[{"abstract":[{"text":"The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.","lang":"eng"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_updated":"2021-01-12T08:20:43Z","volume":365,"type":"journal_article","quality_controlled":0,"title":"Measurements of spontaneous rates of mutations in the recent past and the near future","issue":"1544","doi":"10.1098/rstb.2009.0286","citation":{"apa":"Kondrashov, F., &#38; Kondrashov, A. (2010). Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>","ieee":"F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010.","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>.","ista":"Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.","mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, The, 2010, pp. 1169–76, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>.","short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.","ama":"Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1169-1176. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>"},"publist_id":"6772","intvolume":"       365","extern":1,"author":[{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"}],"day":"27","publisher":"Royal Society, The","date_created":"2018-12-11T11:48:57Z","month":"04","_id":"872","status":"public","year":"2010","date_published":"2010-04-27T00:00:00Z","publication_status":"published","page":"1169 - 1176"},{"year":"2010","_id":"884","month":"01","status":"public","day":"21","publisher":"BioMed Central","date_created":"2018-12-11T11:49:00Z","intvolume":"         5","publist_id":"6762","author":[{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"},{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"full_name":"Ivankov, Dmitry N","first_name":"Dmitry","last_name":"Ivankov"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"}],"extern":1,"publication_status":"published","date_published":"2010-01-21T00:00:00Z","type":"journal_article","volume":5,"date_updated":"2021-01-12T08:21:15Z","abstract":[{"lang":"eng","text":"Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin."}],"publication":"Biology Direct","citation":{"chicago":"Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>.","ieee":"A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","apa":"Kondrashov, A., Povolotskaya, I., Ivankov, D., &#38; Kondrashov, F. (2010). Rate of sequence divergence under constant selection. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>","ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","mla":"Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>.","ama":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence under constant selection. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>","short":"A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010)."},"doi":"10.1186/1745-6150-5-5","quality_controlled":0,"title":"Rate of sequence divergence under constant selection","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"issue":"8","title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution","quality_controlled":"1","doi":"10.1021/am100375w","external_id":{"pmid":["    20735108"]},"oa_version":"None","citation":{"apa":"Wright, I., Higginbotham, A. P., Baker, S., &#38; Donnelly, T. (2010). Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>","ieee":"I. Wright, A. P. Higginbotham, S. Baker, and T. Donnelly, “Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution,” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8. American Chemical Society, pp. 2360–2364, 2010.","chicago":"Wright, Ian, Andrew P Higginbotham, Shenda Baker, and Tom Donnelly. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>.","ista":"Wright I, Higginbotham AP, Baker S, Donnelly T. 2010. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. ACS Applied Materials and Interfaces. 2(8), 2360–2364.","mla":"Wright, Ian, et al. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8, American Chemical Society, 2010, pp. 2360–64, doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>.","short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","ama":"Wright I, Higginbotham AP, Baker S, Donnelly T. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. 2010;2(8):2360-2364. doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>"},"date_updated":"2021-01-12T08:21:17Z","acknowledgement":"This work was supported by the National Science Foundation under Grants PHY-0456898 and PHY-0757989, and acknowledgment is made to the Donors of the Petroleum Research Fund administered by the American Chemical Society for partial support of this research.","publication":"ACS Applied Materials and Interfaces","pmid":1,"abstract":[{"text":"We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":2,"date_published":"2010-07-20T00:00:00Z","publication_status":"published","page":"2360 - 2364","date_created":"2018-12-11T11:44:34Z","publisher":"American Chemical Society","day":"20","author":[{"full_name":"Wright, Ian","first_name":"Ian","last_name":"Wright"},{"first_name":"Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shenda","last_name":"Baker","full_name":"Baker, Shenda"},{"first_name":"Tom","last_name":"Donnelly","full_name":"Donnelly, Tom"}],"extern":"1","intvolume":"         2","publist_id":"7965","year":"2010","status":"public","_id":"89","month":"07"},{"date_published":"2010-02-01T00:00:00Z","publication_status":"published","page":"97 - 108","intvolume":"        11","publist_id":"6755","author":[{"first_name":"Hideki","last_name":"Innan","full_name":"Innan, Hideki"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"extern":1,"publisher":"Nature Publishing Group","day":"01","date_created":"2018-12-11T11:49:03Z","_id":"891","month":"02","status":"public","year":"2010","quality_controlled":0,"title":"The evolution of gene duplications: Classifying and distinguishing between models","issue":"2","doi":"10.1038/nrg2689","citation":{"ama":"Innan H, Kondrashov F. The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. 2010;11(2):97-108. doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>","short":"H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.","mla":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>.","ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","chicago":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>.","ieee":"H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” <i>Nature Reviews Genetics</i>, vol. 11, no. 2. Nature Publishing Group, pp. 97–108, 2010.","apa":"Innan, H., &#38; Kondrashov, F. (2010). The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>"},"abstract":[{"text":"Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.","lang":"eng"}],"publication":"Nature Reviews Genetics","acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","date_updated":"2021-01-12T08:21:19Z","volume":11,"type":"journal_article"},{"publication_status":"published","date_published":"2010-12-31T00:00:00Z","status":"public","_id":"901","month":"12","year":"2010","author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"}],"extern":1,"intvolume":"         5","publist_id":"6749","date_created":"2018-12-11T11:49:06Z","day":"31","publisher":"BioMed Central","doi":"10.1186/1745-6150-5-68","citation":{"ista":"Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 5.","chicago":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>.","ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","apa":"Breen, M., &#38; Kondrashov, F. (2010). Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-68\">https://doi.org/10.1186/1745-6150-5-68</a>","ama":"Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010).","mla":"Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations Are Population-Specific.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-68\">10.1186/1745-6150-5-68</a>."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Mitochondrial pathogenic mutations are population-specific","quality_controlled":0,"type":"journal_article","volume":5,"publication":"Biology Direct","abstract":[{"lang":"eng","text":"Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst)."}],"date_updated":"2021-01-12T08:21:46Z","acknowledgement":"We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science and Innovation, Plan Nacional Program grant BFU2009-09271 for funding."},{"publication_status":"published","date_published":"2010-04-02T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"month":"04","status":"public","year":"2010","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"intvolume":"       104","author":[{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A"},{"full_name":"Abécassis, Benjamin","first_name":"Benjamin","last_name":"Abécassis"},{"full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile","last_name":"Cottin-Bizonne"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"arxiv":1,"date_created":"2021-01-19T10:25:04Z","external_id":{"arxiv":["1004.1256 "],"pmid":["20481918"]},"oa_version":"Preprint","doi":"10.1103/physrevlett.104.138302","quality_controlled":"1","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","scopus_import":"1","article_processing_charge":"No","publication":"Physical Review Letters","pmid":1,"_id":"9012","article_type":"letter_note","extern":"1","day":"02","publisher":"American Physical Society","citation":{"mla":"Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>, vol. 104, no. 13, 138302, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>.","ama":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. 2010;104(13). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010).","ieee":"J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Colloidal motility and pattern formation under rectified diffusiophoresis,” <i>Physical Review Letters</i>, vol. 104, no. 13. American Physical Society, 2010.","chicago":"Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>.","apa":"Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>","ista":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal motility and pattern formation under rectified diffusiophoresis. Physical Review Letters. 104(13), 138302."},"article_number":"138302","issue":"13","volume":104,"type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.","lang":"eng"}],"date_updated":"2023-02-23T13:46:40Z"},{"citation":{"ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. 2010;105(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 105 (2010).","mla":"Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>, vol. 105, no. 8, 088304, American Physical Society , 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>.","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and effective temperature of active colloidal suspensions. Physical Review Letters. 105(8), 088304.","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation and effective temperature of active colloidal suspensions,” <i>Physical Review Letters</i>, vol. 105, no. 8. American Physical Society , 2010.","chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>. American Physical Society , 2010. <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>.","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>"},"issue":"8","article_number":"088304","type":"journal_article","volume":105,"oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","abstract":[{"text":"In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2023-02-23T13:46:42Z","article_type":"letter_note","_id":"9013","extern":"1","publisher":"American Physical Society ","day":"20","doi":"10.1103/physrevlett.105.088304","oa_version":"Preprint","external_id":{"arxiv":["1004.4340"],"pmid":["20868136"]},"title":"Sedimentation and effective temperature of active colloidal suspensions","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"Physical Review Letters","pmid":1,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1004.4340","open_access":"1"}],"date_published":"2010-08-20T00:00:00Z","status":"public","month":"08","year":"2010","author":[{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci"},{"full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile","last_name":"Cottin-Bizonne"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"intvolume":"       105","date_created":"2021-01-19T10:26:33Z","arxiv":1},{"publication":"Ocean Modelling","abstract":[{"lang":"eng","text":"We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well.\r\n\r\nAs for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve."}],"language":[{"iso":"eng"}],"date_updated":"2022-01-24T13:51:35Z","keyword":["Computer Science (miscellaneous)","Geotechnical Engineering and Engineering Geology","Atmospheric Science","Oceanography"],"type":"journal_article","volume":34,"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Ocean turbulence, III: New GISS vertical mixing scheme","quality_controlled":"1","issue":"3-4","citation":{"short":"V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne, Ocean Modelling 34 (2010) 70–91.","ama":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. 2010;34(3-4):70-91. doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>","mla":"Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:<a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">10.1016/j.ocemod.2010.04.006</a>.","ista":"Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010. Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4), 70–91.","apa":"Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A., &#38; Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme. <i>Ocean Modelling</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>","ieee":"V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” <i>Ocean Modelling</i>, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010.","chicago":"Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier, and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” <i>Ocean Modelling</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.ocemod.2010.04.006\">https://doi.org/10.1016/j.ocemod.2010.04.006</a>."},"doi":"10.1016/j.ocemod.2010.04.006","oa_version":"None","extern":"1","author":[{"first_name":"V.M.","last_name":"Canuto","full_name":"Canuto, V.M."},{"full_name":"Howard, A.M.","first_name":"A.M.","last_name":"Howard"},{"last_name":"Cheng","first_name":"Y.","full_name":"Cheng, Y."},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller"},{"full_name":"Leboissetier, A.","last_name":"Leboissetier","first_name":"A."},{"full_name":"Jayne, S.R.","first_name":"S.R.","last_name":"Jayne"}],"intvolume":"        34","publication_identifier":{"issn":["1463-5003"]},"date_created":"2021-02-15T14:40:19Z","publisher":"Elsevier","day":"12","status":"public","article_type":"original","_id":"9145","month":"05","year":"2010","date_published":"2010-05-12T00:00:00Z","page":"70-91","publication_status":"published"},{"article_type":"original","_id":"9146","extern":"1","publisher":"IOP Publishing","day":"09","type":"journal_article","volume":5,"keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.","lang":"eng"}],"date_updated":"2022-01-24T13:51:02Z","citation":{"mla":"O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>, vol. 5, no. 2, 025207, IOP Publishing, 2010, doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","ama":"O’Gorman PA, Muller CJ. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. 2010;5(2). doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>","apa":"O’Gorman, P. A., &#38; Muller, C. J. (2010). How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>","ieee":"P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?,” <i>Environmental Research Letters</i>, vol. 5, no. 2. IOP Publishing, 2010.","chicago":"O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>. IOP Publishing, 2010. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>.","ista":"O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental Research Letters. 5(2), 025207."},"article_number":"025207","issue":"2","month":"04","status":"public","year":"2010","intvolume":"         5","publication_identifier":{"issn":["1748-9326"]},"author":[{"last_name":"O’Gorman","first_name":"P A","full_name":"O’Gorman, P A"},{"first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"date_created":"2021-02-15T14:40:46Z","publication_status":"published","date_published":"2010-04-09T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/5/2/025207","open_access":"1"}],"article_processing_charge":"No","publication":"Environmental Research Letters","oa_version":"Published Version","doi":"10.1088/1748-9326/5/2/025207","quality_controlled":"1","title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":104,"type":"journal_article","article_processing_charge":"No","date_updated":"2021-01-12T08:21:55Z","acknowledgement":"This work was supported by the NSF (DMR-0602684) and the Harvard MRSEC (DMR-0820484).\r\nWe would like to thank Dr. James Butler for helpful conversations.","publication":"Physical Review Letters","abstract":[{"text":"Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"mla":"Angelini, Thomas, et al. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>, vol. 104, no. 16, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>.","short":"T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review Letters 104 (2010).","ama":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. 2010;104(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">10.1103/PhysRevLett.104.168104</a>","apa":"Angelini, T., Hannezo, E. B., Trepat, X., Fredberg, J., &#38; Weitz, D. (2010). Cell migration driven by cooperative substrate deformation patterns. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>","chicago":"Angelini, Thomas, Edouard B Hannezo, Xavier Trepat, Jeffrey Fredberg, and David Weitz. “Cell Migration Driven by Cooperative Substrate Deformation Patterns.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.168104\">https://doi.org/10.1103/PhysRevLett.104.168104</a>.","ieee":"T. Angelini, E. B. Hannezo, X. Trepat, J. Fredberg, and D. Weitz, “Cell migration driven by cooperative substrate deformation patterns,” <i>Physical Review Letters</i>, vol. 104, no. 16. American Physical Society, 2010.","ista":"Angelini T, Hannezo EB, Trepat X, Fredberg J, Weitz D. 2010. Cell migration driven by cooperative substrate deformation patterns. Physical Review Letters. 104(16)."},"oa_version":"None","doi":"10.1103/PhysRevLett.104.168104","issue":"16","title":"Cell migration driven by cooperative substrate deformation patterns","year":"2010","status":"public","month":"04","_id":"920","date_created":"2018-12-11T11:49:12Z","day":"23","publisher":"American Physical Society","extern":"1","author":[{"full_name":"Angelini, Thomas","first_name":"Thomas","last_name":"Angelini"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"first_name":"Jeffrey","last_name":"Fredberg","full_name":"Fredberg, Jeffrey"},{"first_name":"David","last_name":"Weitz","full_name":"Weitz, David"}],"publist_id":"6523","intvolume":"       104","publication_status":"published","date_published":"2010-04-23T00:00:00Z"},{"article_type":"original","_id":"9452","day":"14","publisher":"American Association for the Advancement of Science","extern":"1","page":"916-919","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Multidisciplinary"],"volume":328,"type":"journal_article","date_updated":"2021-12-14T08:35:37Z","abstract":[{"text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>.","ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919."},"issue":"5980","year":"2010","status":"public","month":"05","date_created":"2021-06-04T08:26:08Z","author":[{"full_name":"Zemach, Assaf ","last_name":"Zemach","first_name":"Assaf "},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"intvolume":"       328","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","department":[{"_id":"DaZi"}],"date_published":"2010-05-14T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"Science","external_id":{"pmid":["20395474 "]},"oa_version":"None","doi":"10.1126/science.1186366","scopus_import":"1","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","quality_controlled":"1"},{"article_processing_charge":"No","pmid":1,"publication":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["20937895"]},"doi":"10.1073/pnas.1009695107","oa_version":"Published Version","title":"Local DNA hypomethylation activates genes in rice endosperm","quality_controlled":"1","scopus_import":"1","status":"public","month":"10","year":"2010","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"full_name":"Dotson, Bradley","last_name":"Dotson","first_name":"Bradley"},{"full_name":"Brooks, Matthew D.","last_name":"Brooks","first_name":"Matthew D."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"intvolume":"       107","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_created":"2021-06-07T09:31:01Z","department":[{"_id":"DaZi"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1009695107"}],"date_published":"2010-10-26T00:00:00Z","type":"journal_article","volume":107,"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:40:02Z","citation":{"short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>."},"issue":"43","article_type":"original","_id":"9485","extern":"1","publisher":"National Academy of Sciences","day":"26","page":"18729-18734"},{"citation":{"apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>"},"issue":"17","volume":20,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.","lang":"eng"}],"date_updated":"2021-12-14T08:52:34Z","page":"R780-R785","_id":"9489","article_type":"review","extern":"1","publisher":"Elsevier","day":"14","doi":"10.1016/j.cub.2010.07.007","external_id":{"pmid":["20833323"]},"oa_version":"Published Version","quality_controlled":"1","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","scopus_import":"1","article_processing_charge":"No","pmid":1,"publication":"Current Biology","department":[{"_id":"DaZi"}],"publication_status":"published","date_published":"2010-09-14T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2010.07.007","open_access":"1"}],"month":"09","status":"public","year":"2010","intvolume":"        20","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"date_created":"2021-06-07T09:45:27Z"},{"date_published":"2010-07-20T00:00:00Z","department":[{"_id":"NiBa"}],"date_created":"2021-08-02T09:45:39Z","publisher":"Public Library of Science","day":"20","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Barbier De Reuille, Pierre","first_name":"Pierre","last_name":"Barbier De Reuille"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"related_material":{"record":[{"relation":"used_in_publication","id":"3779","status":"public"}]},"year":"2010","status":"public","_id":"9764","month":"07","title":"Heterosis and the drift load","doi":"10.1371/journal.pbio.1000429.s003","citation":{"ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Heterosis and the drift load. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>","mla":"Rosas, Ulises, et al. <i>Heterosis and the Drift Load</i>. Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>."},"oa_version":"Published Version","date_updated":"2025-09-30T09:42:52Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","article_processing_charge":"No"},{"year":"2010","month":"09","status":"public","date_created":"2018-12-11T11:46:40Z","isi":1,"intvolume":"        64","publist_id":"2780","author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"publication_status":"published","department":[{"_id":"NiBa"}],"corr_author":"1","date_published":"2010-09-01T00:00:00Z","article_processing_charge":"No","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","publication":"Evolution","oa_version":"None","external_id":{"isi":["000281636400017"]},"doi":"10.1111/j.1558-5646.2010.01019.x","scopus_import":"1","quality_controlled":"1","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","_id":"474","publisher":"Wiley-Blackwell","day":"01","page":"2701 - 2715","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":64,"type":"journal_article","date_updated":"2025-09-30T09:50:22Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci."}],"citation":{"ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","apa":"Barton, N. H., Kelleher, J., &#38; Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” <i>Evolution</i>, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>.","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. 2010;64(9):2701-2715. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>."},"issue":"9"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","_id":"488","page":"1 - 12","language":[{"iso":"eng"}],"abstract":[{"text":"Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of &quot;regular&quot; transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. ","lang":"eng"}],"date_updated":"2025-09-30T09:49:32Z","type":"conference","volume":8,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","conference":{"location":"Chennai, India","end_date":"2010-12-18","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2010-12-15"},"citation":{"chicago":"Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>.","ieee":"R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12.","apa":"Alur, R., &#38; Cerny, P. (2010). Expressiveness of streaming string transducers (Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>","ista":"Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 1–12.","mla":"Alur, Rajeev, and Pavol Cerny. <i>Expressiveness of Streaming String Transducers</i>. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>.","ama":"Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>","short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12."},"intvolume":"         8","publist_id":"7331","author":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"date_created":"2018-12-11T11:46:45Z","month":"01","status":"public","year":"2010","date_published":"2010-01-01T00:00:00Z","corr_author":"1","department":[{"_id":"ToHe"}],"pubrep_id":"948","publication_status":"published","article_processing_charge":"No","quality_controlled":"1","title":"Expressiveness of streaming string transducers","alternative_title":["LIPIcs"],"scopus_import":"1","ddc":["005"],"doi":"10.4230/LIPIcs.FSTTCS.2010.1","file_date_updated":"2020-07-14T12:46:35Z","external_id":{"isi":["000310361000001"]},"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf","date_created":"2018-12-12T10:08:29Z","date_updated":"2020-07-14T12:46:35Z","file_id":"4690","creator":"system","content_type":"application/pdf","checksum":"5845be5aa19791830f7407d8853f2df0","file_size":492344,"relation":"main_file"}]},{"page":"30 - 39","_id":"489","day":"09","publisher":"Open Publishing Association","citation":{"ista":"Cristau J, David C, Horn F. 2010. How do we remember the past in randomised strategies? Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 30–39.","ieee":"J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies?,” in <i>Proceedings of GandALF 2010</i>, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.","chicago":"Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies?” In <i>Proceedings of GandALF 2010</i>, 25:30–39. Open Publishing Association, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>.","apa":"Cristau, J., David, C., &#38; Horn, F. (2010). How do we remember the past in randomised strategies? In <i>Proceedings of GandALF 2010</i> (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>","ama":"Cristau J, David C, Horn F. How do we remember the past in randomised strategies? In: <i>Proceedings of GandALF 2010</i>. Vol 25. Open Publishing Association; 2010:30-39. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>","short":"J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39.","mla":"Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?” <i>Proceedings of GandALF 2010</i>, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>."},"conference":{"location":"Minori, Amalfi Coast, Italy","name":"GandALF: Games, Automata, Logic, and Formal Verification","end_date":"2010-06-18","start_date":"2010-06-17"},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":25,"date_updated":"2025-06-11T08:14:27Z","abstract":[{"text":"Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"KrCh"}],"corr_author":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1006.1404"}],"date_published":"2010-06-09T00:00:00Z","year":"2010","status":"public","month":"06","date_created":"2018-12-11T11:46:45Z","arxiv":1,"author":[{"full_name":"Cristau, Julien","first_name":"Julien","last_name":"Cristau"},{"last_name":"David","first_name":"Claire","full_name":"David, Claire"},{"first_name":"Florian","last_name":"Horn","full_name":"Horn, Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7332","intvolume":"        25","external_id":{"arxiv":["1006.1404"]},"doi":"10.4204/EPTCS.25.7","oa_version":"Published Version","scopus_import":"1","alternative_title":["EPTCS"],"title":"How do we remember the past in randomised strategies?","quality_controlled":"1","article_processing_charge":"No","publication":"Proceedings of GandALF 2010"},{"page":"171 - 199","publisher":"Springer","day":"01","_id":"533","issue":"2-3","citation":{"ista":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points. Formal Methods in System Design. 37(2–3), 171–199.","apa":"Hoenicke, J., Leino, K., Podelski, A., Schäf, M., &#38; Wies, T. (2010). Doomed program points. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>","ieee":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.","chicago":"Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” <i>Formal Methods in System Design</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>.","short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199.","ama":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. <i>Formal Methods in System Design</i>. 2010;37(2-3):171-199. doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>","mla":"Hoenicke, Jochen, et al. “Doomed Program Points.” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Any programming error that can be revealed before compiling a program saves precious time for the programmer. While integrated development environments already do a good job by detecting, e.g., data-flow abnormalities, current static analysis tools suffer from false positives (&quot;noise&quot;) or require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, regardless of which state it is started in. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on experiments with a prototype tool."}],"date_updated":"2025-09-30T09:48:58Z","type":"journal_article","volume":37,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-12-01T00:00:00Z","corr_author":"1","department":[{"_id":"ToHe"}],"publication_status":"published","publist_id":"7284","intvolume":"        37","author":[{"full_name":"Hoenicke, Jochen","first_name":"Jochen","last_name":"Hoenicke"},{"full_name":"Leino, Kari","first_name":"Kari","last_name":"Leino"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"last_name":"Schäf","first_name":"Martin","full_name":"Schäf, Martin"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"}],"isi":1,"date_created":"2018-12-11T11:47:01Z","month":"12","status":"public","year":"2010","quality_controlled":"1","title":"Doomed program points","scopus_import":"1","oa_version":"None","doi":"10.1007/s10703-010-0102-0","external_id":{"isi":["000286631700004"]},"publication":"Formal Methods in System Design","article_processing_charge":"No"},{"date_created":"2018-12-12T11:39:03Z","publisher":"IST Austria","day":"07","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"publication_identifier":{"issn":["2664-1690"]},"related_material":{"record":[{"relation":"later_version","status":"public","id":"3366"}]},"year":"2010","status":"public","month":"10","_id":"5388","date_published":"2010-10-07T00:00:00Z","publication_status":"published","page":"17","pubrep_id":"24","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2025-04-15T08:12:00Z","abstract":[{"text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","title":"Quantitative synthesis for concurrent programs","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:42Z","date_created":"2018-12-12T11:53:53Z","file_name":"IST-2010-0004_IST-2010-0004.pdf","access_level":"open_access","file_size":429101,"checksum":"da38782d2388a6fa32109d10bb9bad67","file_id":"5515","creator":"system","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:46:42Z","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p."},"oa_version":"Published Version","doi":"10.15479/AT:IST-2010-0004","ddc":["000","005"]},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","date_updated":"2025-09-30T07:46:05Z","abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2010-0003_IST-2010-0003.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:42Z","date_created":"2018-12-12T11:54:25Z","creator":"system","content_type":"application/pdf","file_id":"5547","file_size":367246,"checksum":"284ded99764e32a583a8ea83fcea254b","relation":"main_file"}],"citation":{"apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>"},"file_date_updated":"2020-07-14T12:46:42Z","doi":"10.15479/AT:IST-2010-0003","oa_version":"Published Version","ddc":["005"],"alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","title":"Simulation distances","year":"2010","status":"public","month":"06","_id":"5389","date_created":"2018-12-12T11:39:03Z","publisher":"IST Austria","day":"04","author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"}],"publication_identifier":{"issn":["2664-1690"]},"related_material":{"record":[{"id":"4393","status":"public","relation":"later_version"},{"status":"public","id":"3249","relation":"later_version"}]},"publication_status":"published","page":"24","pubrep_id":"25","department":[{"_id":"ToHe"}],"date_published":"2010-06-04T00:00:00Z"}]