[{"page":"502 - 513","quality_controlled":0,"publication_status":"published","day":"07","doi":"10.1016/j.cell.2009.05.027","date_published":"2009-08-07T00:00:00Z","month":"08","year":"2009","acknowledgement":"This work was supported by EU contract LSHG-CT-2004-503568 ComBio, the Spanish ministry of education (M.M.C.), and EU-STREP active BioMics (A.D.). Research in the Nedelec lab is funded by the Center for Modeling and Simulation in the Biosciences (http://www.bioms.de), the Volkswagenstiftung, and Human Frontier Science Program grant RGY84.","citation":{"apa":"Dinarina, A., Pugieux, C., Corral, M., Loose, M., Spatz, J., Karsenti, É., &#38; Nédélec, F. (2009). Chromatin shapes the mitotic spindle. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.05.027\">https://doi.org/10.1016/j.cell.2009.05.027</a>","ama":"Dinarina A, Pugieux C, Corral M, et al. Chromatin shapes the mitotic spindle. <i>Cell</i>. 2009;138(3):502-513. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.05.027\">10.1016/j.cell.2009.05.027</a>","ieee":"A. Dinarina <i>et al.</i>, “Chromatin shapes the mitotic spindle,” <i>Cell</i>, vol. 138, no. 3. Cell Press, pp. 502–513, 2009.","ista":"Dinarina A, Pugieux C, Corral M, Loose M, Spatz J, Karsenti É, Nédélec F. 2009. Chromatin shapes the mitotic spindle. Cell. 138(3), 502–513.","mla":"Dinarina, Ana, et al. “Chromatin Shapes the Mitotic Spindle.” <i>Cell</i>, vol. 138, no. 3, Cell Press, 2009, pp. 502–13, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.05.027\">10.1016/j.cell.2009.05.027</a>.","short":"A. Dinarina, C. Pugieux, M. Corral, M. Loose, J. Spatz, É. Karsenti, F. Nédélec, Cell 138 (2009) 502–513.","chicago":"Dinarina, Ana, Céline Pugieux, Maria Corral, Martin Loose, Joachim Spatz, Éric Karsenti, and François Nédélec. “Chromatin Shapes the Mitotic Spindle.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.05.027\">https://doi.org/10.1016/j.cell.2009.05.027</a>."},"status":"public","publisher":"Cell Press","author":[{"full_name":"Dinarina, Ana","last_name":"Dinarina","first_name":"Ana"},{"full_name":"Pugieux, Céline","last_name":"Pugieux","first_name":"Céline"},{"first_name":"Maria","full_name":"Corral, Maria M","last_name":"Corral"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"full_name":"Spatz, Joachim P","last_name":"Spatz","first_name":"Joachim"},{"full_name":"Karsenti, Éric","last_name":"Karsenti","first_name":"Éric"},{"first_name":"François","full_name":"Nédélec, François J","last_name":"Nédélec"}],"title":"Chromatin shapes the mitotic spindle","_id":"1984","extern":1,"issue":"3","type":"journal_article","date_updated":"2021-01-12T06:54:30Z","volume":138,"publication":"Cell","date_created":"2018-12-11T11:55:03Z","publist_id":"5100","abstract":[{"text":"In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14-18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles. We also examined lines of chromatin with various dimensions. Their length determined the number of poles that formed, with a 6 × 18 μm rectangular patch generating normal spindle morphology. Around longer lines, multiple poles formed and the structures were disorganized. While lines thinner than 10 μm generated symmetric structures, thicker lines induced the formation of asymmetric structures where all microtubules are on the same side of the line. Our results show that chromatin defines spindle shape and orientation. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.","lang":"eng"}],"intvolume":"       138"},{"volume":181,"type":"journal_article","date_updated":"2021-01-12T06:55:06Z","intvolume":"       181","date_created":"2018-12-11T11:55:31Z","publication":"Genetics","publist_id":"4971","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"last_name":"Charlesworth","full_name":"Charlesworth, Brian","first_name":"Brian"}],"title":"Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster","issue":"4","_id":"2067","extern":1,"acknowledgement":"This work was funded by a Portuguese Foundation for Science and Technology scholarship to B.V., and B.C. was supported by the Royal Society","year":"2009","status":"public","publisher":"Genetics Society of America","citation":{"apa":"Vicoso, B., &#38; Charlesworth, B. (2009). Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.098004\">https://doi.org/10.1534/genetics.108.098004</a>","ama":"Vicoso B, Charlesworth B. Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. <i>Genetics</i>. 2009;181(4):1699-1701. doi:<a href=\"https://doi.org/10.1534/genetics.108.098004\">10.1534/genetics.108.098004</a>","ieee":"B. Vicoso and B. Charlesworth, “Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster,” <i>Genetics</i>, vol. 181, no. 4. Genetics Society of America, pp. 1699–1701, 2009.","ista":"Vicoso B, Charlesworth B. 2009. Recombination rates may affect the ratio of X to autosomal noncoding polymorphism in African populations of Drosophila melanogaster. Genetics. 181(4), 1699–1701.","chicago":"Vicoso, Beatriz, and Brian Charlesworth. “Recombination Rates May Affect the Ratio of X to Autosomal Noncoding Polymorphism in African Populations of Drosophila Melanogaster.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.098004\">https://doi.org/10.1534/genetics.108.098004</a>.","mla":"Vicoso, Beatriz, and Brian Charlesworth. “Recombination Rates May Affect the Ratio of X to Autosomal Noncoding Polymorphism in African Populations of Drosophila Melanogaster.” <i>Genetics</i>, vol. 181, no. 4, Genetics Society of America, 2009, pp. 1699–701, doi:<a href=\"https://doi.org/10.1534/genetics.108.098004\">10.1534/genetics.108.098004</a>.","short":"B. Vicoso, B. Charlesworth, Genetics 181 (2009) 1699–1701."},"page":"1699 - 1701","quality_controlled":0,"date_published":"2009-04-01T00:00:00Z","month":"04","publication_status":"published","doi":"10.1534/genetics.108.098004","day":"01"},{"month":"05","date_published":"2009-05-01T00:00:00Z","doi":"10.1007/s00239-009-9235-4","day":"01","publication_status":"published","quality_controlled":0,"page":"576 - 583","publisher":"Springer","status":"public","citation":{"ista":"Vicoso B, Charlesworth B. 2009. The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? Journal of Molecular Evolution. 68(5), 576–583.","mla":"Vicoso, Beatriz, and Brian Charlesworth. “The Deficit of Male-Biased Genes on the D. Melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?” <i>Journal of Molecular Evolution</i>, vol. 68, no. 5, Springer, 2009, pp. 576–83, doi:<a href=\"https://doi.org/10.1007/s00239-009-9235-4\">10.1007/s00239-009-9235-4</a>.","short":"B. Vicoso, B. Charlesworth, Journal of Molecular Evolution 68 (2009) 576–583.","chicago":"Vicoso, Beatriz, and Brian Charlesworth. “The Deficit of Male-Biased Genes on the D. Melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?” <i>Journal of Molecular Evolution</i>. Springer, 2009. <a href=\"https://doi.org/10.1007/s00239-009-9235-4\">https://doi.org/10.1007/s00239-009-9235-4</a>.","apa":"Vicoso, B., &#38; Charlesworth, B. (2009). The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? <i>Journal of Molecular Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s00239-009-9235-4\">https://doi.org/10.1007/s00239-009-9235-4</a>","ama":"Vicoso B, Charlesworth B. The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation? <i>Journal of Molecular Evolution</i>. 2009;68(5):576-583. doi:<a href=\"https://doi.org/10.1007/s00239-009-9235-4\">10.1007/s00239-009-9235-4</a>","ieee":"B. Vicoso and B. Charlesworth, “The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?,” <i>Journal of Molecular Evolution</i>, vol. 68, no. 5. Springer, pp. 576–583, 2009."},"acknowledgement":"This work was funded by a Portuguese Foundation for Science and Technology scholarship to B.V., and B.C. was supported by the Royal Society","year":"2009","_id":"2068","extern":1,"issue":"5","title":"The deficit of male-biased genes on the D. melanogaster X chromosome is expression-dependent: A consequence of dosage compensation?","author":[{"full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"}],"abstract":[{"text":"In Drosophila, there is a consistent deficit of male-biased genes on the X chromosome. It has been suggested that male-biased genes may evolve from initially unbiased genes as a result of increased expression levels in males. If transcription rates are limited, a large increase in expression in the testis may be harder to achieve for single-copy X-linked genes than for autosomal genes, because they are already hypertranscribed due to dosage compensation. This hypothesis predicts that the larger the increase in expression required to make a male-biased gene, the lower the chance of this being achievable if it is located on the X chromosome. Consequently, highly expressed male-biased genes should be located on the X chromosome less often than lowly expressed male-biased genes. This pattern is observed in our analysis of publicly available data, where microarray data or EST data are used to detect male-biased genes in D. melanogaster and to measure their expression levels. This is consistent with the idea that limitations in transcription rates may prevent male-biased genes from accumulating on the X chromosome.","lang":"eng"}],"intvolume":"        68","publist_id":"4970","publication":"Journal of Molecular Evolution","date_created":"2018-12-11T11:55:31Z","volume":68,"date_updated":"2021-01-12T06:55:06Z","type":"journal_article"},{"status":"public","publisher":"Wiley-Blackwell","citation":{"apa":"Vicoso, B., &#38; Charlesworth, B. (2009). Effective population size and the faster-X effect: An extended model. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00719.x\">https://doi.org/10.1111/j.1558-5646.2009.00719.x</a>","ama":"Vicoso B, Charlesworth B. Effective population size and the faster-X effect: An extended model. <i>Evolution</i>. 2009;63(9):2413-2426. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00719.x\">10.1111/j.1558-5646.2009.00719.x</a>","ieee":"B. Vicoso and B. Charlesworth, “Effective population size and the faster-X effect: An extended model,” <i>Evolution</i>, vol. 63, no. 9. Wiley-Blackwell, pp. 2413–2426, 2009.","ista":"Vicoso B, Charlesworth B. 2009. Effective population size and the faster-X effect: An extended model. Evolution. 63(9), 2413–2426.","short":"B. Vicoso, B. Charlesworth, Evolution 63 (2009) 2413–2426.","chicago":"Vicoso, Beatriz, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: An Extended Model.” <i>Evolution</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00719.x\">https://doi.org/10.1111/j.1558-5646.2009.00719.x</a>.","mla":"Vicoso, Beatriz, and Brian Charlesworth. “Effective Population Size and the Faster-X Effect: An Extended Model.” <i>Evolution</i>, vol. 63, no. 9, Wiley-Blackwell, 2009, pp. 2413–26, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00719.x\">10.1111/j.1558-5646.2009.00719.x</a>."},"acknowledgement":"This work was funded by a Portuguese Foundation for Science and Technology scholarship to BV, and BC was supported by the Royal Society","year":"2009","month":"09","date_published":"2009-09-01T00:00:00Z","publication_status":"published","day":"01","doi":"10.1111/j.1558-5646.2009.00719.x","quality_controlled":0,"page":"2413 - 2426","abstract":[{"lang":"eng","text":"Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/N eA &gt; 3/4. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution."}],"intvolume":"        63","date_created":"2018-12-11T11:55:32Z","publication":"Evolution","publist_id":"4968","volume":63,"type":"journal_article","date_updated":"2021-01-12T06:55:06Z","title":"Effective population size and the faster-X effect: An extended model","_id":"2069","issue":"9","extern":1,"author":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"},{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"}]},{"author":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bachtrog, Doris","last_name":"Bachtrog","first_name":"Doris"}],"issue":"5","_id":"2070","extern":1,"title":"Progress and prospects toward our understanding of the evolution of dosage compensation","volume":17,"date_updated":"2021-01-12T06:55:07Z","type":"journal_article","intvolume":"        17","abstract":[{"lang":"eng","text":"In many eukaryotic organisms, gender is determined by a pair of heteromorphic sex chromosomes. Degeneration of the non-recombining Y chromosome is a general facet of sex chromosome evolution. Selective pressure to restore expression levels of X-linked genes relative to autosomes accompanies Y-chromosome degeneration, thus driving the evolution of dosage compensation mechanisms. This review focuses on evolutionary aspects of dosage compensation, in light of recent advances in comparative and functional genomics that have substantially increased our understanding of the molecular mechanisms of dosage compensation and how it evolved. We review processes involved in sex chromosome evolution, and discuss the dynamic interaction between Y degeneration and the acquisition of dosage compensation. We compare mechanisms of dosage compensation and the origin of dosage compensation genes between different taxa and comment on sex chromosomes that apparently lack compensation mechanisms. Finally, we discuss how dosage compensation systems can also influence the evolution of well-established sex chromosomes."}],"publist_id":"4969","date_created":"2018-12-11T11:55:32Z","publication":"Chromosome Research","page":"585 - 602","quality_controlled":0,"month":"07","date_published":"2009-07-01T00:00:00Z","doi":"10.1007/s10577-009-9053-y","day":"01","publication_status":"published","acknowledgement":"This research is funded by NIH Grant GM076007 and a Sloan Research Fellowship and a David and Lucile Packard Fellowship to D.B.","year":"2009","publisher":"Springer","status":"public","citation":{"chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Progress and Prospects toward Our Understanding of the Evolution of Dosage Compensation.” <i>Chromosome Research</i>. Springer, 2009. <a href=\"https://doi.org/10.1007/s10577-009-9053-y\">https://doi.org/10.1007/s10577-009-9053-y</a>.","short":"B. Vicoso, D. Bachtrog, Chromosome Research 17 (2009) 585–602.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Progress and Prospects toward Our Understanding of the Evolution of Dosage Compensation.” <i>Chromosome Research</i>, vol. 17, no. 5, Springer, 2009, pp. 585–602, doi:<a href=\"https://doi.org/10.1007/s10577-009-9053-y\">10.1007/s10577-009-9053-y</a>.","ista":"Vicoso B, Bachtrog D. 2009. Progress and prospects toward our understanding of the evolution of dosage compensation. Chromosome Research. 17(5), 585–602.","ieee":"B. Vicoso and D. Bachtrog, “Progress and prospects toward our understanding of the evolution of dosage compensation,” <i>Chromosome Research</i>, vol. 17, no. 5. Springer, pp. 585–602, 2009.","ama":"Vicoso B, Bachtrog D. Progress and prospects toward our understanding of the evolution of dosage compensation. <i>Chromosome Research</i>. 2009;17(5):585-602. doi:<a href=\"https://doi.org/10.1007/s10577-009-9053-y\">10.1007/s10577-009-9053-y</a>","apa":"Vicoso, B., &#38; Bachtrog, D. (2009). Progress and prospects toward our understanding of the evolution of dosage compensation. <i>Chromosome Research</i>. Springer. <a href=\"https://doi.org/10.1007/s10577-009-9053-y\">https://doi.org/10.1007/s10577-009-9053-y</a>"}},{"main_file_link":[{"url":"https://arxiv.org/abs/0811.0695","open_access":"1"}],"status":"public","citation":{"apa":"Mark, M., Danzl, J. G., Haller, E., Gustavsson, M., Bouloufa, N., Dulieu, O., … Nägerl, H. (2009). Dark resonances for ground-state transfer of molecular quantum gases. <i>Applied Physics B: Lasers and Optics</i>. Springer. <a href=\"https://doi.org/10.1007/s00340-009-3407-1\">https://doi.org/10.1007/s00340-009-3407-1</a>","ama":"Mark M, Danzl JG, Haller E, et al. Dark resonances for ground-state transfer of molecular quantum gases. <i>Applied Physics B: Lasers and Optics</i>. 2009;95(2):219-225. doi:<a href=\"https://doi.org/10.1007/s00340-009-3407-1\">10.1007/s00340-009-3407-1</a>","ieee":"M. Mark <i>et al.</i>, “Dark resonances for ground-state transfer of molecular quantum gases,” <i>Applied Physics B: Lasers and Optics</i>, vol. 95, no. 2. Springer, pp. 219–225, 2009.","ista":"Mark M, Danzl JG, Haller E, Gustavsson M, Bouloufa N, Dulieu O, Salami H, Bergeman T, Ritsch H, Hart R, Nägerl H. 2009. Dark resonances for ground-state transfer of molecular quantum gases. Applied Physics B: Lasers and Optics. 95(2), 219–225.","mla":"Mark, Manfred, et al. “Dark Resonances for Ground-State Transfer of Molecular Quantum Gases.” <i>Applied Physics B: Lasers and Optics</i>, vol. 95, no. 2, Springer, 2009, pp. 219–25, doi:<a href=\"https://doi.org/10.1007/s00340-009-3407-1\">10.1007/s00340-009-3407-1</a>.","short":"M. Mark, J.G. Danzl, E. Haller, M. Gustavsson, N. Bouloufa, O. Dulieu, H. Salami, T. Bergeman, H. Ritsch, R. Hart, H. Nägerl, Applied Physics B: Lasers and Optics 95 (2009) 219–225.","chicago":"Mark, Manfred, Johann G Danzl, Elmar Haller, Mattias Gustavsson, Nadia Bouloufa, Olivier Dulieu, Houssam Salami, et al. “Dark Resonances for Ground-State Transfer of Molecular Quantum Gases.” <i>Applied Physics B: Lasers and Optics</i>. Springer, 2009. <a href=\"https://doi.org/10.1007/s00340-009-3407-1\">https://doi.org/10.1007/s00340-009-3407-1</a>."},"acknowledgement":"We are indebted to R. Grimm for generous support and we thank E. Tiemann for valuable discussions and C. Amiot for providing the FTS data of LAC on Cs2. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (BMWF)\r\nand the Austrian Science Fund (FWF) in the form of a START prize grant and by the European Science Foundation (ESF) in the framework of the EuroQUAM collective research project QuDipMol. R.H. acknowledges support by the European Union in the form of a Marie Curie International Incoming Fellowship (IIF). The work at Stony Brook was supported by the US NSF, under grant PHY0652459.","month":"05","day":"01","doi":"10.1007/s00340-009-3407-1","publication_status":"published","arxiv":1,"oa_version":"None","language":[{"iso":"eng"}],"abstract":[{"text":"One possible way to produce ultra-cold, high-phase-space-density quantum gases of molecules in the rovibronic ground state is given by molecule association from quantum-degenerate atomic gases on a Feshbach resonance and subsequent coherent optical multi-photon transfer into the rovibronic ground state. In ultra-cold samples of Cs2 molecules, we observe two-photon dark resonances that connect the intermediate rovibrational level |v=73,J=2 with the rovibrational ground state |v=0,J=0 of the singlet X 1 ∑ g + ground-state potential. For precise dark resonance spectroscopy we exploit the fact that it is possible to efficiently populate the level |v=73,J=2 by two-photon transfer from the dissociation threshold with the stimulated Raman adiabatic passage (STIRAP) technique. We find that at least one of the two-photon resonances is sufficiently strong to allow future implementation of coherent STIRAP transfer of a molecular quantum gas to the rovibrational ground state |v=0,J=0.","lang":"eng"}],"publication":"Applied Physics B: Lasers and Optics","date_created":"2018-12-11T11:49:49Z","date_updated":"2021-01-12T06:47:50Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dark resonances for ground-state transfer of molecular quantum gases","oa":1,"publisher":"Springer","year":"2009","date_published":"2009-05-01T00:00:00Z","article_processing_charge":"No","page":"219 - 225","intvolume":"        95","publist_id":"6350","volume":95,"_id":"1038","external_id":{"arxiv":["0811.0695"]},"extern":"1","issue":"2","author":[{"first_name":"Manfred","last_name":"Mark","full_name":"Mark, Manfred"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"first_name":"Elmar","full_name":"Haller, Elmar","last_name":"Haller"},{"full_name":"Gustavsson, Mattias","last_name":"Gustavsson","first_name":"Mattias"},{"full_name":"Bouloufa, Nadia","last_name":"Bouloufa","first_name":"Nadia"},{"full_name":"Dulieu, Olivier","last_name":"Dulieu","first_name":"Olivier"},{"first_name":"Houssam","full_name":"Salami, Houssam","last_name":"Salami"},{"full_name":"Bergeman, Thomas","last_name":"Bergeman","first_name":"Thomas"},{"last_name":"Ritsch","full_name":"Ritsch, Helmut","first_name":"Helmut"},{"first_name":"Russell","last_name":"Hart","full_name":"Hart, Russell"},{"last_name":"Nägerl","full_name":"Nägerl, Hanns","first_name":"Hanns"}]},{"date_published":"2009-01-01T00:00:00Z","article_processing_charge":"No","page":"1224 - 1227","publisher":"American Association for the Advancement of Science","year":"2009","_id":"1040","issue":"5945","external_id":{"arxiv":["1006.0739"]},"extern":"1","author":[{"first_name":"Elmar","full_name":"Haller, Elmar","last_name":"Haller"},{"last_name":"Gustavsson","full_name":"Gustavsson, Mattias","first_name":"Mattias"},{"full_name":"Mark, Manfred","last_name":"Mark","first_name":"Manfred"},{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"first_name":"Guido","full_name":"Pupillo, Guido","last_name":"Pupillo"},{"first_name":"Hanns","last_name":"Nägerl","full_name":"Nägerl, Hanns"}],"intvolume":"       325","publist_id":"6348","volume":325,"month":"01","publication_status":"published","day":"01","doi":"10.1126/science.1175850","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"None","main_file_link":[{"url":"https://arxiv.org/abs/1006.0739","open_access":"1"}],"status":"public","citation":{"apa":"Haller, E., Gustavsson, M., Mark, M., Danzl, J. G., Hart, R., Pupillo, G., &#38; Nägerl, H. (2009). Realization of an excited, strongly correlated quantum gas Phase. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1175850\">https://doi.org/10.1126/science.1175850</a>","ama":"Haller E, Gustavsson M, Mark M, et al. Realization of an excited, strongly correlated quantum gas Phase. <i>Science</i>. 2009;325(5945):1224-1227. doi:<a href=\"https://doi.org/10.1126/science.1175850\">10.1126/science.1175850</a>","ieee":"E. Haller <i>et al.</i>, “Realization of an excited, strongly correlated quantum gas Phase,” <i>Science</i>, vol. 325, no. 5945. American Association for the Advancement of Science, pp. 1224–1227, 2009.","ista":"Haller E, Gustavsson M, Mark M, Danzl JG, Hart R, Pupillo G, Nägerl H. 2009. Realization of an excited, strongly correlated quantum gas Phase. Science. 325(5945), 1224–1227.","mla":"Haller, Elmar, et al. “Realization of an Excited, Strongly Correlated Quantum Gas Phase.” <i>Science</i>, vol. 325, no. 5945, American Association for the Advancement of Science, 2009, pp. 1224–27, doi:<a href=\"https://doi.org/10.1126/science.1175850\">10.1126/science.1175850</a>.","short":"E. Haller, M. Gustavsson, M. Mark, J.G. Danzl, R. Hart, G. Pupillo, H. Nägerl, Science 325 (2009) 1224–1227.","chicago":"Haller, Elmar, Mattias Gustavsson, Manfred Mark, Johann G Danzl, Russell Hart, Guido Pupillo, and Hanns Nägerl. “Realization of an Excited, Strongly Correlated Quantum Gas Phase.” <i>Science</i>. American Association for the Advancement of Science, 2009. <a href=\"https://doi.org/10.1126/science.1175850\">https://doi.org/10.1126/science.1175850</a>."},"acknowledgement":"We thank S. Giorgini and C. Menotti for helpful discussions and for providing the theory curves shown in Fig. 3A. We are indebted to R. Grimm for generous support and to H. Häffner and his group for the loan of a charge-coupled device camera. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (Bundesministerium für Wissenschaft und Forschung) and the Austrian Science Fund (Fonds zur Förderung der wissenschaftlichen Forschung) in the form of a START prize grant and by the European Union through the Specific Targeted Research Project FP7-ICT-2007-C project NAME-QUAM (Nanodesigning of Atomic and Molecular Quantum Matter) and within the framework of the EuroQUASAR collective research project Quantum-Degenerate Gases for Precision Measurements. R.H. is supported by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme.","title":"Realization of an excited, strongly correlated quantum gas Phase","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"lang":"eng","text":"Ultracold atomic physics offers myriad possibilities to study strongly correlated many-body systems in lower dimensions. Typically, only ground-state phases are accessible. Using a tunable quantum gas of bosonic cesium atoms, we realized and controlled in one-dimensional geometry a highly excited quantum phase that is stabilized in the presence of attractive interactions by maintaining and strengthening quantum correlations across a confinement-induced resonance. We diagnosed the crossover from repulsive to attractive interactions in terms of the stiffness and energy of the system. Our results open up the experimental study of metastable, excited, many-body phases with strong correlations and their dynamical properties."}],"publication":"Science","date_created":"2018-12-11T11:49:50Z","type":"journal_article","date_updated":"2021-01-12T06:47:51Z"},{"author":[{"orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Manfred","full_name":"Mark, Manfred","last_name":"Mark"},{"first_name":"Elmar","full_name":"Haller, Elmar","last_name":"Haller"},{"first_name":"Mattias","last_name":"Gustavsson","full_name":"Gustavsson, Mattias"},{"full_name":"Hart, Russell","last_name":"Hart","first_name":"Russell"},{"last_name":"Liem","full_name":"Liem, Andreas","first_name":"Andreas"},{"first_name":"Holger","full_name":"Zellmer, Holger","last_name":"Zellmer"},{"full_name":"Nägerl, Hanns","last_name":"Nägerl","first_name":"Hanns"}],"oa":1,"title":"Deeply bound ultracold molecules in an optical lattice","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","_id":"1041","external_id":{"arxiv":["0812.5070"]},"volume":11,"type":"journal_article","date_updated":"2021-01-12T06:47:51Z","intvolume":"        11","abstract":[{"lang":"eng","text":"We demonstrate efficient transfer of ultracold molecules into a deeply bound rovibrational level of the singlet ground state potential in the presence of an optical lattice. The overall molecule creation efficiency is 25%, and the transfer efficiency to the rovibrational level |v = 73, J = 2) is above 80%. We find that the molecules in |v = 73, J = 2) are trapped in the optical lattice, and that the lifetime in the lattice is limited by optical excitation by the lattice light. The molecule trapping time for a lattice depth of 15 atomic recoil energies is about 20 ms. We determine the trapping frequency by the lattice phase and amplitude modulation technique. It will now be possible to transfer the molecules to the rovibrational ground state |v = 0, J = 0) in the presence of the optical lattice."}],"date_created":"2018-12-11T11:49:50Z","publication":"New Journal of Physics","publist_id":"6349","article_processing_charge":"No","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"None","date_published":"2009-03-14T00:00:00Z","month":"03","publication_status":"published","doi":"10.1088/1367-2630/11/5/055036","day":"14","year":"2009","acknowledgement":"We are indebted to R Grimm for generous support and we thank S Knoop, N Boloufa, and O Dulieu for valuable discussions. We gratefully acknowledge funding by the Austrian Ministry of Science and Research (BMWF) and the Austrian Science Fund (FWF) in the form of a START prize grant. RH acknowledges support by the European Union in the form of a Marie-Curie International Incoming Fellowship (IIF).","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0812.5070"}],"publisher":"IOP Publishing Ltd.","citation":{"mla":"Danzl, Johann G., et al. “Deeply Bound Ultracold Molecules in an Optical Lattice.” <i>New Journal of Physics</i>, vol. 11, IOP Publishing Ltd., 2009, doi:<a href=\"https://doi.org/10.1088/1367-2630/11/5/055036\">10.1088/1367-2630/11/5/055036</a>.","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, A. Liem, H. Zellmer, H. Nägerl, New Journal of Physics 11 (2009).","chicago":"Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, Andreas Liem, Holger Zellmer, and Hanns Nägerl. “Deeply Bound Ultracold Molecules in an Optical Lattice.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2009. <a href=\"https://doi.org/10.1088/1367-2630/11/5/055036\">https://doi.org/10.1088/1367-2630/11/5/055036</a>.","ista":"Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Liem A, Zellmer H, Nägerl H. 2009. Deeply bound ultracold molecules in an optical lattice. New Journal of Physics. 11.","ieee":"J. G. Danzl <i>et al.</i>, “Deeply bound ultracold molecules in an optical lattice,” <i>New Journal of Physics</i>, vol. 11. IOP Publishing Ltd., 2009.","ama":"Danzl JG, Mark M, Haller E, et al. Deeply bound ultracold molecules in an optical lattice. <i>New Journal of Physics</i>. 2009;11. doi:<a href=\"https://doi.org/10.1088/1367-2630/11/5/055036\">10.1088/1367-2630/11/5/055036</a>","apa":"Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., Liem, A., … Nägerl, H. (2009). Deeply bound ultracold molecules in an optical lattice. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/11/5/055036\">https://doi.org/10.1088/1367-2630/11/5/055036</a>"}},{"type":"journal_article","date_updated":"2021-01-12T06:47:52Z","abstract":[{"text":"One possibility for the creation of ultracold, high phase space density quantum gases of molecules in the rovibronic ground state relies on first associating weakly-bound molecules from quantum-degenerate atomic gases on a Feshbach resonance and then transferring the molecules via several steps of coherent two-photon stimulated Raman adiabatic passage (STIRAP) into the rovibronic ground state. Here, in ultracold samples of Cs2 Feshbach molecules produced out of ultracold samples of Cs atoms, we observe several optical transitions to deeply-bound rovibrational levels of the excited 0 u+ molecular potentials with high resolution. At least one of these transitions, although rather weak, allows efficient STIRAP transfer into the deeply-bound vibrational level v = 73&gt; of the singlet X 1Σg+ ground state potential, as recently demonstrated (J. G. Danzl, E. Haller, M. Gustavsson, M. J. Mark, R. Hart, N. Bouloufa, O. Dulieu, H. Ritsch, and H.-C. Nägerl, Science, 2008, 321, 1062). From this level, the rovibrational ground state v = 0, J = 0&gt; can be reached with one more transfer step. In total, our results show that coherent ground state transfer for Cs2 is possible using a maximum of two successive two-photon STIRAP processes or one single four-photon STIRAP process.","lang":"eng"}],"date_created":"2018-12-11T11:49:51Z","publication":"Faraday Discussions","oa":1,"title":"Precision molecular spectroscopy for ground state transfer of molecular quantum gases","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We are indebted to R. Grimm for generous support and we thank T. Bergeman, H.\r\nSalami, J. Hutson, J. Aldegunde, and E. Tiemann for valuable discussions. We\r\ngratefully acknowledge funding by the Austrian Ministry of Science and Research\r\n(BMWF) and the Austrian Science Fund (FWF) in the form of a START prize grant\r\nand by the European Science Foundation (ESF) in the framework of the EuroQUAM collective research project QuDipMol. R. H. acknowledges support by\r\nthe European Union in form of a Marie Curie International Incoming Fellowship\r\n(IIF).","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0811.2374"}],"citation":{"ista":"Danzl JG, Mark M, Haller E, Gustavsson M, Bouloufa N, Dulieu O, Ritsch H, Hart R, Nägerl H. 2009. Precision molecular spectroscopy for ground state transfer of molecular quantum gases. Faraday Discussions. 142, 283–295.","short":"J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, N. Bouloufa, O. Dulieu, H. Ritsch, R. Hart, H. Nägerl, Faraday Discussions 142 (2009) 283–295.","mla":"Danzl, Johann G., et al. “Precision Molecular Spectroscopy for Ground State Transfer of Molecular Quantum Gases.” <i>Faraday Discussions</i>, vol. 142, Royal Society of Chemistry, 2009, pp. 283–95, doi:<a href=\"https://doi.org/10.1039/b820542f\">10.1039/b820542f</a>.","chicago":"Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Nadia Bouloufa, Olivier Dulieu, Helmut Ritsch, Russell Hart, and Hanns Nägerl. “Precision Molecular Spectroscopy for Ground State Transfer of Molecular Quantum Gases.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2009. <a href=\"https://doi.org/10.1039/b820542f\">https://doi.org/10.1039/b820542f</a>.","ama":"Danzl JG, Mark M, Haller E, et al. Precision molecular spectroscopy for ground state transfer of molecular quantum gases. <i>Faraday Discussions</i>. 2009;142:283-295. doi:<a href=\"https://doi.org/10.1039/b820542f\">10.1039/b820542f</a>","apa":"Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Bouloufa, N., Dulieu, O., … Nägerl, H. (2009). Precision molecular spectroscopy for ground state transfer of molecular quantum gases. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/b820542f\">https://doi.org/10.1039/b820542f</a>","ieee":"J. G. Danzl <i>et al.</i>, “Precision molecular spectroscopy for ground state transfer of molecular quantum gases,” <i>Faraday Discussions</i>, vol. 142. Royal Society of Chemistry, pp. 283–295, 2009."},"arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","month":"01","publication_status":"published","doi":"10.1039/b820542f","day":"01","volume":142,"intvolume":"       142","publist_id":"6347","author":[{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"first_name":"Manfred","full_name":"Mark, Manfred","last_name":"Mark"},{"first_name":"Elmar","full_name":"Haller, Elmar","last_name":"Haller"},{"full_name":"Gustavsson, Mattias","last_name":"Gustavsson","first_name":"Mattias"},{"first_name":"Nadia","full_name":"Bouloufa, Nadia","last_name":"Bouloufa"},{"first_name":"Olivier","last_name":"Dulieu","full_name":"Dulieu, Olivier"},{"first_name":"Helmut","last_name":"Ritsch","full_name":"Ritsch, Helmut"},{"first_name":"Russell","full_name":"Hart, Russell","last_name":"Hart"},{"last_name":"Nägerl","full_name":"Nägerl, Hanns","first_name":"Hanns"}],"_id":"1043","extern":"1","external_id":{"arxiv":["0811.2374"]},"year":"2009","publisher":"Royal Society of Chemistry","article_processing_charge":"No","page":"283 - 295","date_published":"2009-01-01T00:00:00Z"},{"publisher":"Microtome Publishing","status":"public","main_file_link":[{"url":"https://hal.inria.fr/hal-00773608","open_access":"1"}],"citation":{"short":"M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research 10 (2009) 71–106.","mla":"Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>, vol. 10, Microtome Publishing, 2009, pp. 71–106.","chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>. Microtome Publishing, 2009.","ista":"Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations for MAP estimation of discrete MRFs,” <i>Journal of Machine Learning Research</i>, vol. 10. Microtome Publishing, pp. 71–106, 2009.","ama":"Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. 2009;10:71-106.","apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2009). An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. Microtome Publishing."},"year":"2009","month":"01","date_published":"2009-01-01T00:00:00Z","day":"01","publication_status":"published","quality_controlled":0,"page":"71 - 106","abstract":[{"text":"The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.\n\nWe show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.","lang":"eng"}],"intvolume":"        10","publist_id":"3484","date_created":"2018-12-11T12:01:57Z","publication":"Journal of Machine Learning Research","volume":10,"date_updated":"2021-01-12T07:41:44Z","type":"journal_article","_id":"3197","extern":1,"title":"An analysis of convex relaxations for MAP estimation of discrete MRFs","author":[{"last_name":"Kumar","full_name":"Kumar, M Pawan","first_name":"M Pawan"},{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"last_name":"Torr","full_name":"Torr, Philip H","first_name":"Philip"}],"oa":1},{"conference":{"name":"ICCV: International Conference on Computer Vision"},"author":[{"first_name":"Sara","full_name":"Vicente, Sara","last_name":"Vicente"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}],"_id":"3199","extern":1,"title":"Joint optimization of segmentation and appearance models","date_updated":"2021-01-12T07:41:44Z","type":"conference","publist_id":"3482","date_created":"2018-12-11T12:01:58Z","abstract":[{"text":"Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additionally a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of real world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm.","lang":"eng"}],"quality_controlled":0,"page":"755 - 762","doi":"10.1109/ICCV.2009.5459287","day":"01","publication_status":"published","month":"05","date_published":"2009-05-01T00:00:00Z","year":"2009","citation":{"short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762.","mla":"Vicente, Sara, et al. <i>Joint Optimization of Segmentation and Appearance Models</i>. IEEE, 2009, pp. 755–62, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>.","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Joint Optimization of Segmentation and Appearance Models,” 755–62. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>.","ista":"Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation and appearance models. ICCV: International Conference on Computer Vision, 755–762.","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Joint optimization of segmentation and appearance models,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 755–762.","apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2009). Joint optimization of segmentation and appearance models (pp. 755–762). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>","ama":"Vicente S, Kolmogorov V, Rother C. Joint optimization of segmentation and appearance models. In: IEEE; 2009:755-762. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>"},"publisher":"IEEE","status":"public","main_file_link":[{"open_access":"0","url":"http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf"}]},{"citation":{"ieee":"V. Kolmogorov and A. Shioura, “New algorithms for convex cost tension problem with application to computer vision,” <i>Discrete Optimization</i>, vol. 6, no. 4. Elsevier, pp. 378–393, 2009.","apa":"Kolmogorov, V., &#38; Shioura, A. (2009). New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>","ama":"Kolmogorov V, Shioura A. New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. 2009;6(4):378-393. doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>","mla":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>, vol. 6, no. 4, Elsevier, 2009, pp. 378–93, doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>.","short":"V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393.","chicago":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>.","ista":"Kolmogorov V, Shioura A. 2009. New algorithms for convex cost tension problem with application to computer vision. Discrete Optimization. 6(4), 378–393."},"publisher":"Elsevier","status":"public","year":"2009","day":"01","doi":"10.1016/j.disopt.2009.04.006","publication_status":"published","date_published":"2009-11-01T00:00:00Z","month":"11","quality_controlled":0,"page":"378 - 393","publist_id":"3483","publication":"Discrete Optimization","date_created":"2018-12-11T12:01:58Z","intvolume":"         6","abstract":[{"text":"Motivated by various applications to computer vision, we consider the convex cost tension problem, which is the dual of the convex cost flow problem. In this paper, we first propose a primal algorithm for computing an optimal solution of the problem. Our primal algorithm iteratively updates primal variables by solving associated minimum cut problems. We show that the time complexity of the primal algorithm is O (K {dot operator} T (n, m)), where K is the range of primal variables and T (n, m) is the time needed to compute a minimum cut in a graph with n nodes and m edges. We then develop an improved version of the primal algorithm, called the primal-dual algorithm, by making good use of dual variables in addition to primal variables. Although its time complexity is the same as that of the primal algorithm, we can expect a better performance in practice. We finally consider an application to a computer vision problem called the panoramic image stitching.","lang":"eng"}],"date_updated":"2021-01-12T07:41:45Z","type":"journal_article","volume":6,"extern":1,"_id":"3200","issue":"4","title":"New algorithms for convex cost tension problem with application to computer vision","author":[{"first_name":"Vladimir","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"last_name":"Shioura","full_name":"Shioura, Akiyoshi","first_name":"Akiyoshi"}]},{"title":"A global perspective on MAP inference for low level vision","extern":1,"_id":"3203","author":[{"last_name":"Woodford","full_name":"Woodford, Oliver J","first_name":"Oliver"},{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"},{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"conference":{"name":"ICCV: International Conference on Computer Vision"},"date_created":"2018-12-11T12:01:59Z","publist_id":"3481","abstract":[{"text":"In recent years the Markov Random Field (MRF) has become the de facto probabilistic model for low-level vision applications. However, in a maximum a posteriori (MAP) framework, MRFs inherently encourage delta function marginal statistics. By contrast, many low-level vision problems have heavy tailed marginal statistics, making the MRF model unsuitable. In this paper we introduce a more general Marginal Probability Field (MPF), of which the MRF is a special, linear case, and show that convex energy MPFs can be used to encourage arbitrary marginal statistics. We introduce a flexible, extensible framework for effectively optimizing the resulting NP-hard MAP problem, based around dual-decomposition and a modified mincost flow algorithm, and which achieves global optimality in some instances. We use a range of applications, including image denoising and texture synthesis, to demonstrate the benefits of this class of MPF over MRFs.","lang":"eng"}],"type":"conference","date_updated":"2021-01-12T07:41:46Z","publication_status":"published","day":"01","doi":"10.1109/ICCV.2009.5459434","month":"05","date_published":"2009-05-01T00:00:00Z","quality_controlled":0,"page":"2319 - 2326","citation":{"short":"O. Woodford, C. Rother, V. Kolmogorov, in:, IEEE, 2009, pp. 2319–2326.","mla":"Woodford, Oliver, et al. <i>A Global Perspective on MAP Inference for Low Level Vision</i>. IEEE, 2009, pp. 2319–26, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">10.1109/ICCV.2009.5459434</a>.","chicago":"Woodford, Oliver, Carsten Rother, and Vladimir Kolmogorov. “A Global Perspective on MAP Inference for Low Level Vision,” 2319–26. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">https://doi.org/10.1109/ICCV.2009.5459434</a>.","ista":"Woodford O, Rother C, Kolmogorov V. 2009. A global perspective on MAP inference for low level vision. ICCV: International Conference on Computer Vision, 2319–2326.","ieee":"O. Woodford, C. Rother, and V. Kolmogorov, “A global perspective on MAP inference for low level vision,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 2319–2326.","apa":"Woodford, O., Rother, C., &#38; Kolmogorov, V. (2009). A global perspective on MAP inference for low level vision (pp. 2319–2326). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">https://doi.org/10.1109/ICCV.2009.5459434</a>","ama":"Woodford O, Rother C, Kolmogorov V. A global perspective on MAP inference for low level vision. In: IEEE; 2009:2319-2326. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459434\">10.1109/ICCV.2009.5459434</a>"},"status":"public","publisher":"IEEE","year":"2009"},{"month":"05","date_published":"2009-05-28T00:00:00Z","publication_status":"published","doi":"10.1007/978-3-642-01001-9_34","day":"28","page":"590 - 609","quality_controlled":0,"status":"public","publisher":"Springer","citation":{"ama":"Kiltz E, Pietrzak KZ, Stam M, Yung M. A new randomness extraction paradigm for hybrid encryption. In: Vol 5479. Springer; 2009:590-609. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">10.1007/978-3-642-01001-9_34</a>","apa":"Kiltz, E., Pietrzak, K. Z., Stam, M., &#38; Yung, M. (2009). A new randomness extraction paradigm for hybrid encryption (Vol. 5479, pp. 590–609). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">https://doi.org/10.1007/978-3-642-01001-9_34</a>","ieee":"E. Kiltz, K. Z. Pietrzak, M. Stam, and M. Yung, “A new randomness extraction paradigm for hybrid encryption,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 590–609.","ista":"Kiltz E, Pietrzak KZ, Stam M, Yung M. 2009. A new randomness extraction paradigm for hybrid encryption. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 590–609.","short":"E. Kiltz, K.Z. Pietrzak, M. Stam, M. Yung, in:, Springer, 2009, pp. 590–609.","chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, Martijn Stam, and Moti Yung. “A New Randomness Extraction Paradigm for Hybrid Encryption,” 5479:590–609. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">https://doi.org/10.1007/978-3-642-01001-9_34</a>.","mla":"Kiltz, Eike, et al. <i>A New Randomness Extraction Paradigm for Hybrid Encryption</i>. Vol. 5479, Springer, 2009, pp. 590–609, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_34\">10.1007/978-3-642-01001-9_34</a>."},"year":"2009","title":"A new randomness extraction paradigm for hybrid encryption","alternative_title":["LNCS"],"extern":1,"_id":"3230","author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","last_name":"Pietrzak"},{"first_name":"Martijn","full_name":"Stam, Martijn","last_name":"Stam"},{"first_name":"Moti","last_name":"Yung","full_name":"Yung, Moti"}],"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"intvolume":"      5479","abstract":[{"lang":"eng","text":"We present a new approach to the design of IND-CCA2 secure hybrid encryption schemes in the standard model. Our approach provides an efficient generic transformation from 1-universal to 2-universal hash proof systems. The transformation involves a randomness extractor based on a 4-wise independent hash function as the key derivation function. Our methodology can be instantiated with efficient schemes based on standard intractability assumptions such as Decisional Diffie-Hellman, Quadratic Residuosity, and Paillier's Decisional Composite Residuosity. Interestingly, our framework also allows to prove IND-CCA2 security of a hybrid version of 1991's Damgård's ElGamal public-key encryption scheme under the DDH assumption. "}],"date_created":"2018-12-11T12:02:09Z","publist_id":"3449","volume":5479,"type":"conference","date_updated":"2021-01-12T07:41:58Z"},{"author":[{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"}],"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"alternative_title":["LNCS"],"title":"On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model","extern":1,"_id":"3231","type":"conference","date_updated":"2021-01-12T07:41:58Z","volume":5479,"date_created":"2018-12-11T12:02:09Z","publist_id":"3450","intvolume":"      5479","abstract":[{"lang":"eng","text":"We investigate the security of &quot;padding-based&quot; encryption schemes in the standard model. This class contains all public-key encryption schemes where the encryption algorithm first applies some invertible public transformation to the message (the &quot;padding&quot;), followed by a trapdoor permutation. In particular, this class contains OAEP and its variants. Our main result is a black-box impossibility result showing that one cannot prove any such padding-based scheme chosen-ciphertext secure even assuming the existence of ideal trapdoor permutations. The latter is a strong ideal abstraction of trapdoor permutations which inherits all security properties of uniform random permutations. "}],"page":"389 - 406","quality_controlled":0,"publication_status":"published","doi":"10.1007/978-3-642-01001-9_23","day":"28","month":"05","date_published":"2009-05-28T00:00:00Z","year":"2009","citation":{"ista":"Kiltz E, Pietrzak KZ. 2009. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 5479, 389–406.","mla":"Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model</i>. Vol. 5479, Springer, 2009, pp. 389–406, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">10.1007/978-3-642-01001-9_23</a>.","chicago":"Kiltz, Eike, and Krzysztof Z Pietrzak. “On the Security of Padding Based Encryption Schemes Why We Cannot Prove OAEP Secure in the Standard Model,” 5479:389–406. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">https://doi.org/10.1007/978-3-642-01001-9_23</a>.","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2009, pp. 389–406.","apa":"Kiltz, E., &#38; Pietrzak, K. Z. (2009). On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model (Vol. 5479, pp. 389–406). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">https://doi.org/10.1007/978-3-642-01001-9_23</a>","ama":"Kiltz E, Pietrzak KZ. On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model. In: Vol 5479. Springer; 2009:389-406. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_23\">10.1007/978-3-642-01001-9_23</a>","ieee":"E. Kiltz and K. Z. Pietrzak, “On the security of padding based encryption schemes Why We cannot prove OAEP secure in the standard model,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2009, vol. 5479, pp. 389–406."},"status":"public","publisher":"Springer"},{"publication_status":"published","day":"28","doi":"10.1007/978-3-642-01001-9_27","date_published":"2009-05-28T00:00:00Z","month":"05","quality_controlled":0,"page":"462 - 482","citation":{"ista":"Pietrzak KZ. 2009. A leakage resilient mode of operation. CRYPTO: International Cryptology Conference, LNCS, vol. 5479, 462–482.","chicago":"Pietrzak, Krzysztof Z. “A Leakage Resilient Mode of Operation,” 5479:462–82. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">https://doi.org/10.1007/978-3-642-01001-9_27</a>.","mla":"Pietrzak, Krzysztof Z. <i>A Leakage Resilient Mode of Operation</i>. Vol. 5479, Springer, 2009, pp. 462–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">10.1007/978-3-642-01001-9_27</a>.","short":"K.Z. Pietrzak, in:, Springer, 2009, pp. 462–482.","ama":"Pietrzak KZ. A leakage resilient mode of operation. In: Vol 5479. Springer; 2009:462-482. doi:<a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">10.1007/978-3-642-01001-9_27</a>","apa":"Pietrzak, K. Z. (2009). A leakage resilient mode of operation (Vol. 5479, pp. 462–482). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-01001-9_27\">https://doi.org/10.1007/978-3-642-01001-9_27</a>","ieee":"K. Z. Pietrzak, “A leakage resilient mode of operation,” presented at the CRYPTO: International Cryptology Conference, 2009, vol. 5479, pp. 462–482."},"status":"public","publisher":"Springer","year":"2009","title":"A leakage resilient mode of operation","alternative_title":["LNCS"],"extern":1,"_id":"3232","author":[{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}],"conference":{"name":"CRYPTO: International Cryptology Conference"},"date_created":"2018-12-11T12:02:09Z","publist_id":"3448","intvolume":"      5479","abstract":[{"text":"A weak pseudorandom function (wPRF) is a cryptographic primitive similar to - but weaker than - a pseudorandom function: for wPRFs one only requires that the output is pseudorandom when queried on random inputs.We show that unlike &quot;normal&quot; PRFs, wPRFs are seedincompressible, in the sense that the output of a wPRF is pseudorandom even if a bounded amount of information about the key is leaked. As an application of this result we construct a simple mode of operation which - when instantiated with any wPRF - gives a leakage-resilient stream-cipher. The implementation of such a cipher is secure against every side-channel attack, as long as the amount of information leaked per round is bounded, but overall can be arbitrary large. The construction is simpler than the previous one (Dziembowski-Pietrzak FOCS'08) as it only uses a single primitive (a wPRF) in a straight forward manner. ","lang":"eng"}],"type":"conference","date_updated":"2021-01-12T07:41:59Z","volume":5479},{"type":"journal_article","date_updated":"2021-01-12T07:42:26Z","volume":284,"publication":"Journal of Biological Chemistry","date_created":"2018-12-11T12:02:30Z","publist_id":"3353","abstract":[{"text":"Galactofuranose (Galf) containing molecules have been described at the cell surface of several eukaryotes and shown to contribute to the virulence of the parasite Leishmania major and the fungus Aspergillus fumigatus. It is anticipated that a number of the surface glycoconjugates such as N-glycans or glycolipids are galactofuranosylated in the Golgi apparatus. This raises the question of how the substrate for galactofuranosylation reactions, UDP-Galf, which is synthesized in the cytosol, translocates into the organelles of the secretory pathway. Here we report the first identification of a Golgi-localized nucleotide sugar transporter, named GlfB, with specificity for a UDP-Galf. In vitro transport assays established binding of UDP-Galf to GlfB and excluded transport of several other nucleotide sugars. Furthermore, the implication of glfB in the galactofuranosylation of A. fumigatus glycoconjugates and galactomannan was demonstrated by a targeted gene deletion approach. Our data reveal a direct connection between galactomannan and the organelles of the secretory pathway that strongly suggests that the cell wall-bound polysaccharide originates from its glycosylphosphatidylinositol-anchored form.","lang":"eng"}],"intvolume":"       284","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5795-0133","first_name":"Philipp S"},{"first_name":"Thilo","full_name":"Dörk Bousset, Thilo","last_name":"Dörk Bousset"},{"first_name":"Vincent","full_name":"Ferrières, Vincent","last_name":"Ferrières"},{"first_name":"Françoise","last_name":"Routier","full_name":"Routier, Françoise"}],"title":"A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"49","_id":"3292","extern":"1","year":"2009","citation":{"chicago":"Engel, Jakob, Philipp S Schmalhorst, Thilo Dörk Bousset, Vincent Ferrières, and Françoise Routier. “A Single UDP Galactofuranose Transporter Is Required for Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2009. <a href=\"https://doi.org/10.1074/jbc.M109.070219 \">https://doi.org/10.1074/jbc.M109.070219 </a>.","short":"J. Engel, P.S. Schmalhorst, T. Dörk Bousset, V. Ferrières, F. Routier, Journal of Biological Chemistry 284 (2009) 33859–33868.","mla":"Engel, Jakob, et al. “A Single UDP Galactofuranose Transporter Is Required for Galactofuranosylation in Aspergillus Fumigatus.” <i>Journal of Biological Chemistry</i>, vol. 284, no. 49, American Society for Biochemistry and Molecular Biology, 2009, pp. 33859–68, doi:<a href=\"https://doi.org/10.1074/jbc.M109.070219 \">10.1074/jbc.M109.070219 </a>.","ista":"Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. 2009. A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. Journal of Biological Chemistry. 284(49), 33859–33868.","ieee":"J. Engel, P. S. Schmalhorst, T. Dörk Bousset, V. Ferrières, and F. Routier, “A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus,” <i>Journal of Biological Chemistry</i>, vol. 284, no. 49. American Society for Biochemistry and Molecular Biology, pp. 33859–33868, 2009.","ama":"Engel J, Schmalhorst PS, Dörk Bousset T, Ferrières V, Routier F. A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. <i>Journal of Biological Chemistry</i>. 2009;284(49):33859-33868. doi:<a href=\"https://doi.org/10.1074/jbc.M109.070219 \">10.1074/jbc.M109.070219 </a>","apa":"Engel, J., Schmalhorst, P. S., Dörk Bousset, T., Ferrières, V., &#38; Routier, F. (2009). A single UDP galactofuranose transporter is required for galactofuranosylation in Aspergillus fumigatus. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M109.070219 \">https://doi.org/10.1074/jbc.M109.070219 </a>"},"status":"public","publisher":"American Society for Biochemistry and Molecular Biology","page":"33859 - 33868","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"None","publication_status":"published","day":"04","doi":"10.1074/jbc.M109.070219 ","month":"12","date_published":"2009-12-04T00:00:00Z"},{"author":[{"last_name":"Chakraborty Tuhin","full_name":"Chakraborty Tuhin, Subhra","first_name":"Subhra"},{"full_name":"Sarit Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","first_name":"Sarit"},{"first_name":"Obaid","last_name":"Siddiqi","full_name":"Siddiqi, Obaid"}],"_id":"3293","extern":1,"issue":"1-2","title":"Sensory correlates of imaginal conditioning in Drosophila melanogaster","volume":23,"date_updated":"2021-01-12T07:42:27Z","type":"journal_article","intvolume":"        23","abstract":[{"lang":"eng","text":"Chemotactic responses of Drosophila to certain esters and alcohols are experience dependent. When the flies are exposed after eclosion to these chemicals, the odorants become strongly attractive. We show that behavioral conditioning is accompanied by an increase in the electrophysiological responses of single neurons in sensilla basiconica. Sensitization involves odorants that act on a common olfactory receptor. The possible mechanism of imaginal conditioning and its ecological and evolutionary significance are discussed."}],"publist_id":"3348","publication":"Journal of Neurogenetics","date_created":"2018-12-11T12:02:30Z","page":"210 - 9","quality_controlled":0,"date_published":"2009-01-01T00:00:00Z","month":"01","day":"01","doi":"10.1080/01677060802491559 ","publication_status":"published","year":"2009","publisher":"Informa Healthcare","status":"public","citation":{"ieee":"S. Chakraborty Tuhin, S. Goswami, and O. Siddiqi, “Sensory correlates of imaginal conditioning in Drosophila melanogaster,” <i>Journal of Neurogenetics</i>, vol. 23, no. 1–2. Informa Healthcare, pp. 210–9, 2009.","ama":"Chakraborty Tuhin S, Goswami S, Siddiqi O. Sensory correlates of imaginal conditioning in Drosophila melanogaster. <i>Journal of Neurogenetics</i>. 2009;23(1-2):210-219. doi:<a href=\"https://doi.org/10.1080/01677060802491559 \">10.1080/01677060802491559 </a>","apa":"Chakraborty Tuhin, S., Goswami, S., &#38; Siddiqi, O. (2009). Sensory correlates of imaginal conditioning in Drosophila melanogaster. <i>Journal of Neurogenetics</i>. Informa Healthcare. <a href=\"https://doi.org/10.1080/01677060802491559 \">https://doi.org/10.1080/01677060802491559 </a>","mla":"Chakraborty Tuhin, Subhra, et al. “Sensory Correlates of Imaginal Conditioning in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>, vol. 23, no. 1–2, Informa Healthcare, 2009, pp. 210–19, doi:<a href=\"https://doi.org/10.1080/01677060802491559 \">10.1080/01677060802491559 </a>.","short":"S. Chakraborty Tuhin, S. Goswami, O. Siddiqi, Journal of Neurogenetics 23 (2009) 210–9.","chicago":"Chakraborty Tuhin, Subhra, Sarit Goswami, and Obaid Siddiqi. “Sensory Correlates of Imaginal Conditioning in Drosophila Melanogaster.” <i>Journal of Neurogenetics</i>. Informa Healthcare, 2009. <a href=\"https://doi.org/10.1080/01677060802491559 \">https://doi.org/10.1080/01677060802491559 </a>.","ista":"Chakraborty Tuhin S, Goswami S, Siddiqi O. 2009. Sensory correlates of imaginal conditioning in Drosophila melanogaster. Journal of Neurogenetics. 23(1–2), 210–9."}},{"status":"public","publisher":"Academic Press","citation":{"chicago":"Weissman, Daniel, Michael Desai, Daniel Fisher, and Marcus Feldman. “The Rate at Which Asexual Populations Cross Fitness Valleys.” <i>Theoretical Population Biology</i>. Academic Press, 2009. <a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">https://doi.org/10.1016/j.tpb.2009.02.006</a>.","short":"D. Weissman, M. Desai, D. Fisher, M. Feldman, Theoretical Population Biology 75 (2009) 286–300.","mla":"Weissman, Daniel, et al. “The Rate at Which Asexual Populations Cross Fitness Valleys.” <i>Theoretical Population Biology</i>, vol. 75, no. 4, Academic Press, 2009, pp. 286–300, doi:<a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">10.1016/j.tpb.2009.02.006</a>.","ista":"Weissman D, Desai M, Fisher D, Feldman M. 2009. The rate at which asexual populations cross fitness valleys. Theoretical Population Biology. 75(4), 286–300.","ieee":"D. Weissman, M. Desai, D. Fisher, and M. Feldman, “The rate at which asexual populations cross fitness valleys,” <i>Theoretical Population Biology</i>, vol. 75, no. 4. Academic Press, pp. 286–300, 2009.","apa":"Weissman, D., Desai, M., Fisher, D., &#38; Feldman, M. (2009). The rate at which asexual populations cross fitness valleys. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">https://doi.org/10.1016/j.tpb.2009.02.006</a>","ama":"Weissman D, Desai M, Fisher D, Feldman M. The rate at which asexual populations cross fitness valleys. <i>Theoretical Population Biology</i>. 2009;75(4):286-300. doi:<a href=\"https://doi.org/10.1016/j.tpb.2009.02.006\">10.1016/j.tpb.2009.02.006</a>"},"year":"2009","month":"06","date_published":"2009-06-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.tpb.2009.02.006","day":"01","page":"286 - 300","quality_controlled":0,"abstract":[{"lang":"eng","text":"Complex traits often involve interactions between different genetic loci. This can lead to sign epistasis, whereby mutations that are individually deleterious or neutral combine to confer a fitness benefit. In order to acquire the beneficial genotype, an asexual population must cross a fitness valley or plateau by first acquiring the deleterious or neutral intermediates. Here, we present a complete, intuitive theoretical description of the valley-crossing process across the full spectrum of possible parameter regimes. We calculate the rate at which a population crosses a fitness valley or plateau of arbitrary width, as a function of the mutation rates, the population size, and the fitnesses of the intermediates. We find that when intermediates are close to neutral, a large population can cross even wide fitness valleys remarkably quickly, so that valley-crossing dynamics may be common even when mutations that directly increase fitness are also possible. Thus the evolutionary dynamics of large populations can be sensitive to the structure of an extended region of the fitness landscape — the population may not take directly uphill paths in favor of paths across valleys and plateaus that lead eventually to fitter genotypes. In smaller populations, we find that below a threshold size, which depends on the width of the fitness valley and the strength of selection against intermediate genotypes, valley-crossing is much less likely and hence the evolutionary dynamics are less influenced by distant regions of the fitness landscape."}],"intvolume":"        75","date_created":"2018-12-11T12:02:34Z","publication":"Theoretical Population Biology","publist_id":"3336","volume":75,"type":"journal_article","date_updated":"2021-01-12T07:42:31Z","title":"The rate at which asexual populations cross fitness valleys","_id":"3304","issue":"4","extern":1,"author":[{"last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Daniel Weissman","first_name":"Daniel"},{"full_name":"Desai, Michael M","last_name":"Desai","first_name":"Michael"},{"first_name":"Daniel","last_name":"Fisher","full_name":"Fisher, Daniel S"},{"last_name":"Feldman","full_name":"Feldman, Marcus W","first_name":"Marcus"}]},{"intvolume":"        14","abstract":[{"lang":"eng","text":"\n\nMastitis, a worldwide endemic disease of dairy cows, is an important cause of decreased efficiency in milk production. Early medical treatment can reduce the nonreversible losses in milk production caused by this infection. Various diagnostic tests for mastitis are available, including a test measuring the electrical conductivity of milk (MEC test), the industry standard of somatic cell counting (SCC test), a bacteriological test, and a recently developed test measuring mammary associated amyloid A (MAA test). None of these tests is considered a gold standard, however. The aim of the present study was to determine which of these tests provides the best results, and at what cost, to improve the efficiency of milk production. For this study, 25 cows were tested at all four quarters of the udder with each of the aforementioned mastitis diagnostic tests. Based on the data, the disease prevalence as well as the sensitivity and the specificity of the four tests were estimated with a Bayesian approach by extending the Hui and Walter model with two independent tests and two populations to a model with four partially dependent tests and one population. This model was further combined with a receiver operating characteristics analysis to estimate the overall test accuracy."}],"date_created":"2018-12-11T12:02:35Z","publication":"Journal of Agricultural Biological and Environmental Statistics","publist_id":"3331","volume":14,"type":"journal_article","date_updated":"2021-01-12T07:42:33Z","title":"Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard","_id":"3309","extern":1,"issue":"1","author":[{"last_name":"Uhler","full_name":"Caroline Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline"}],"status":"public","publisher":"Springer","citation":{"apa":"Uhler, C. (2009). Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. <i>Journal of Agricultural Biological and Environmental Statistics</i>. Springer. <a href=\"https://doi.org/10.1198/jabes.2009.0005\">https://doi.org/10.1198/jabes.2009.0005</a>","ama":"Uhler C. Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. <i>Journal of Agricultural Biological and Environmental Statistics</i>. 2009;14(1):79-98. doi:<a href=\"https://doi.org/10.1198/jabes.2009.0005\">10.1198/jabes.2009.0005</a>","ieee":"C. Uhler, “Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard,” <i>Journal of Agricultural Biological and Environmental Statistics</i>, vol. 14, no. 1. Springer, pp. 79–98, 2009.","ista":"Uhler C. 2009. Mastitis in dairy production: Estimation of sensitivity, specificity and disease prevalence in the absence of a gold standard. Journal of Agricultural Biological and Environmental Statistics. 14(1), 79–98.","chicago":"Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity, Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal of Agricultural Biological and Environmental Statistics</i>. Springer, 2009. <a href=\"https://doi.org/10.1198/jabes.2009.0005\">https://doi.org/10.1198/jabes.2009.0005</a>.","mla":"Uhler, Caroline. “Mastitis in Dairy Production: Estimation of Sensitivity, Specificity and Disease Prevalence in the Absence of a Gold Standard.” <i>Journal of Agricultural Biological and Environmental Statistics</i>, vol. 14, no. 1, Springer, 2009, pp. 79–98, doi:<a href=\"https://doi.org/10.1198/jabes.2009.0005\">10.1198/jabes.2009.0005</a>.","short":"C. Uhler, Journal of Agricultural Biological and Environmental Statistics 14 (2009) 79–98."},"year":"2009","month":"03","date_published":"2009-03-01T00:00:00Z","publication_status":"published","day":"01","doi":"10.1198/jabes.2009.0005","quality_controlled":0,"page":"79 - 98"}]