'s problem in the context of nuclear physics 35 years ago, it has attracted great interest in many areas of physics3-8. However, the observation of Efimov quantum states has remained an elusive goal3,5. Here we report the observation of an Efimov resonance in an ultracold gas of caesium atoms. The resonance occurs in the range of large negative two-body scattering lengths, arising from the coupling of three free atoms to an Efimov trimer. Experimentally, we observe its signature as a giant three-body recombination loss9,10 when the strength of the two-body interaction is varied. We also detect a minimum 9,11,12 in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point with which to explore the universal properties of resonantly interacting few-body systems7. While Feshbach resonances13,14 have provided the key to control quantum-mechanical interactions on the two-body level, Efimov resonances connect ultracold matter15 to the world of few-body quantum phenomena.","lang":"eng"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","acknowledgement":"We thank E. Braaten, C. Greene, B. Esry, H. Hammer and T. Ko ̈hler for many discussions and E. Kneringer for support regarding the data analysis. We acknowledge support by the Austrian Science Fund (FWF) within Spezialforschungsbereich 15 and within the Lise Meitner programme, and by the\r\nEuropean Union in the frame of the TMR networks ‘Cold Molecules’ and ‘FASTNet’. M.M. is supported within the Doktorandenprogramm of the Austrian\r\nAcademy of Sciences."},{"day":"01","title":"Experimental evidence for Efimov quantum states","doi":"10.1063/1.2400657","intvolume":"       869","month":"01","date_created":"2018-12-11T11:49:48Z","author":[{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"},{"full_name":"Kraemer, Tobias","last_name":"Kraemer","first_name":"Tobias"},{"full_name":"Mark, Michael","last_name":"Mark","first_name":"Michael"},{"full_name":"Waldburger, Philipp","first_name":"Philipp","last_name":"Waldburger"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Engeser","first_name":"Bastian","full_name":"Engeser, Bastian"},{"full_name":"Lange, Adam","first_name":"Adam","last_name":"Lange"},{"first_name":"Karl","last_name":"Pilch","full_name":"Pilch, Karl"},{"full_name":"Jaakkola, Antti","last_name":"Jaakkola","first_name":"Antti"},{"full_name":"Chin, Cheng","first_name":"Cheng","last_name":"Chin"},{"last_name":"Grimm","first_name":"Rudolf","full_name":"Grimm, Rudolf"}],"volume":869,"type":"conference","publication_status":"published","status":"public","date_updated":"2021-01-12T06:47:49Z","publist_id":"6355","date_published":"2006-01-01T00:00:00Z","_id":"1034","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","citation":{"short":"H. Nägerl, T. Kraemer, M. Mark, P. Waldburger, J.G. Danzl, B. Engeser, A. Lange, K. Pilch, A. Jaakkola, C. Chin, R. Grimm, in:, AIP, 2006, pp. 269–277.","ista":"Nägerl H, Kraemer T, Mark M, Waldburger P, Danzl JG, Engeser B, Lange A, Pilch K, Jaakkola A, Chin C, Grimm R. 2006. Experimental evidence for Efimov quantum states. ICAP: International Conference on Atomic Physics vol. 869, 269–277.","chicago":"Nägerl, Hanns, Tobias Kraemer, Michael Mark, Philipp Waldburger, Johann G Danzl, Bastian Engeser, Adam Lange, et al. “Experimental Evidence for Efimov Quantum States,” 869:269–77. AIP, 2006. <a href=\"https://doi.org/10.1063/1.2400657\">https://doi.org/10.1063/1.2400657</a>.","ieee":"H. Nägerl <i>et al.</i>, “Experimental evidence for Efimov quantum states,” presented at the ICAP: International Conference on Atomic Physics, 2006, vol. 869, pp. 269–277.","ama":"Nägerl H, Kraemer T, Mark M, et al. Experimental evidence for Efimov quantum states. In: Vol 869. AIP; 2006:269-277. doi:<a href=\"https://doi.org/10.1063/1.2400657\">10.1063/1.2400657</a>","mla":"Nägerl, Hanns, et al. <i>Experimental Evidence for Efimov Quantum States</i>. Vol. 869, AIP, 2006, pp. 269–77, doi:<a href=\"https://doi.org/10.1063/1.2400657\">10.1063/1.2400657</a>.","apa":"Nägerl, H., Kraemer, T., Mark, M., Waldburger, P., Danzl, J. G., Engeser, B., … Grimm, R. (2006). Experimental evidence for Efimov quantum states (Vol. 869, pp. 269–277). Presented at the ICAP: International Conference on Atomic Physics, AIP. <a href=\"https://doi.org/10.1063/1.2400657\">https://doi.org/10.1063/1.2400657</a>"},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/cond-mat/0611629","open_access":"1"}],"conference":{"name":"ICAP: International Conference on Atomic Physics"},"abstract":[{"text":"Three interacting particles form a system which is well known for its complex physical behavior. A landmark theoretical result in few-body quantum physics is Efimov\\'s prediction of a universal set of weakly bound trimer states appearing for three identical bosons with a resonant two-body interaction [1, 2]. Surprisingly, these states even exist in the absence of a corresponding two-body bound state and their precise nature is largely independent of the particular type of the two-body interaction potential. Efimov\\'s scenario has attracted great interest in many areas of physics; an experimental test however has not been achieved. We report the observation of an Efimov resonance in an ultracold thermal gas of cesium atoms [3]. The resonance occurs in the range of large negative two-body scattering lengths and arises from the coupling of three free atoms to an Efimov trimer. We observe its signature as a giant three-body recombination loss when the strength of the two-body interaction is varied near a Feshbach resonance. This resonance develops into a continuum resonance at non-zero collision energies, and we observe a shift of the resonance position as a function of temperature. We also report on a minimum in the recombination loss for positive scattering lengths, indicating destructive interference of decay pathways. Our results confirm central theoretical predictions of Efimov physics and represent a starting point from which to explore the universal properties of resonantly interacting few-body systems.","lang":"eng"}],"year":"2006","page":"269 - 277","extern":"1","article_processing_charge":"No","publisher":"AIP","acknowledgement":"We thank E. Braaten, C. Greene, B. Esry, H. Hammer, and T. Köhl\r\ner for many stimulat-\r\ning and fruitful discussions and E. Kneringer for support re\r\ngarding the data analysis. We\r\nacknowledge support by the Austrian Science Fund (FWF) with\r\nin Spezialforschungs-\r\nbereich 15 and within the Lise Meitner program, and by the Eur\r\nopean Union in the frame\r\nof the TMR networks “Cold Molecules” and “FASTNet”. M.M. is s\r\nupported within the\r\nDoktorandenprogramm of the Austrian Academy of Sciences.","language":[{"iso":"eng"}]},{"date_created":"2022-08-19T07:20:31Z","doi":"10.1145/1148170.1148222","month":"08","title":"Finding near-duplicate web pages: A large-scale evaluation of algorithms","day":"01","date_updated":"2023-02-17T13:49:03Z","status":"public","publication_status":"published","type":"conference","scopus_import":"1","author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"citation":{"apa":"Henzinger, M. H. (2006). Finding near-duplicate web pages: A large-scale evaluation of algorithms. In <i>29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval</i> (pp. 284–291). Seattle, WA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1148170.1148222\">https://doi.org/10.1145/1148170.1148222</a>","mla":"Henzinger, Monika H. “Finding Near-Duplicate Web Pages: A Large-Scale Evaluation of Algorithms.” <i>29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval</i>, Association for Computing Machinery, 2006, pp. 284–91, doi:<a href=\"https://doi.org/10.1145/1148170.1148222\">10.1145/1148170.1148222</a>.","ama":"Henzinger MH. Finding near-duplicate web pages: A large-scale evaluation of algorithms. In: <i>29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval</i>. Association for Computing Machinery; 2006:284-291. doi:<a href=\"https://doi.org/10.1145/1148170.1148222\">10.1145/1148170.1148222</a>","ieee":"M. H. Henzinger, “Finding near-duplicate web pages: A large-scale evaluation of algorithms,” in <i>29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval</i>, Seattle, WA, United States, 2006, pp. 284–291.","chicago":"Henzinger, Monika H. “Finding Near-Duplicate Web Pages: A Large-Scale Evaluation of Algorithms.” In <i>29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval</i>, 284–91. Association for Computing Machinery, 2006. <a href=\"https://doi.org/10.1145/1148170.1148222\">https://doi.org/10.1145/1148170.1148222</a>.","ista":"Henzinger MH. 2006. Finding near-duplicate web pages: A large-scale evaluation of algorithms. 29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. SIGIR: International Conference on Research and Development in Information Retrieval, 284–291.","short":"M.H. Henzinger, in:, 29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, Association for Computing Machinery, 2006, pp. 284–291."},"oa_version":"None","_id":"11929","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2006-08-01T00:00:00Z","quality_controlled":"1","publication":"29th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","article_processing_charge":"No","extern":"1","page":"284-291","abstract":[{"text":"Broder et al.'s [3] shingling algorithm and Charikar's [4] random projection based approach are considered \"state-of-the-art\" algorithms for finding near-duplicate web pages. Both algorithms were either developed at or used by popular web search engines. We compare the two algorithms on a very large scale, namely on a set of 1.6B distinct web pages. The results show that neither of the algorithms works well for finding near-duplicate pairs on the same site, while both achieve high precision for near-duplicate pairs on different sites. Since Charikar's algorithm finds more near-duplicate pairs on different sites, it achieves a better precision overall, namely 0.50 versus 0.38 for Broder et al.'s algorithm. We present a combined algorithm which achieves precision 0.79 with 79% of the recall of the other algorithms.","lang":"eng"}],"year":"2006","conference":{"name":"SIGIR: International Conference on Research and Development in Information Retrieval","end_date":"2006-08-11","location":"Seattle, WA, United States","start_date":"2006-08-06"}},{"publication_status":"published","type":"book_chapter","volume":2,"author":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"full_name":"Sawhney, Ravi K","last_name":"Sawhney","first_name":"Ravi"},{"full_name":"Stark, Martin","first_name":"Martin","last_name":"Stark"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"date_updated":"2021-01-12T07:43:15Z","publist_id":"2998","status":"public","title":"Atomic force microscopy","day":"28","date_created":"2018-12-11T12:03:09Z","intvolume":"         2","month":"09","extern":1,"page":"213 - 284","year":"2006","publisher":"World Scientific Publishing","quality_controlled":0,"_id":"3404","date_published":"2006-09-28T00:00:00Z","alternative_title":["Manuals in Biomedical Research"],"publication":"Techniques in Microscopy for Biomedical Applications","citation":{"ista":"Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical Research, vol. 2, 213–284.","short":"H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.","chicago":"Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic Force Microscopy.” In <i>Techniques in Microscopy for Biomedical Applications</i>, 2:213–84. World Scientific Publishing, 2006.","ama":"Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: <i>Techniques in Microscopy for Biomedical Applications</i>. Vol 2. World Scientific Publishing; 2006:213-284.","ieee":"H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,” in <i>Techniques in Microscopy for Biomedical Applications</i>, vol. 2, World Scientific Publishing, 2006, pp. 213–284.","mla":"Janovjak, Harald L., et al. “Atomic Force Microscopy.” <i>Techniques in Microscopy for Biomedical Applications</i>, vol. 2, World Scientific Publishing, 2006, pp. 213–84.","apa":"Janovjak, H. L., Sawhney, R., Stark, M., &#38; Mueller, D. (2006). Atomic force microscopy. In <i>Techniques in Microscopy for Biomedical Applications</i> (Vol. 2, pp. 213–284). World Scientific Publishing."}},{"doi":"10.1016/j.jmb.2005.12.065","month":"03","intvolume":"       357","date_created":"2018-12-11T12:03:12Z","day":"24","issue":"2","title":"Bacteriorhodopsin folds into the membrane against an external force","status":"public","publist_id":"2988","date_updated":"2021-01-12T07:43:18Z","author":[{"last_name":"Kessler","first_name":"Max","full_name":"Kessler, Max"},{"first_name":"Kay","last_name":"Gottschalk","full_name":"Gottschalk, Kay E"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"},{"full_name":"Gaub, Hermann","first_name":"Hermann","last_name":"Gaub"}],"volume":357,"publication_status":"published","type":"journal_article","citation":{"ista":"Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 357(2), 644–654.","short":"M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 644–654.","chicago":"Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” <i>Journal of Molecular Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jmb.2005.12.065\">https://doi.org/10.1016/j.jmb.2005.12.065</a>.","ieee":"M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin folds into the membrane against an external force,” <i>Journal of Molecular Biology</i>, vol. 357, no. 2. Elsevier, pp. 644–654, 2006.","ama":"Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin folds into the membrane against an external force. <i>Journal of Molecular Biology</i>. 2006;357(2):644-654. doi:<a href=\"https://doi.org/10.1016/j.jmb.2005.12.065\">10.1016/j.jmb.2005.12.065</a>","mla":"Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an External Force.” <i>Journal of Molecular Biology</i>, vol. 357, no. 2, Elsevier, 2006, pp. 644–54, doi:<a href=\"https://doi.org/10.1016/j.jmb.2005.12.065\">10.1016/j.jmb.2005.12.065</a>.","apa":"Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., &#38; Gaub, H. (2006). Bacteriorhodopsin folds into the membrane against an external force. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2005.12.065\">https://doi.org/10.1016/j.jmb.2005.12.065</a>"},"publication":"Journal of Molecular Biology","date_published":"2006-03-24T00:00:00Z","_id":"3413","quality_controlled":0,"publisher":"Elsevier","abstract":[{"text":"Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.\n\nHere we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.\n\nWe discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state.","lang":"eng"}],"year":"2006","extern":1,"page":"644 - 654"},{"citation":{"apa":"Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., &#38; Mueller, D. (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2005.10.028\">https://doi.org/10.1016/j.jmb.2005.10.028</a>","mla":"Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” <i>Journal of Molecular Biology</i>, vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:<a href=\"https://doi.org/10.1016/j.jmb.2005.10.028\">10.1016/j.jmb.2005.10.028</a>.","ieee":"A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli,” <i>Journal of Molecular Biology</i>, vol. 355, no. 1. Elsevier, pp. 2–8, 2006.","ama":"Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. <i>Journal of Molecular Biology</i>. 2006;355(1):2-8. doi:<a href=\"https://doi.org/10.1016/j.jmb.2005.10.028\">10.1016/j.jmb.2005.10.028</a>","chicago":"Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” <i>Journal of Molecular Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jmb.2005.10.028\">https://doi.org/10.1016/j.jmb.2005.10.028</a>.","short":"A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 2–8.","ista":"Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 355(1), 2–8."},"publication":"Journal of Molecular Biology","_id":"3414","quality_controlled":0,"date_published":"2006-01-06T00:00:00Z","publisher":"Elsevier","abstract":[{"lang":"eng","text":"Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter."}],"year":"2006","extern":1,"page":"2 - 8","doi":"10.1016/j.jmb.2005.10.028","intvolume":"       355","month":"01","date_created":"2018-12-11T12:03:12Z","day":"06","title":"Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli","issue":"1","status":"public","date_updated":"2021-01-12T07:43:19Z","publist_id":"2987","author":[{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Ziegler,  Christine","last_name":"Ziegler","first_name":"Christine"},{"first_name":"Werner","last_name":"Kühlbrandt","full_name":"Kühlbrandt, Werner"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}],"volume":355,"type":"journal_article","publication_status":"published"},{"day":"01","title":"Imaging and detecting molecular interactions of single membrane proteins","intvolume":"        27","doi":"10.1016/j.neurobiolaging.2005.03.031","month":"01","date_created":"2018-12-11T12:03:12Z","author":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"last_name":"Kedrov","first_name":"Alexej","full_name":"Kedrov, Alexej"},{"full_name":"Cisneros, David","last_name":"Cisneros","first_name":"David"},{"full_name":"Sapra, Tanuj K","last_name":"Sapra","first_name":"Tanuj"},{"full_name":"Struckmeier, Jens","first_name":"Jens","last_name":"Struckmeier"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"volume":27,"publication_status":"published","type":"review","status":"public","date_updated":"2019-04-26T07:22:27Z","publist_id":"2986","publication":"Neurobiology of Aging","_id":"3415","quality_controlled":0,"date_published":"2006-01-01T00:00:00Z","citation":{"chicago":"Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” <i>Neurobiology of Aging</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.neurobiolaging.2005.03.031\">https://doi.org/10.1016/j.neurobiolaging.2005.03.031</a>.","ista":"Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 27, 546–561.","short":"H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 546–561.","mla":"Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” <i>Neurobiology of Aging</i>, vol. 27, Elsevier, 2006, pp. 546–61, doi:<a href=\"https://doi.org/10.1016/j.neurobiolaging.2005.03.031\">10.1016/j.neurobiolaging.2005.03.031</a>.","apa":"Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., &#38; Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. <i>Neurobiology of Aging</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neurobiolaging.2005.03.031\">https://doi.org/10.1016/j.neurobiolaging.2005.03.031</a>","ieee":"H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” <i>Neurobiology of Aging</i>, vol. 27. Elsevier, pp. 546–561, 2006.","ama":"Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. <i>Neurobiology of Aging</i>. 2006;27:546-561. doi:<a href=\"https://doi.org/10.1016/j.neurobiolaging.2005.03.031\">10.1016/j.neurobiolaging.2005.03.031</a>"},"year":"2006","page":"546 - 561","extern":1,"publisher":"Elsevier"},{"citation":{"chicago":"Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” <i>ArXiv</i>. ArXiv, 2006.","short":"G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.","ista":"Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, .","apa":"Tkačik, G., Schneidman, E., Berry, M., &#38; Bialek, W. (2006). Ising models for networks of real neurons. <i>ArXiv</i>. ArXiv.","mla":"Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” <i>ArXiv</i>, ArXiv, 2006, pp. 1–4.","ieee":"G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” <i>ArXiv</i>. ArXiv, pp. 1–4, 2006.","ama":"Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. <i>ArXiv</i>. 2006:1-4."},"publication":"ArXiv","date_published":"2006-11-22T00:00:00Z","_id":"3431","quality_controlled":0,"publisher":"ArXiv","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/q-bio/0611072"}],"extern":1,"page":"1 - 4","abstract":[{"text":"Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses.","lang":"eng"}],"year":"2006","month":"11","date_created":"2018-12-11T12:03:18Z","day":"22","title":"Ising models for networks of real neurons","status":"public","publist_id":"2969","date_updated":"2021-01-12T07:43:25Z","author":[{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"E.","last_name":"Schneidman","full_name":"Schneidman, E."},{"first_name":"M.","last_name":"Berry","full_name":"Berry, M. J."},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William S"}],"type":"preprint","publication_status":"published"},{"date_created":"2018-12-11T12:03:19Z","intvolume":"        16","doi":"10.1016/j.gde.2006.10.006","month":"12","title":"Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution","issue":"6","day":"01","date_updated":"2021-01-12T07:43:27Z","publist_id":"2963","status":"public","volume":16,"publication_status":"published","type":"journal_article","author":[{"full_name":"Betancourt, Andrea J","last_name":"Betancourt","first_name":"Andrea"},{"last_name":"Bollback","first_name":"Jonathan P","full_name":"Jonathan Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"chicago":"Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.gde.2006.10.006\">https://doi.org/10.1016/j.gde.2006.10.006</a>.","short":"A. Betancourt, J.P. Bollback, Current Opinion in Genetics &#38; Development 16 (2006) 618–623.","ista":"Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics &#38; Development. 16(6), 618–623.","mla":"Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:<a href=\"https://doi.org/10.1016/j.gde.2006.10.006\">10.1016/j.gde.2006.10.006</a>.","apa":"Betancourt, A., &#38; Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2006.10.006\">https://doi.org/10.1016/j.gde.2006.10.006</a>","ieee":"A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.","ama":"Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. <i>Current Opinion in Genetics &#38; Development</i>. 2006;16(6):618-623. doi:<a href=\"https://doi.org/10.1016/j.gde.2006.10.006\">10.1016/j.gde.2006.10.006</a>"},"date_published":"2006-12-01T00:00:00Z","_id":"3437","quality_controlled":0,"publication":"Current Opinion in Genetics & Development","publisher":"Elsevier","year":"2006","abstract":[{"lang":"eng","text":"The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models."}],"extern":1,"page":"618 - 623"},{"publication_status":"published","type":"conference","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jagadeesan, Rhada","last_name":"Jagadeesan","first_name":"Rhada"},{"last_name":"Pitcher","first_name":"Corin","full_name":"Pitcher, Corin"}],"publist_id":"2938","date_updated":"2021-01-12T07:43:32Z","status":"public","title":"Games for controls","day":"31","date_created":"2018-12-11T12:03:23Z","doi":"10.1109/CSFW.2006.14","month":"07","page":"70 - 82","extern":1,"year":"2006","abstract":[{"text":"We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control.","lang":"eng"}],"conference":{"name":"CSF: Computer Security Foundations"},"publisher":"IEEE","_id":"3449","date_published":"2006-07-31T00:00:00Z","quality_controlled":0,"citation":{"ieee":"K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.","ama":"Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:<a href=\"https://doi.org/10.1109/CSFW.2006.14\">10.1109/CSFW.2006.14</a>","mla":"Chatterjee, Krishnendu, et al. <i>Games for Controls</i>. IEEE, 2006, pp. 70–82, doi:<a href=\"https://doi.org/10.1109/CSFW.2006.14\">10.1109/CSFW.2006.14</a>.","apa":"Chatterjee, K., Jagadeesan, R., &#38; Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. <a href=\"https://doi.org/10.1109/CSFW.2006.14\">https://doi.org/10.1109/CSFW.2006.14</a>","ista":"Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.","short":"K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.","chicago":"Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. <a href=\"https://doi.org/10.1109/CSFW.2006.14\">https://doi.org/10.1109/CSFW.2006.14</a>."}},{"_id":"3463","date_published":"2006-12-01T00:00:00Z","quality_controlled":0,"publication":"Pflugers Archiv : European Journal of Physiology","citation":{"ieee":"J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review),” <i>Pflugers Archiv : European Journal of Physiology</i>, vol. 453, no. 3. Springer, pp. 361–372, 2006.","ama":"Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). <i>Pflugers Archiv : European Journal of Physiology</i>. 2006;453(3):361-372. doi:<a href=\"https://doi.org/10.1007/s00424-006-0093-2\">10.1007/s00424-006-0093-2</a>","mla":"Bischofberger, Joseph, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” <i>Pflugers Archiv : European Journal of Physiology</i>, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:<a href=\"https://doi.org/10.1007/s00424-006-0093-2\">10.1007/s00424-006-0093-2</a>.","apa":"Bischofberger, J., Engel, D., Frotscher, M., &#38; Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). <i>Pflugers Archiv : European Journal of Physiology</i>. Springer. <a href=\"https://doi.org/10.1007/s00424-006-0093-2\">https://doi.org/10.1007/s00424-006-0093-2</a>","short":"J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–372.","ista":"Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review). Pflugers Archiv : European Journal of Physiology. 453(3), 361–372.","chicago":"Bischofberger, Joseph, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network. (Review).” <i>Pflugers Archiv : European Journal of Physiology</i>. Springer, 2006. <a href=\"https://doi.org/10.1007/s00424-006-0093-2\">https://doi.org/10.1007/s00424-006-0093-2</a>."},"abstract":[{"lang":"eng","text":"It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network."}],"year":"2006","extern":1,"page":"361 - 372","publisher":"Springer","issue":"3","title":"Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. (Review)","day":"01","date_created":"2018-12-11T12:03:28Z","month":"12","intvolume":"       453","doi":"10.1007/s00424-006-0093-2","volume":453,"type":"review","publication_status":"published","author":[{"full_name":"Bischofberger, Joseph","last_name":"Bischofberger","first_name":"Joseph"},{"last_name":"Engel","first_name":"Dominique","full_name":"Engel, Dominique"},{"first_name":"Michael","last_name":"Frotscher","full_name":"Frotscher, Michael"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2019-04-26T07:22:28Z","publist_id":"2924","status":"public"},{"alternative_title":["LNCS "],"_id":"3499","date_published":"2006-09-28T00:00:00Z","quality_controlled":0,"citation":{"ama":"Chatterjee K. Nash equilibrium for upward-closed objectives. In: Vol 4207. Springer; 2006:271-286. doi:<a href=\"https://doi.org/10.1007/11874683_18\">10.1007/11874683_18</a>","ieee":"K. Chatterjee, “Nash equilibrium for upward-closed objectives,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 271–286.","mla":"Chatterjee, Krishnendu. <i>Nash Equilibrium for Upward-Closed Objectives</i>. Vol. 4207, Springer, 2006, pp. 271–86, doi:<a href=\"https://doi.org/10.1007/11874683_18\">10.1007/11874683_18</a>.","apa":"Chatterjee, K. (2006). Nash equilibrium for upward-closed objectives (Vol. 4207, pp. 271–286). Presented at the CSL: Computer Science Logic, Springer. <a href=\"https://doi.org/10.1007/11874683_18\">https://doi.org/10.1007/11874683_18</a>","short":"K. Chatterjee, in:, Springer, 2006, pp. 271–286.","ista":"Chatterjee K. 2006. Nash equilibrium for upward-closed objectives. CSL: Computer Science Logic, LNCS , vol. 4207, 271–286.","chicago":"Chatterjee, Krishnendu. “Nash Equilibrium for Upward-Closed Objectives,” 4207:271–86. Springer, 2006. <a href=\"https://doi.org/10.1007/11874683_18\">https://doi.org/10.1007/11874683_18</a>."},"conference":{"name":"CSL: Computer Science Logic"},"page":"271 - 286","extern":1,"year":"2006","abstract":[{"text":"We study infinite stochastic games played by n-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players’ goals are not necessarily conflicting), and undiscounted. We show that if each player has an upward-closed objective, then there exists an ε-Nash equilibrium in memoryless strategies, for every ε&gt;0; and exact Nash equilibria need not exist. Upward-closure of an objective means that if a set Z of infinitely repeating states is winning, then all supersets of Z of infinitely repeating states are also winning. Memoryless strategies are strategies that are independent of history of plays and depend only on the current state. We also study the complexity of finding values (payoff profile) of an ε-Nash equilibrium. We show that the values of an ε-Nash equilibrium in nonzero-sum concurrent games with upward-closed objectives for all players can be computed by computing ε-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives for all players and a polynomial procedure. As a consequence we establish that values of an ε-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME. ","lang":"eng"}],"publisher":"Springer","acknowledgement":"This research was supported in part by the NSF grants CCR-0225610 and CCR- 0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.","day":"28","title":"Nash equilibrium for upward-closed objectives","doi":"10.1007/11874683_18","intvolume":"      4207","month":"09","date_created":"2018-12-11T12:03:39Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","publication_status":"published","volume":4207,"status":"public","date_updated":"2021-01-12T07:43:52Z","publist_id":"2888"},{"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Nir Piterman. “Algorithms for Büchi Games.” ACM, 2006.","short":"K. Chatterjee, T.A. Henzinger, N. Piterman, in:, ACM, 2006.","ista":"Chatterjee K, Henzinger TA, Piterman N. 2006. Algorithms for Büchi Games. GDV: Games in Design and Verification.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Büchi Games</i>. ACM, 2006.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Piterman, N. (2006). Algorithms for Büchi Games. Presented at the GDV: Games in Design and Verification, ACM.","ama":"Chatterjee K, Henzinger TA, Piterman N. Algorithms for Büchi Games. In: ACM; 2006.","ieee":"K. Chatterjee, T. A. Henzinger, and N. Piterman, “Algorithms for Büchi Games,” presented at the GDV: Games in Design and Verification, 2006."},"_id":"3500","date_published":"2006-08-21T00:00:00Z","quality_controlled":0,"publisher":"ACM","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610 and the SNSF under the Indo-Swiss Joint Research Programme.","conference":{"name":"GDV: Games in Design and Verification"},"main_file_link":[{"url":"http://www.cs.le.ac.uk/people/np183/publications/2006/CHP06.pdf","open_access":"0"}],"extern":1,"abstract":[{"text":"The classical algorithm for solving Bu ̈chi games requires time O(n · m) for game graphs with n states and m edges. For game graphs with constant outdegree, the best known algorithm has running time O(n2/logn). We present two new algorithms for Bu ̈chi games. First, we give an algorithm that performs at most O(m) more work than the classical algorithm, but runs in time O(n) on infinitely many graphs of constant outdegree on which the classical algorithm requires time O(n2). Second, we give an algorithm with running time O(n · m · log δ(n)/ log n), where 1 ≤ δ(n) ≤ n is the outdegree of the game graph. Note that this algorithm performs asymptotically better than the classical algorithm if δ(n) = O(log n).","lang":"eng"}],"year":"2006","month":"08","date_created":"2018-12-11T12:03:39Z","day":"21","title":"Algorithms for Büchi Games","status":"public","publist_id":"2887","date_updated":"2021-01-12T07:43:53Z","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"}],"publication_status":"published","type":"conference"},{"type":"patent","ipc":"G06F 7/60 ; G06F 17/10 ; G06F 101/00","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Fu","first_name":"Ping","full_name":"Fu, Ping"},{"last_name":"Nekhayev","first_name":"Dmitry","full_name":"Nekhayev, Dmitry"},{"last_name":"Facello","first_name":"Michael","full_name":"Facello, Michael"},{"full_name":"Williams, Steven","first_name":"Steven","last_name":"Williams"}],"publist_id":"2877","date_updated":"2022-01-05T12:58:26Z","publication_date":"2006-02-07","status":"public","title":"Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism","day":"07","date_created":"2018-12-11T12:03:42Z","month":"02","extern":"1","year":"2006","abstract":[{"text":"Embodiments automatically generate an accurate network of watertight NURBS patches from polygonal models of objects while automatically detecting and preserving character lines thereon. These embodiments generate from an initial triangulation of the surface, a hierarchy of progressively coarser triangulations of the surface by performing a sequence of edge contractions using a greedy algorithm that selects edge contractions by their numerical properties. Operations are also performed to connect the triangulations in the hierarchy using homeomorphisms that preserve the topology of the initial triangulation in the coarsest triangulation. A desired quadrangulation of the surface can then be generated by homeomorphically mapping edges of a coarsest triangulation in the hierarchy back to the initial triangulation. This quadrangulation is topologically consistent with the initial triangulation and is defined by a plurality of quadrangular patches. These quadrangular patches are linked together by a (U, V) mesh that is guaranteed to be continuous at patch boundaries. A grid is then preferably fit to each of the quadrangles in the resulting quadrangulation by decomposing each of the quadrangles into k.sup.2 smaller quadrangles. A watertight NURBS model may be generated from the resulting quadrangulation.","lang":"eng"}],"main_file_link":[{"url":"https://patents.google.com/patent/US6996505","open_access":"1"}],"oa":1,"article_processing_charge":"No","ipn":"US6996505B1","applicant":["Raindrop Geomagic, Inc."],"date_published":"2006-02-07T00:00:00Z","_id":"3510","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, S. Williams, (2006).","ista":"Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. 2006. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.","chicago":"Edelsbrunner, Herbert, Ping Fu, Dmitry Nekhayev, Michael Facello, and Steven Williams. “Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism,” 2006.","ama":"Edelsbrunner H, Fu P, Nekhayev D, Facello M, Williams S. Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism. 2006.","ieee":"H. Edelsbrunner, P. Fu, D. Nekhayev, M. Facello, and S. Williams, “Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.” 2006.","apa":"Edelsbrunner, H., Fu, P., Nekhayev, D., Facello, M., &#38; Williams, S. (2006). Method, apparatus and computer program products for automatically generating NURBS models of triangulated surfaces using homeomorphism.","mla":"Edelsbrunner, Herbert, et al. <i>Method, Apparatus and Computer Program Products for Automatically Generating NURBS Models of Triangulated Surfaces Using Homeomorphism</i>. 2006."},"oa_version":"Published Version"}]