[{"month":"04","title":"Measurements of spontaneous rates of mutations in the recent past and the near future","date_published":"2010-04-27T00:00:00Z","publisher":"Royal Society, The","date_updated":"2021-01-12T08:20:43Z","page":"1169 - 1176","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_status":"published","publist_id":"6772","_id":"872","extern":1,"author":[{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"}],"intvolume":"       365","volume":365,"type":"journal_article","citation":{"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.","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>","short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.","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.","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>.","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>.","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>"},"quality_controlled":0,"issue":"1544","doi":"10.1098/rstb.2009.0286","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","status":"public","day":"27","year":"2010","date_created":"2018-12-11T11:48:57Z"},{"volume":5,"type":"journal_article","intvolume":"         5","author":[{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"full_name":"Ivankov, Dmitry N","last_name":"Ivankov","first_name":"Dmitry"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"extern":1,"_id":"884","publist_id":"6762","publication_status":"published","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T08:21:15Z","publisher":"BioMed Central","date_published":"2010-01-21T00:00:00Z","title":"Rate of sequence divergence under constant selection","month":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:00Z","year":"2010","status":"public","publication":"Biology Direct","day":"21","doi":"10.1186/1745-6150-5-5","quality_controlled":0,"citation":{"ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","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).","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.","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>.","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>","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>."}},{"year":"2010","date_created":"2018-12-11T11:44:34Z","publication":"ACS Applied Materials and Interfaces","day":"20","status":"public","issue":"8","doi":"10.1021/am100375w","quality_controlled":"1","citation":{"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>.","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>","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>.","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>","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.","short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","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."},"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.","volume":2,"type":"journal_article","extern":"1","intvolume":"         2","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","author":[{"first_name":"Ian","last_name":"Wright","full_name":"Wright, Ian"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham"},{"full_name":"Baker, Shenda","last_name":"Baker","first_name":"Shenda"},{"first_name":"Tom","last_name":"Donnelly","full_name":"Donnelly, Tom"}],"_id":"89","pmid":1,"publist_id":"7965","abstract":[{"lang":"eng","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."}],"external_id":{"pmid":["    20735108"]},"publication_status":"published","page":"2360 - 2364","publisher":"American Chemical Society","date_updated":"2021-01-12T08:21:17Z","title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution","language":[{"iso":"eng"}],"month":"07","date_published":"2010-07-20T00:00:00Z"},{"quality_controlled":0,"citation":{"ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","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>","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.","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>.","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>","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>."},"publication":"Nature Reviews Genetics","status":"public","day":"01","doi":"10.1038/nrg2689","issue":"2","date_created":"2018-12-11T11:49:03Z","year":"2010","date_updated":"2021-01-12T08:21:19Z","publisher":"Nature Publishing Group","date_published":"2010-02-01T00:00:00Z","title":"The evolution of gene duplications: Classifying and distinguishing between models","month":"02","publication_status":"published","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"}],"page":"97 - 108","_id":"891","publist_id":"6755","type":"journal_article","volume":11,"acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","intvolume":"        11","author":[{"full_name":"Innan, Hideki","last_name":"Innan","first_name":"Hideki"},{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"extern":1},{"publisher":"BioMed Central","date_updated":"2021-01-12T08:21:46Z","title":"Mitochondrial pathogenic mutations are population-specific","month":"12","date_published":"2010-12-31T00:00:00Z","abstract":[{"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).","lang":"eng"}],"publication_status":"published","_id":"901","publist_id":"6749","type":"journal_article","volume":5,"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.","extern":1,"author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"intvolume":"         5","quality_controlled":0,"citation":{"ieee":"M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","short":"M. Breen, F. Kondrashov, Biology Direct 5 (2010).","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>","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>.","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>","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>."},"day":"31","status":"public","publication":"Biology Direct","doi":"10.1186/1745-6150-5-68","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"year":"2010","date_created":"2018-12-11T11:49:06Z"},{"pmid":1,"volume":104,"author":[{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci"},{"full_name":"Abécassis, Benjamin","last_name":"Abécassis","first_name":"Benjamin"},{"full_name":"Cottin-Bizonne, Cécile","last_name":"Cottin-Bizonne","first_name":"Cécile"},{"full_name":"Ybert, Christophe","first_name":"Christophe","last_name":"Ybert"},{"full_name":"Bocquet, Lydéric","last_name":"Bocquet","first_name":"Lydéric"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","extern":"1","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","external_id":{"pmid":["20481918"],"arxiv":["1004.1256 "]},"publication_status":"published","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"}],"article_processing_charge":"No","publication":"Physical Review Letters","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"doi":"10.1103/physrevlett.104.138302","issue":"13","article_number":"138302","date_created":"2021-01-19T10:25:04Z","year":"2010","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"quality_controlled":"1","scopus_import":"1","_id":"9012","type":"journal_article","intvolume":"       104","oa_version":"Preprint","article_type":"letter_note","date_updated":"2023-02-23T13:46:40Z","arxiv":1,"publisher":"American Physical Society","date_published":"2010-04-02T00:00:00Z","language":[{"iso":"eng"}],"month":"04","oa":1,"status":"public","day":"02","citation":{"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.","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>","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.","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010).","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>.","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>","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>."}},{"day":"20","status":"public","citation":{"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.","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>","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.","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>.","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>","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>."},"article_type":"letter_note","intvolume":"       105","oa_version":"Preprint","type":"journal_article","_id":"9013","scopus_import":"1","oa":1,"language":[{"iso":"eng"}],"month":"08","date_published":"2010-08-20T00:00:00Z","publisher":"American Physical Society ","arxiv":1,"date_updated":"2023-02-23T13:46:42Z","year":"2010","date_created":"2021-01-19T10:26:33Z","article_number":"088304","issue":"8","doi":"10.1103/physrevlett.105.088304","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication":"Physical Review Letters","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1004.4340","open_access":"1"}],"extern":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"last_name":"Cottin-Bizonne","first_name":"Cécile","full_name":"Cottin-Bizonne, Cécile"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"volume":105,"pmid":1,"article_processing_charge":"No","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"}],"publication_status":"published","external_id":{"arxiv":["1004.4340"],"pmid":["20868136"]},"title":"Sedimentation and effective temperature of active colloidal suspensions"},{"_id":"9145","type":"journal_article","volume":34,"article_type":"original","extern":"1","author":[{"first_name":"V.M.","last_name":"Canuto","full_name":"Canuto, V.M."},{"last_name":"Howard","first_name":"A.M.","full_name":"Howard, A.M."},{"first_name":"Y.","last_name":"Cheng","full_name":"Cheng, Y."},{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"last_name":"Leboissetier","first_name":"A.","full_name":"Leboissetier, A."},{"last_name":"Jayne","first_name":"S.R.","full_name":"Jayne, S.R."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        34","oa_version":"None","publisher":"Elsevier","date_updated":"2022-01-24T13:51:35Z","title":"Ocean turbulence, III: New GISS vertical mixing scheme","language":[{"iso":"eng"}],"month":"05","keyword":["Computer Science (miscellaneous)","Geotechnical Engineering and Engineering Geology","Atmospheric Science","Oceanography"],"date_published":"2010-05-12T00:00:00Z","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."}],"publication_status":"published","page":"70-91","article_processing_charge":"No","publication":"Ocean Modelling","day":"12","status":"public","issue":"3-4","doi":"10.1016/j.ocemod.2010.04.006","publication_identifier":{"issn":["1463-5003"]},"year":"2010","date_created":"2021-02-15T14:40:19Z","quality_controlled":"1","citation":{"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>.","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>.","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>","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>","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.","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.","short":"V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne, Ocean Modelling 34 (2010) 70–91."}},{"_id":"9146","type":"journal_article","article_type":"original","intvolume":"         5","oa_version":"Published Version","publisher":"IOP Publishing","date_updated":"2022-01-24T13:51:02Z","month":"04","language":[{"iso":"eng"}],"date_published":"2010-04-09T00:00:00Z","oa":1,"day":"09","status":"public","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>.","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>.","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>","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.","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>","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.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010)."},"volume":5,"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"O’Gorman, P A","first_name":"P A","last_name":"O’Gorman"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","last_name":"Muller","first_name":"Caroline J"}],"title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"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"}],"publication_status":"published","article_processing_charge":"No","publication":"Environmental Research Letters","issue":"2","publication_identifier":{"issn":["1748-9326"]},"doi":"10.1088/1748-9326/5/2/025207","article_number":"025207","year":"2010","date_created":"2021-02-15T14:40:46Z","main_file_link":[{"url":"https://doi.org/10.1088/1748-9326/5/2/025207","open_access":"1"}],"quality_controlled":"1"},{"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>.","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>.","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).","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>","short":"T. Angelini, E.B. Hannezo, X. Trepat, J. Fredberg, D. Weitz, Physical Review Letters 104 (2010).","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."},"date_created":"2018-12-11T11:49:12Z","year":"2010","doi":"10.1103/PhysRevLett.104.168104","issue":"16","day":"23","status":"public","publication":"Physical Review Letters","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","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."}],"date_published":"2010-04-23T00:00:00Z","month":"04","title":"Cell migration driven by cooperative substrate deformation patterns","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:21:55Z","publisher":"American Physical Society","intvolume":"       104","author":[{"full_name":"Angelini, Thomas","first_name":"Thomas","last_name":"Angelini"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"full_name":"Fredberg, Jeffrey","first_name":"Jeffrey","last_name":"Fredberg"},{"first_name":"David","last_name":"Weitz","full_name":"Weitz, David"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","extern":"1","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.","type":"journal_article","volume":104,"publist_id":"6523","_id":"920"},{"volume":328,"extern":"1","author":[{"first_name":"Assaf ","last_name":"Zemach","full_name":"Zemach, Assaf "},{"full_name":"McDaniel, Ivy E.","first_name":"Ivy E.","last_name":"McDaniel"},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"abstract":[{"lang":"eng","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."}],"publication_status":"published","external_id":{"pmid":["20395474 "]},"page":"916-919","article_processing_charge":"No","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","keyword":["Multidisciplinary"],"year":"2010","date_created":"2021-06-04T08:26:08Z","publication":"Science","issue":"5980","doi":"10.1126/science.1186366","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"quality_controlled":"1","type":"journal_article","article_type":"original","oa_version":"None","intvolume":"       328","_id":"9452","scopus_import":"1","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:35:37Z","language":[{"iso":"eng"}],"month":"05","date_published":"2010-05-14T00:00:00Z","status":"public","day":"14","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>.","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>.","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>","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>","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","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."}},{"status":"public","day":"26","citation":{"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>","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>.","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>.","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.","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>","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."},"type":"journal_article","article_type":"original","intvolume":"       107","oa_version":"Published Version","_id":"9485","scopus_import":"1","oa":1,"publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:40:02Z","month":"10","language":[{"iso":"eng"}],"date_published":"2010-10-26T00:00:00Z","year":"2010","date_created":"2021-06-07T09:31:01Z","publication":"Proceedings of the National Academy of Sciences","issue":"43","doi":"10.1073/pnas.1009695107","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"volume":107,"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"last_name":"Silva","first_name":"Pedro","full_name":"Silva, Pedro"},{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Dotson, Bradley","first_name":"Bradley","last_name":"Dotson"},{"full_name":"Brooks, Matthew D.","first_name":"Matthew D.","last_name":"Brooks"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"pmid":1,"abstract":[{"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.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["20937895"]},"page":"18729-18734","article_processing_charge":"No","title":"Local DNA hypomethylation activates genes in rice endosperm"},{"date_created":"2021-06-07T09:45:27Z","year":"2010","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"doi":"10.1016/j.cub.2010.07.007","issue":"17","publication":"Current Biology","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zemach","first_name":"Assaf","full_name":"Zemach, Assaf"},{"first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"extern":"1","volume":20,"pmid":1,"article_processing_charge":"No","page":"R780-R785","publication_status":"published","external_id":{"pmid":["20833323"]},"abstract":[{"lang":"eng","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."}],"title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","status":"public","day":"14","citation":{"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>.","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>.","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>","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>","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","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."},"oa_version":"Published Version","intvolume":"        20","article_type":"review","type":"journal_article","scopus_import":"1","_id":"9489","oa":1,"date_published":"2010-09-14T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2021-12-14T08:52:34Z","department":[{"_id":"DaZi"}],"publisher":"Elsevier"},{"article_processing_charge":"No","date_published":"2010-07-20T00:00:00Z","title":"Heterosis and the drift load","month":"07","date_updated":"2025-09-30T09:42:52Z","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille","first_name":"Pierre"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"type":"research_data_reference","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3779"}]},"_id":"9764","citation":{"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>","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>.","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>.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","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.","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>","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>."},"date_created":"2021-08-02T09:45:39Z","year":"2010","doi":"10.1371/journal.pbio.1000429.s003","day":"20","status":"public"},{"oa":1,"date_updated":"2021-01-12T08:11:44Z","arxiv":1,"publisher":"APS","date_published":"2010-11-18T00:00:00Z","month":"11","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":"        82","article_type":"original","_id":"7078","citation":{"ieee":"E. K. H. Salje <i>et al.</i>, “Tin telluride: A weakly co-elastic metal,” <i>Physical Review B</i>, vol. 82, no. 18. APS, 2010.","short":"E.K.H. Salje, D.J. Safarik, K.A. Modic, J.E. Gubernatis, J.C. Cooley, R.D. Taylor, B. Mihaila, A. Saxena, T. Lookman, J.L. Smith, R.A. Fisher, M. Pasternak, C.P. Opeil, T. Siegrist, P.B. Littlewood, J.C. Lashley, Physical Review B 82 (2010).","ama":"Salje EKH, Safarik DJ, Modic KA, et al. Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. 2010;82(18). doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>","ista":"Salje EKH, Safarik DJ, Modic KA, Gubernatis JE, Cooley JC, Taylor RD, Mihaila B, Saxena A, Lookman T, Smith JL, Fisher RA, Pasternak M, Opeil CP, Siegrist T, Littlewood PB, Lashley JC. 2010. Tin telluride: A weakly co-elastic metal. Physical Review B. 82(18), 184112.","apa":"Salje, E. K. H., Safarik, D. J., Modic, K. A., Gubernatis, J. E., Cooley, J. C., Taylor, R. D., … Lashley, J. C. (2010). Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. APS. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>","chicago":"Salje, E. K. H., D. J. Safarik, Kimberly A Modic, J. E. Gubernatis, J. C. Cooley, R. D. Taylor, B. Mihaila, et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>. APS, 2010. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>.","mla":"Salje, E. K. H., et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>, vol. 82, no. 18, 184112, APS, 2010, doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>."},"status":"public","day":"18","external_id":{"arxiv":["1011.1445"]},"publication_status":"published","abstract":[{"text":"We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other.","lang":"eng"}],"article_processing_charge":"No","title":"Tin telluride: A weakly co-elastic metal","volume":82,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Salje","first_name":"E. K. H.","full_name":"Salje, E. K. H."},{"full_name":"Safarik, D. J.","last_name":"Safarik","first_name":"D. J."},{"full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A","last_name":"Modic"},{"full_name":"Gubernatis, J. E.","last_name":"Gubernatis","first_name":"J. E."},{"full_name":"Cooley, J. C.","first_name":"J. C.","last_name":"Cooley"},{"first_name":"R. D.","last_name":"Taylor","full_name":"Taylor, R. D."},{"full_name":"Mihaila, B.","last_name":"Mihaila","first_name":"B."},{"full_name":"Saxena, A.","last_name":"Saxena","first_name":"A."},{"full_name":"Lookman, T.","first_name":"T.","last_name":"Lookman"},{"last_name":"Smith","first_name":"J. L.","full_name":"Smith, J. L."},{"first_name":"R. A.","last_name":"Fisher","full_name":"Fisher, R. A."},{"full_name":"Pasternak, M.","first_name":"M.","last_name":"Pasternak"},{"first_name":"C. P.","last_name":"Opeil","full_name":"Opeil, C. P."},{"last_name":"Siegrist","first_name":"T.","full_name":"Siegrist, T."},{"full_name":"Littlewood, P. B.","last_name":"Littlewood","first_name":"P. B."},{"full_name":"Lashley, J. C.","first_name":"J. C.","last_name":"Lashley"}],"extern":"1","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1011.1445","open_access":"1"}],"article_number":"184112","date_created":"2019-11-19T13:46:28Z","year":"2010","publication":"Physical Review B","publication_identifier":{"issn":["1098-0121","1550-235X"]},"doi":"10.1103/physrevb.82.184112","issue":"18"},{"citation":{"apa":"Drymiotis, F. R., Drye, T. B., Wang, Y., He, J., Rhodes, D., Modic, K. A., … Zhang, Q. R. (2010). Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures. <i>Journal of Applied Physics</i>. AIP. <a href=\"https://doi.org/10.1063/1.3284946\">https://doi.org/10.1063/1.3284946</a>","chicago":"Drymiotis, Fivos R., Tyler B. Drye, Yisha Wang, Jian He, Daniel Rhodes, Kimberly A Modic, Samantha Cawthorne, and Qiu Run Zhang. “Structure Formation and Very Low Thermal Conductivity in Pb:Te:Ag:Se Mixtures.” <i>Journal of Applied Physics</i>. AIP, 2010. <a href=\"https://doi.org/10.1063/1.3284946\">https://doi.org/10.1063/1.3284946</a>.","mla":"Drymiotis, Fivos R., et al. “Structure Formation and Very Low Thermal Conductivity in Pb:Te:Ag:Se Mixtures.” <i>Journal of Applied Physics</i>, vol. 107, no. 3, 033519, AIP, 2010, doi:<a href=\"https://doi.org/10.1063/1.3284946\">10.1063/1.3284946</a>.","ieee":"F. R. Drymiotis <i>et al.</i>, “Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures,” <i>Journal of Applied Physics</i>, vol. 107, no. 3. AIP, 2010.","short":"F.R. Drymiotis, T.B. Drye, Y. Wang, J. He, D. Rhodes, K.A. Modic, S. Cawthorne, Q.R. Zhang, Journal of Applied Physics 107 (2010).","ama":"Drymiotis FR, Drye TB, Wang Y, et al. Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures. <i>Journal of Applied Physics</i>. 2010;107(3). doi:<a href=\"https://doi.org/10.1063/1.3284946\">10.1063/1.3284946</a>","ista":"Drymiotis FR, Drye TB, Wang Y, He J, Rhodes D, Modic KA, Cawthorne S, Zhang QR. 2010. Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures. Journal of Applied Physics. 107(3), 033519."},"quality_controlled":"1","issue":"3","publication_identifier":{"issn":["0021-8979","1089-7550"]},"doi":"10.1063/1.3284946","publication":"Journal of Applied Physics","status":"public","day":"09","year":"2010","date_created":"2019-11-19T13:47:24Z","article_number":"033519","title":"Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures","month":"02","language":[{"iso":"eng"}],"date_published":"2010-02-09T00:00:00Z","publisher":"AIP","date_updated":"2021-01-12T08:11:44Z","article_processing_charge":"No","abstract":[{"text":"We have observed that reacting Pb:Te:Ag:Se in a 1:1:1.9:1 molar ratio gives rise to what appears to be a predominantly single-phase alloy, which crystallizes in the PbSe cF8 fcc structure. However, further investigation of the structure using energy dispersive x-ray analysis reveals the presence of two phases, PbSe and β-Ag2Te, with identical lattice parameters. The total thermal conductivity of the formed alloy is remarkably low for a crystalline material, κT<0.6W∕mK at 675K, it is reproducible, and in addition, the compound has good mechanical properties.","lang":"eng"}],"publication_status":"published","_id":"7079","extern":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Drymiotis, Fivos R.","first_name":"Fivos R.","last_name":"Drymiotis"},{"full_name":"Drye, Tyler B.","first_name":"Tyler B.","last_name":"Drye"},{"last_name":"Wang","first_name":"Yisha","full_name":"Wang, Yisha"},{"full_name":"He, Jian","last_name":"He","first_name":"Jian"},{"full_name":"Rhodes, Daniel","last_name":"Rhodes","first_name":"Daniel"},{"first_name":"Kimberly A","last_name":"Modic","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"},{"first_name":"Samantha","last_name":"Cawthorne","full_name":"Cawthorne, Samantha"},{"first_name":"Qiu Run","last_name":"Zhang","full_name":"Zhang, Qiu Run"}],"intvolume":"       107","oa_version":"None","type":"journal_article","volume":107},{"year":"2010","date_created":"2020-01-15T12:21:06Z","article_number":"A180","issue":"12","doi":"10.1149/1.3494045","publication_identifier":{"issn":["1099-0062"]},"publication":"Electrochemical and Solid-State Letters","day":"04","status":"public","citation":{"mla":"Giordani, V., et al. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts in Li–O2 Cells.” <i>Electrochemical and Solid-State Letters</i>, vol. 13, no. 12, A180, The Electrochemical Society, 2010, doi:<a href=\"https://doi.org/10.1149/1.3494045\">10.1149/1.3494045</a>.","apa":"Giordani, V., Freunberger, S. A., Bruce, P. G., Tarascon, J.-M., &#38; Larcher, D. (2010). H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. <i>Electrochemical and Solid-State Letters</i>. The Electrochemical Society. <a href=\"https://doi.org/10.1149/1.3494045\">https://doi.org/10.1149/1.3494045</a>","chicago":"Giordani, V., Stefan Alexander Freunberger, P. G. Bruce, J.-M. Tarascon, and D. Larcher. “H2O2 Decomposition Reaction as Selecting Tool for Catalysts in Li–O2 Cells.” <i>Electrochemical and Solid-State Letters</i>. The Electrochemical Society, 2010. <a href=\"https://doi.org/10.1149/1.3494045\">https://doi.org/10.1149/1.3494045</a>.","ama":"Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. <i>Electrochemical and Solid-State Letters</i>. 2010;13(12). doi:<a href=\"https://doi.org/10.1149/1.3494045\">10.1149/1.3494045</a>","ista":"Giordani V, Freunberger SA, Bruce PG, Tarascon J-M, Larcher D. 2010. H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells. Electrochemical and Solid-State Letters. 13(12), A180.","ieee":"V. Giordani, S. A. Freunberger, P. G. Bruce, J.-M. Tarascon, and D. Larcher, “H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells,” <i>Electrochemical and Solid-State Letters</i>, vol. 13, no. 12. The Electrochemical Society, 2010.","short":"V. Giordani, S.A. Freunberger, P.G. Bruce, J.-M. Tarascon, D. Larcher, Electrochemical and Solid-State Letters 13 (2010)."},"quality_controlled":"1","article_type":"letter_note","extern":"1","author":[{"last_name":"Giordani","first_name":"V.","full_name":"Giordani, V."},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger"},{"full_name":"Bruce, P. G.","first_name":"P. G.","last_name":"Bruce"},{"last_name":"Tarascon","first_name":"J.-M.","full_name":"Tarascon, J.-M."},{"full_name":"Larcher, D.","first_name":"D.","last_name":"Larcher"}],"oa_version":"None","intvolume":"        13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13,"type":"journal_article","_id":"7318","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2) catalyzed by transition metal oxide powders has been compared with the charging voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear relationship between Ln k (rate constant for the H2O2 decomposition) and the charging voltage has been found, despite differences in media and possible mechanistic differences. The results suggest that the decomposition may be a reliable, useful, and fast screening tool for materials that promote the charging process of the Li-O2 battery and may ultimately give insight into the charging mechanism."}],"publication_status":"published","language":[{"iso":"eng"}],"title":"H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells","month":"10","date_published":"2010-10-04T00:00:00Z","publisher":"The Electrochemical Society","date_updated":"2021-01-12T08:13:01Z"},{"_id":"754","publist_id":"6900","acknowledgement":"The work of Dan Alistarh is supported by the Swiss NCCR MICS project. The work of Hagit Attiya is supported in part by the Israel Science Foundation (grant number 953/06).","type":"conference","volume":"6343 LNCS","extern":"1","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Attiya","first_name":"Hagit","full_name":"Attiya, Hagit"},{"full_name":"Gilbert, Seth","first_name":"Seth","last_name":"Gilbert"},{"first_name":"Andrei","last_name":"Giurgiu","full_name":"Giurgiu, Andrei"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publisher":"Springer","date_updated":"2023-02-23T13:10:21Z","language":[{"iso":"eng"}],"title":"Fast randomized test-and-set and renaming","month":"01","date_published":"2010-01-01T00:00:00Z","abstract":[{"text":"Most people believe that renaming is easy: simply choose a name at random; if more than one process selects the same name, then try again. We highlight the issues that occur when trying to implement such a scheme and shed new light on the read-write complexity of randomized renaming in an asynchronous environment. At the heart of our new perspective stands an adaptive implementation of a randomized test-and-set object, that has poly-logarithmic step complexity per operation, with high probability. Interestingly, our implementation is anonymous, as it does not require process identifiers. Based on this implementation, we present two new randomized renaming algorithms. The first ensures a tight namespace of n names using O( n log4 n) total steps, with high probability. This significantly improves on the complexity of the best previously known namespace-optimal algorithms. The second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2 (1 + ε) ) total steps, both with high probability, where k is the total contention in the execution. It is the first adaptive randomized renaming algorithm, and it improves on existing deterministic solutions by providing a smaller namespace, and by lowering step complexity.","lang":"eng"}],"publication_status":"published","page":"94 - 108","article_processing_charge":"No","day":"01","status":"public","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-15763-9_9","year":"2010","date_created":"2018-12-11T11:48:19Z","conference":{"name":"DISC: Distributed Computing"},"citation":{"ieee":"D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, and R. Guerraoui, “Fast randomized test-and-set and renaming,” presented at the DISC: Distributed Computing, 2010, vol. 6343 LNCS, pp. 94–108.","short":"D.-A. Alistarh, H. Attiya, S. Gilbert, A. Giurgiu, R. Guerraoui, in:, Springer, 2010, pp. 94–108.","ama":"Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. Fast randomized test-and-set and renaming. In: Vol 6343 LNCS. Springer; 2010:94-108. doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">10.1007/978-3-642-15763-9_9</a>","ista":"Alistarh D-A, Attiya H, Gilbert S, Giurgiu A, Guerraoui R. 2010. Fast randomized test-and-set and renaming. DISC: Distributed Computing, LNCS, vol. 6343 LNCS, 94–108.","apa":"Alistarh, D.-A., Attiya, H., Gilbert, S., Giurgiu, A., &#38; Guerraoui, R. (2010). Fast randomized test-and-set and renaming (Vol. 6343 LNCS, pp. 94–108). Presented at the DISC: Distributed Computing, Springer. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">https://doi.org/10.1007/978-3-642-15763-9_9</a>","chicago":"Alistarh, Dan-Adrian, Hagit Attiya, Seth Gilbert, Andrei Giurgiu, and Rachid Guerraoui. “Fast Randomized Test-and-Set and Renaming,” 6343 LNCS:94–108. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">https://doi.org/10.1007/978-3-642-15763-9_9</a>.","mla":"Alistarh, Dan-Adrian, et al. <i>Fast Randomized Test-and-Set and Renaming</i>. Vol. 6343 LNCS, Springer, 2010, pp. 94–108, doi:<a href=\"https://doi.org/10.1007/978-3-642-15763-9_9\">10.1007/978-3-642-15763-9_9</a>."}},{"issue":"PART 2","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-14162-1_10","day":"01","status":"public","year":"2010","date_created":"2018-12-11T11:48:20Z","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming"},"citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>How Efficient Can Gossip Be? (On the Cost of Resilient Information Exchange)</i>. Vol. 6199 LNCS, no. PART 2, Springer, 2010, pp. 115–26, doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">10.1007/978-3-642-14162-1_10</a>.","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, and Morteza Zadimoghaddam. “How Efficient Can Gossip Be? (On the Cost of Resilient Information Exchange),” 6199 LNCS:115–26. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">https://doi.org/10.1007/978-3-642-14162-1_10</a>.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., &#38; Zadimoghaddam, M. (2010). How efficient can gossip be? (On the cost of resilient information exchange) (Vol. 6199 LNCS, pp. 115–126). Presented at the ICALP: International Colloquium on Automota, Languages and Programming, Springer. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">https://doi.org/10.1007/978-3-642-14162-1_10</a>","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Zadimoghaddam M. How efficient can gossip be? (On the cost of resilient information exchange). In: Vol 6199 LNCS. Springer; 2010:115-126. doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_10\">10.1007/978-3-642-14162-1_10</a>","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Zadimoghaddam M. 2010. How efficient can gossip be? (On the cost of resilient information exchange). ICALP: International Colloquium on Automota, Languages and Programming, LNCS, vol. 6199 LNCS, 115–126.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, and M. Zadimoghaddam, “How efficient can gossip be? (On the cost of resilient information exchange),” presented at the ICALP: International Colloquium on Automota, Languages and Programming, 2010, vol. 6199 LNCS, no. PART 2, pp. 115–126.","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, M. Zadimoghaddam, in:, Springer, 2010, pp. 115–126."},"publist_id":"6901","_id":"755","extern":"1","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Gilbert, Seth","last_name":"Gilbert","first_name":"Seth"},{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"first_name":"Morteza","last_name":"Zadimoghaddam","full_name":"Zadimoghaddam, Morteza"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","acknowledgement":"We would like to thank Prof. Hagit Attiya and the anonymous reviewers for their useful comments on earlier drafts of this paper.","type":"conference","volume":"6199 LNCS","title":"How efficient can gossip be? (On the cost of resilient information exchange)","language":[{"iso":"eng"}],"month":"01","date_published":"2010-01-01T00:00:00Z","publisher":"Springer","date_updated":"2023-02-23T13:10:40Z","page":"115 - 126","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Gossip, also known as epidemic dissemination, is becoming an increasingly popular technique in distributed systems. Yet, it has remained a partially open question: how robust are such protocols? We consider a natural extension of the random phone-call model (introduced by Karp et al. [1]), and we analyze two different notions of robustness: the ability to tolerate adaptive failures, and the ability to tolerate oblivious failures. For adaptive failures, we present a new gossip protocol, TrickleGossip, which achieves near-optimal O(n log 3 n) message complexity. To the best of our knowledge, this is the first epidemic-style protocol that can tolerate adaptive failures. We also show a direct relation between resilience and message complexity, demonstrating that gossip protocols which tolerate a large number of adaptive failures need to use a super-linear number of messages with high probability. For oblivious failures, we present a new gossip protocol, CoordinatedGossip, that achieves optimal O(n) message complexity. This protocol makes novel use of the universe reduction technique to limit the message complexity."}],"publication_status":"published"},{"abstract":[{"lang":"eng","text":"This paper studies non-cryptographic authenticated broadcast in radio networks subject to malicious failures. We introduce two protocols that address this problem. The first, NeighborWatchRB, makes use of a novel strategy in which honest devices monitor their neighbors for malicious behavior. Second, we present a more robust variant, MultiPathRB, that tolerates the maximum possible density of malicious devices per region, using an elaborate voting strategy. We also introduce a new proof technique to show that both protocols ensure asymptotically optimal running time. We demonstrate the fault tolerance of our protocols through extensive simulation. Simulations show the practical superiority of the NeighborWatchRB protocol (an advantage hidden in the constants of the asymptotic complexity). The NeighborWatchRB protocol even performs relatively well when compared to the simple, fast epidemic protocols commonly used in the radio setting, protocols that tolerate no malicious faults. We therefore believe that the overhead for ensuring authenticated broadcast is reasonable, especially in applications that use authenticated broadcast only when necessary, such as distributing an authenticated digest."}],"publication_status":"published","page":"50 - 59","article_processing_charge":"No","publisher":"ACM","date_updated":"2023-02-23T13:10:56Z","language":[{"iso":"eng"}],"title":"Securing every bit: Authenticated broadcast in radio networks","month":"01","date_published":"2010-01-01T00:00:00Z","type":"conference","acknowledgement":"The authors would like to thank Prof. Guevara Noubir for his useful comments on earlier\r\ndrafts of this paper.","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Seth","last_name":"Gilbert","full_name":"Gilbert, Seth"},{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"last_name":"Milošević","first_name":"Žarko","full_name":"Milošević, Žarko"},{"full_name":"Newport, Calvin","last_name":"Newport","first_name":"Calvin"}],"_id":"756","publist_id":"6902","citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>Securing Every Bit: Authenticated Broadcast in Radio Networks</i>. ACM, 2010, pp. 50–59, doi:<a href=\"https://doi.org/10.1145/1810479.1810489\">10.1145/1810479.1810489</a>.","apa":"Alistarh, D.-A., Gilbert, S., Guerraoui, R., Milošević, Ž., &#38; Newport, C. (2010). Securing every bit: Authenticated broadcast in radio networks (pp. 50–59). Presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, ACM. <a href=\"https://doi.org/10.1145/1810479.1810489\">https://doi.org/10.1145/1810479.1810489</a>","chicago":"Alistarh, Dan-Adrian, Seth Gilbert, Rachid Guerraoui, Žarko Milošević, and Calvin Newport. “Securing Every Bit: Authenticated Broadcast in Radio Networks,” 50–59. ACM, 2010. <a href=\"https://doi.org/10.1145/1810479.1810489\">https://doi.org/10.1145/1810479.1810489</a>.","ista":"Alistarh D-A, Gilbert S, Guerraoui R, Milošević Ž, Newport C. 2010. Securing every bit: Authenticated broadcast in radio networks. SPAA: Symposium on Parallelism in Algorithms and Architectures, 50–59.","ama":"Alistarh D-A, Gilbert S, Guerraoui R, Milošević Ž, Newport C. Securing every bit: Authenticated broadcast in radio networks. In: ACM; 2010:50-59. doi:<a href=\"https://doi.org/10.1145/1810479.1810489\">10.1145/1810479.1810489</a>","short":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, Ž. Milošević, C. Newport, in:, ACM, 2010, pp. 50–59.","ieee":"D.-A. Alistarh, S. Gilbert, R. Guerraoui, Ž. Milošević, and C. Newport, “Securing every bit: Authenticated broadcast in radio networks,” presented at the SPAA: Symposium on Parallelism in Algorithms and Architectures, 2010, pp. 50–59."},"conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"year":"2010","date_created":"2018-12-11T11:48:20Z","status":"public","day":"01","doi":"10.1145/1810479.1810489"}]