--- _id: '7329' abstract: - lang: eng text: A novel measurement principle for measuring the current distribution in polymer electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other known techniques, for the first time for a resolution smaller than the channel/rib scale of the flow field in PEFCs. The current density is obtained by considering the electron conductors in the cell as a two-dimensional resistor with the voltage drop caused by the current. The method was applied to a cell operated on oxygen up to high current densities. The results show that the ohmic resistances govern the current distribution in the low current regime, whereas mass transport limitations hamper the current production under the land at high loads. article_processing_charge: No article_type: original author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Mathias full_name: Reum, Mathias last_name: Reum - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Freunberger SA, Reum M, Wokaun A, Büchi FN. Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. 2006;8(9):1435-1438. doi:10.1016/j.elecom.2006.05.032 apa: Freunberger, S. A., Reum, M., Wokaun, A., & Büchi, F. N. (2006). Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. Elsevier. https://doi.org/10.1016/j.elecom.2006.05.032 chicago: Freunberger, Stefan Alexander, Mathias Reum, Alexander Wokaun, and Felix N. Büchi. “Expanding Current Distribution Measurement in PEFCs to Sub-Millimeter Resolution.” Electrochemistry Communications. Elsevier, 2006. https://doi.org/10.1016/j.elecom.2006.05.032. ieee: S. A. Freunberger, M. Reum, A. Wokaun, and F. N. Büchi, “Expanding current distribution measurement in PEFCs to sub-millimeter resolution,” Electrochemistry Communications, vol. 8, no. 9. Elsevier, pp. 1435–1438, 2006. ista: Freunberger SA, Reum M, Wokaun A, Büchi FN. 2006. Expanding current distribution measurement in PEFCs to sub-millimeter resolution. Electrochemistry Communications. 8(9), 1435–1438. mla: Freunberger, Stefan Alexander, et al. “Expanding Current Distribution Measurement in PEFCs to Sub-Millimeter Resolution.” Electrochemistry Communications, vol. 8, no. 9, Elsevier, 2006, pp. 1435–38, doi:10.1016/j.elecom.2006.05.032. short: S.A. Freunberger, M. Reum, A. Wokaun, F.N. Büchi, Electrochemistry Communications 8 (2006) 1435–1438. date_created: 2020-01-15T12:23:22Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T08:13:06Z day: '01' doi: 10.1016/j.elecom.2006.05.032 extern: '1' intvolume: ' 8' issue: '9' language: - iso: eng month: '09' oa_version: None page: 1435-1438 publication: Electrochemistry Communications publication_identifier: issn: - 1388-2481 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Expanding current distribution measurement in PEFCs to sub-millimeter resolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2006' ... --- _id: '7330' abstract: - lang: eng text: Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries (<2.0) and standard electrochemical components show a high degree of inhomogeneity in the current density distribution over the active area. An inhomogeneous current density distribution leads to a non-uniform utilization of the active area, which could negatively affect the time of life of the cells. Furthermore, it is also believed to lower cell performance. In this work, the homogenization of the current density, realized by means of tailored cathodes with along-the-air-channel redistributed catalyst loadings, is investigated. The air stoichiometry range for which a homogenization of the current density is achieved depends upon the gradient with which the catalyst is redistributed along the air channel. A gentle increasing catalyst loading profile homogenizes the current density at relatively higher air stoichiometries, while a steeper profile is suited better for lower air stoichiometries. The results show that a homogenization of the current density by means of redistributed catalyst loading has negative effects on cell performance. Model calculations corroborate the experimental findings on homogenization of the current density and deliver an explanation for the decrease in cell performance. article_processing_charge: No article_type: original author: - first_name: M. full_name: Santis, M. last_name: Santis - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: A. full_name: Reiner, A. last_name: Reiner - first_name: F.N. full_name: Büchi, F.N. last_name: Büchi citation: ama: Santis M, Freunberger SA, Reiner A, Büchi FN. Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. 2006;51(25):5383-5393. doi:10.1016/j.electacta.2006.02.008 apa: Santis, M., Freunberger, S. A., Reiner, A., & Büchi, F. N. (2006). Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. Elsevier. https://doi.org/10.1016/j.electacta.2006.02.008 chicago: Santis, M., Stefan Alexander Freunberger, A. Reiner, and F.N. Büchi. “Homogenization of the Current Density in Polymer Electrolyte Fuel Cells by In-Plane Cathode Catalyst Gradients.” Electrochimica Acta. Elsevier, 2006. https://doi.org/10.1016/j.electacta.2006.02.008. ieee: M. Santis, S. A. Freunberger, A. Reiner, and F. N. Büchi, “Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients,” Electrochimica Acta, vol. 51, no. 25. Elsevier, pp. 5383–5393, 2006. ista: Santis M, Freunberger SA, Reiner A, Büchi FN. 2006. Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients. Electrochimica Acta. 51(25), 5383–5393. mla: Santis, M., et al. “Homogenization of the Current Density in Polymer Electrolyte Fuel Cells by In-Plane Cathode Catalyst Gradients.” Electrochimica Acta, vol. 51, no. 25, Elsevier, 2006, pp. 5383–93, doi:10.1016/j.electacta.2006.02.008. short: M. Santis, S.A. Freunberger, A. Reiner, F.N. Büchi, Electrochimica Acta 51 (2006) 5383–5393. date_created: 2020-01-15T12:23:34Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T08:13:07Z day: '01' doi: 10.1016/j.electacta.2006.02.008 extern: '1' intvolume: ' 51' issue: '25' language: - iso: eng month: '07' oa_version: None page: 5383-5393 publication: Electrochimica Acta publication_identifier: issn: - 0013-4686 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2006' ... --- _id: '7332' abstract: - lang: eng text: A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities. article_number: A396 article_processing_charge: No article_type: original author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Marco full_name: Santis, Marco last_name: Santis - first_name: Ingo A. full_name: Schneider, Ingo A. last_name: Schneider - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. 2006;153(2). doi:10.1149/1.2150150 apa: Freunberger, S. A., Santis, M., Schneider, I. A., Wokaun, A., & Büchi, F. N. (2006). In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2150150 chicago: Freunberger, Stefan Alexander, Marco Santis, Ingo A. Schneider, Alexander Wokaun, and Felix N. Büchi. “In-Plane Effects in Large-Scale PEMFCs.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2150150. ieee: S. A. Freunberger, M. Santis, I. A. Schneider, A. Wokaun, and F. N. Büchi, “In-plane effects in large-scale PEMFCs,” Journal of The Electrochemical Society, vol. 153, no. 2. The Electrochemical Society, 2006. ista: Freunberger SA, Santis M, Schneider IA, Wokaun A, Büchi FN. 2006. In-plane effects in large-scale PEMFCs. Journal of The Electrochemical Society. 153(2), A396. mla: Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEMFCs.” Journal of The Electrochemical Society, vol. 153, no. 2, A396, The Electrochemical Society, 2006, doi:10.1149/1.2150150. short: S.A. Freunberger, M. Santis, I.A. Schneider, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006). date_created: 2020-01-15T12:24:00Z date_published: 2006-01-04T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '04' doi: 10.1149/1.2150150 extern: '1' intvolume: ' 153' issue: '2' language: - iso: eng month: '01' oa_version: None publication: Journal of The Electrochemical Society publication_identifier: issn: - 0013-4651 publication_status: published publisher: The Electrochemical Society quality_controlled: '1' status: public title: In-plane effects in large-scale PEMFCs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2006' ... --- _id: '7331' abstract: - lang: eng text: A previously developed mathematical model for water management and current density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to investigate the effects of cooling strategies on cell performance. The model describes a two-dimensional slice through the cell along the channels and through the entire cell sandwich including the coolant channels and the bipolar plate. Arbitrary flow arrangements of fuel, oxidant, and coolant stream directions can be described. Due to the serious impact of temperature on all processes in the PEFC, both the relative direction of the coolant stream to the gas streams and its mass flow turns out to significantly affect the cell performance. Besides influencing the electrochemical reaction and all kinds of mass transfer temperature, variations predominantly alter the local membrane hydration distribution and subseqently its conductivity. article_number: A909 article_processing_charge: No article_type: original author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Alexander full_name: Wokaun, Alexander last_name: Wokaun - first_name: Felix N. full_name: Büchi, Felix N. last_name: Büchi citation: ama: 'Freunberger SA, Wokaun A, Büchi FN. In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. 2006;153(5). doi:10.1149/1.2185282' apa: 'Freunberger, S. A., Wokaun, A., & Büchi, F. N. (2006). In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2185282' chicago: 'Freunberger, Stefan Alexander, Alexander Wokaun, and Felix N. Büchi. “In-Plane Effects in Large-Scale PEFCs: II. The Influence of Cooling Strategy on Cell Performance.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2185282.' ieee: 'S. A. Freunberger, A. Wokaun, and F. N. Büchi, “In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance,” Journal of The Electrochemical Society, vol. 153, no. 5. The Electrochemical Society, 2006.' ista: 'Freunberger SA, Wokaun A, Büchi FN. 2006. In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance. Journal of The Electrochemical Society. 153(5), A909.' mla: 'Freunberger, Stefan Alexander, et al. “In-Plane Effects in Large-Scale PEFCs: II. The Influence of Cooling Strategy on Cell Performance.” Journal of The Electrochemical Society, vol. 153, no. 5, A909, The Electrochemical Society, 2006, doi:10.1149/1.2185282.' short: S.A. Freunberger, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006). date_created: 2020-01-15T12:23:46Z date_published: 2006-03-27T00:00:00Z date_updated: 2021-01-12T08:13:08Z day: '27' doi: 10.1149/1.2185282 extern: '1' intvolume: ' 153' issue: '5' language: - iso: eng month: '03' oa_version: None publication: Journal of The Electrochemical Society publication_identifier: issn: - 0013-4651 publication_status: published publisher: The Electrochemical Society quality_controlled: '1' status: public title: 'In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 153 year: '2006' ... --- _id: '854' abstract: - lang: eng text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch - the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene. acknowledgement: |- FAK is supported by the NSF Graduate Research Fellowship. We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images. author: - first_name: Evgeny full_name: Rogaev, Evgeny I last_name: Rogaev - first_name: Yuri full_name: Moliaka, Yuri K last_name: Moliaka - first_name: Boris full_name: Malyarchuk, Boris A last_name: Malyarchuk - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Miroslava full_name: Derenko, Miroslava V last_name: Derenko - first_name: Ilya full_name: Chumakov, Ilya M last_name: Chumakov - first_name: Anastasia full_name: Grigorenko, Anastasia P last_name: Grigorenko citation: ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410. doi:10.1371/journal.pbio.0040073 apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov, I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0040073 chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology. Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073. ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library of Science, pp. 0403–0410, 2006. ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 4(3), 0403–0410. mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073. short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 0403–0410. date_created: 2018-12-11T11:48:51Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T08:19:58Z day: '01' doi: 10.1371/journal.pbio.0040073 extern: 1 intvolume: ' 4' issue: '3' month: '03' page: 0403 - 0410 publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '6794' quality_controlled: 0 status: public title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius type: journal_article volume: 4 year: '2006' ... --- _id: '868' abstract: - lang: eng text: 'Background: The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in animal tissues has been reported. In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study. Results: Using sequence similarity searches, we identified MS genes in arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in the numerous sequenced genomes of placental mammals. The regions of the placental mammals'' genomes expected to code for malate synthase, as determined by comparison of the gene orders in vertebrate genomes, show clear similarity to the opossum MS sequence but contain stop codons, indicating that the MS gene became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable in animals other than the nematodes that possess a bifunctional, fused ICL-MS gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal gene transfer events that probably went in both directions between several bacterial and eukaryotic lineages. The strongest evidence was obtained for the acquisition of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the corresponding operonic organization by the common ancestor of the nematodes. Conclusion: The distribution of the MS and ICL genes in animals suggests that either they encode alternative enzymes of the glyoxylate cycle that are not orthologous to the known MS and ICL or the animal MS acquired a new function that remains to be characterized. Regardless of the ultimate solution to this conundrum, the genes for the glyoxylate cycle enzymes present a remarkable variety of evolutionary events including unusual horizontal gene transfer from bacteria to animals.' acknowledgement: The authors thank Alexey Kondrashov for suggesting the possibility of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for critical reading of this manuscript. FAK is a National Science Foundation Graduate Fellow. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin - first_name: Igor full_name: Morgunov, Igor G last_name: Morgunov - first_name: Tatiana full_name: Finogenova, Tatiana V last_name: Finogenova - first_name: Marie full_name: Kondrashova, Marie N last_name: Kondrashova citation: ama: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 2006;1. doi:10.1186/1745-6150-1-31 apa: Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., & Kondrashova, M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-1-31 chicago: Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct. BioMed Central, 2006. https://doi.org/10.1186/1745-6150-1-31. ieee: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova, “Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation,” Biology Direct, vol. 1. BioMed Central, 2006. ista: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation. Biology Direct. 1. mla: Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31. short: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology Direct 1 (2006). date_created: 2018-12-11T11:48:56Z date_published: 2006-10-23T00:00:00Z date_updated: 2021-01-12T08:20:31Z day: '23' doi: 10.1186/1745-6150-1-31 extern: 1 intvolume: ' 1' license: https://creativecommons.org/licenses/by/4.0/ month: '10' publication: Biology Direct publication_status: published publisher: BioMed Central publist_id: '6778' quality_controlled: 0 status: public title: Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 1 year: '2006' ... --- _id: '873' abstract: - lang: eng text: New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10-9-10-10 per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 2006;239(2):141-151. doi:10.1016/j.jtbi.2005.08.033 apa: Kondrashov, F., & Kondrashov, A. (2006). Role of selection in fixation of gene duplications. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.08.033 chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.08.033. ieee: F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,” Journal of Theoretical Biology, vol. 239, no. 2. Elsevier, pp. 141–151, 2006. ista: Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications. Journal of Theoretical Biology. 239(2), 141–151. mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier, 2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033. short: F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151. date_created: 2018-12-11T11:48:57Z date_published: 2006-03-21T00:00:00Z date_updated: 2021-01-12T08:20:47Z day: '21' doi: 10.1016/j.jtbi.2005.08.033 extern: 1 intvolume: ' 239' issue: '2' month: '03' page: 141 - 151 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '6773' quality_controlled: 0 status: public title: Role of selection in fixation of gene duplications type: journal_article volume: 239 year: '2006' ... --- _id: '8489' abstract: - lang: eng text: Structure elucidation of proteins by either NMR or X‐ray crystallography often requires the screening of a large number of samples for promising protein constructs and optimum solution conditions. For large‐scale screening of protein samples in solution, robust methods are needed that allow a rapid assessment of the folding of a polypeptide under diverse sample conditions. Here we present HET‐SOFAST NMR, a highly sensitive new method for semi‐quantitative characterization of the structural compactness and heterogeneity of polypeptide chains in solution. On the basis of one‐dimensional 1H HET‐SOFAST NMR data, obtained on well‐folded, molten globular, partially‐ and completely unfolded proteins, we define empirical thresholds that can be used as quantitative benchmarks for protein compactness. For 15N‐enriched protein samples, two‐dimensional 1H‐15N HET‐SOFAST correlation spectra provide site‐specific information about the structural heterogeneity along the polypeptide chain. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Vincent full_name: Forge, Vincent last_name: Forge - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Schanda P, Forge V, Brutscher B. HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance in Chemistry. 2006;44(S1):S177-S184. doi:10.1002/mrc.1825 apa: Schanda, P., Forge, V., & Brutscher, B. (2006). HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance in Chemistry. Wiley. https://doi.org/10.1002/mrc.1825 chicago: Schanda, Paul, Vincent Forge, and Bernhard Brutscher. “HET-SOFAST NMR for Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.” Magnetic Resonance in Chemistry. Wiley, 2006. https://doi.org/10.1002/mrc.1825. ieee: P. Schanda, V. Forge, and B. Brutscher, “HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains,” Magnetic Resonance in Chemistry, vol. 44, no. S1. Wiley, pp. S177–S184, 2006. ista: Schanda P, Forge V, Brutscher B. 2006. HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains. Magnetic Resonance in Chemistry. 44(S1), S177–S184. mla: Schanda, Paul, et al. “HET-SOFAST NMR for Fast Detection of Structural Compactness and Heterogeneity along Polypeptide Chains.” Magnetic Resonance in Chemistry, vol. 44, no. S1, Wiley, 2006, pp. S177–84, doi:10.1002/mrc.1825. short: P. Schanda, V. Forge, B. Brutscher, Magnetic Resonance in Chemistry 44 (2006) S177–S184. date_created: 2020-09-18T10:13:42Z date_published: 2006-07-06T00:00:00Z date_updated: 2021-01-12T08:19:37Z day: '06' doi: 10.1002/mrc.1825 extern: '1' intvolume: ' 44' issue: S1 language: - iso: eng month: '07' oa_version: None page: S177-S184 publication: Magnetic Resonance in Chemistry publication_identifier: issn: - 0749-1581 - 1097-458X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2006' ... --- _id: '8488' abstract: - lang: eng text: We demonstrate for different protein samples that three-dimensional HNCO and HNCA correlation spectra may be recorded in a few minutes acquisition time using the band-selective excitation short-transient sequences presented here. This opens new perspectives for the NMR structural investigation of unstable protein samples and real-time site-resolved studies of protein kinetics. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Hélène full_name: Van Melckebeke, Hélène last_name: Van Melckebeke - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Schanda P, Van Melckebeke H, Brutscher B. Speeding up three-dimensional protein NMR experiments to a few minutes. Journal of the American Chemical Society. 2006;128(28):9042-9043. doi:10.1021/ja062025p apa: Schanda, P., Van Melckebeke, H., & Brutscher, B. (2006). Speeding up three-dimensional protein NMR experiments to a few minutes. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja062025p chicago: Schanda, Paul, Hélène Van Melckebeke, and Bernhard Brutscher. “Speeding up Three-Dimensional Protein NMR Experiments to a Few Minutes.” Journal of the American Chemical Society. American Chemical Society, 2006. https://doi.org/10.1021/ja062025p. ieee: P. Schanda, H. Van Melckebeke, and B. Brutscher, “Speeding up three-dimensional protein NMR experiments to a few minutes,” Journal of the American Chemical Society, vol. 128, no. 28. American Chemical Society, pp. 9042–9043, 2006. ista: Schanda P, Van Melckebeke H, Brutscher B. 2006. Speeding up three-dimensional protein NMR experiments to a few minutes. Journal of the American Chemical Society. 128(28), 9042–9043. mla: Schanda, Paul, et al. “Speeding up Three-Dimensional Protein NMR Experiments to a Few Minutes.” Journal of the American Chemical Society, vol. 128, no. 28, American Chemical Society, 2006, pp. 9042–43, doi:10.1021/ja062025p. short: P. Schanda, H. Van Melckebeke, B. Brutscher, Journal of the American Chemical Society 128 (2006) 9042–9043. date_created: 2020-09-18T10:13:36Z date_published: 2006-06-21T00:00:00Z date_updated: 2021-01-12T08:19:37Z day: '21' doi: 10.1021/ja062025p extern: '1' intvolume: ' 128' issue: '28' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '06' oa_version: None page: 9042-9043 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Speeding up three-dimensional protein NMR experiments to a few minutes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2006' ... --- _id: '8490' abstract: - lang: eng text: We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer. article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Bernhard full_name: Brutscher, Bernhard last_name: Brutscher citation: ama: Schanda P, Brutscher B. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance. 2006;178(2):334-339. doi:10.1016/j.jmr.2005.10.007 apa: Schanda, P., & Brutscher, B. (2006). Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2005.10.007 chicago: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance. Elsevier, 2006. https://doi.org/10.1016/j.jmr.2005.10.007. ieee: P. Schanda and B. Brutscher, “Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR,” Journal of Magnetic Resonance, vol. 178, no. 2. Elsevier, pp. 334–339, 2006. ista: Schanda P, Brutscher B. 2006. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance. 178(2), 334–339. mla: Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” Journal of Magnetic Resonance, vol. 178, no. 2, Elsevier, 2006, pp. 334–39, doi:10.1016/j.jmr.2005.10.007. short: P. Schanda, B. Brutscher, Journal of Magnetic Resonance 178 (2006) 334–339. date_created: 2020-09-18T10:13:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T08:19:38Z day: '01' doi: 10.1016/j.jmr.2005.10.007 extern: '1' intvolume: ' 178' issue: '2' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '02' oa_version: None page: 334-339 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier status: public title: Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 178 year: '2006' ... --- _id: '8514' abstract: - lang: eng text: We study the extent to which the Hausdorff dimension of a compact subset of an infinite-dimensional Banach space is affected by a typical mapping into a finite-dimensional space. It is possible that the dimension drops under all such mappings, but the amount by which it typically drops is controlled by the ‘thickness exponent’ of the set, which was defined by Hunt and Kaloshin (Nonlinearity12 (1999), 1263–1275). More precisely, let $X$ be a compact subset of a Banach space $B$ with thickness exponent $\tau$ and Hausdorff dimension $d$. Let $M$ be any subspace of the (locally) Lipschitz functions from $B$ to $\mathbb{R}^{m}$ that contains the space of bounded linear functions. We prove that for almost every (in the sense of prevalence) function $f \in M$, the Hausdorff dimension of $f(X)$ is at least $\min\{ m, d / (1 + \tau) \}$. We also prove an analogous result for a certain part of the dimension spectra of Borel probability measures supported on $X$. The factor $1 / (1 + \tau)$ can be improved to $1 / (1 + \tau / 2)$ if $B$ is a Hilbert space. Since dimension cannot increase under a (locally) Lipschitz function, these theorems become dimension preservation results when $\tau = 0$. We conjecture that many of the attractors associated with the evolution equations of mathematical physics have thickness exponent zero. We also discuss the sharpness of our results in the case $\tau > 0$. article_processing_charge: No article_type: original author: - first_name: WILLIAM full_name: OTT, WILLIAM last_name: OTT - first_name: BRIAN full_name: HUNT, BRIAN last_name: HUNT - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: OTT W, HUNT B, Kaloshin V. The effect of projections on fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems. 2006;26(3):869-891. doi:10.1017/s0143385705000714 apa: OTT, W., HUNT, B., & Kaloshin, V. (2006). The effect of projections on fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/s0143385705000714 chicago: OTT, WILLIAM, BRIAN HUNT, and Vadim Kaloshin. “The Effect of Projections on Fractal Sets and Measures in Banach Spaces.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2006. https://doi.org/10.1017/s0143385705000714. ieee: W. OTT, B. HUNT, and V. Kaloshin, “The effect of projections on fractal sets and measures in Banach spaces,” Ergodic Theory and Dynamical Systems, vol. 26, no. 3. Cambridge University Press, pp. 869–891, 2006. ista: OTT W, HUNT B, Kaloshin V. 2006. The effect of projections on fractal sets and measures in Banach spaces. Ergodic Theory and Dynamical Systems. 26(3), 869–891. mla: OTT, WILLIAM, et al. “The Effect of Projections on Fractal Sets and Measures in Banach Spaces.” Ergodic Theory and Dynamical Systems, vol. 26, no. 3, Cambridge University Press, 2006, pp. 869–91, doi:10.1017/s0143385705000714. short: W. OTT, B. HUNT, V. Kaloshin, Ergodic Theory and Dynamical Systems 26 (2006) 869–891. date_created: 2020-09-18T10:48:52Z date_published: 2006-06-01T00:00:00Z date_updated: 2021-01-12T08:19:48Z day: '01' doi: 10.1017/s0143385705000714 extern: '1' intvolume: ' 26' issue: '3' language: - iso: eng month: '06' oa_version: None page: 869-891 publication: Ergodic Theory and Dynamical Systems publication_identifier: issn: - 0143-3857 - 1469-4417 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: The effect of projections on fractal sets and measures in Banach spaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2006' ... --- _id: '8515' abstract: - lang: eng text: "We consider the evolution of a set carried by a space periodic incompressible stochastic flow in a Euclidean space. We\r\nreport on three main results obtained in [8, 9, 10] concerning long time behaviour for a typical realization of the stochastic flow. First, at time t most of the particles are at a distance of order √t away from the origin. Moreover, we prove a Central Limit Theorem for the evolution of a measure carried by the flow, which holds for almost every realization of the flow. Second, we show the existence of a zero measure full Hausdorff dimension set of points, which\r\nescape to infinity at a linear rate. Third, in the 2-dimensional case, we study the set of points visited by the original set by time t. Such a set, when scaled down by the factor of t, has a limiting non random shape." article_processing_charge: No author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: D. full_name: DOLGOPYAT, D. last_name: DOLGOPYAT - first_name: L. full_name: KORALOV, L. last_name: KORALOV citation: ama: 'Kaloshin V, DOLGOPYAT D, KORALOV L. Long time behaviour of periodic stochastic flows. In: XIVth International Congress on Mathematical Physics. World Scientific; 2006:290-295. doi:10.1142/9789812704016_0026' apa: 'Kaloshin, V., DOLGOPYAT, D., & KORALOV, L. (2006). Long time behaviour of periodic stochastic flows. In XIVth International Congress on Mathematical Physics (pp. 290–295). Lisbon, Portugal: World Scientific. https://doi.org/10.1142/9789812704016_0026' chicago: Kaloshin, Vadim, D. DOLGOPYAT, and L. KORALOV. “Long Time Behaviour of Periodic Stochastic Flows.” In XIVth International Congress on Mathematical Physics, 290–95. World Scientific, 2006. https://doi.org/10.1142/9789812704016_0026. ieee: V. Kaloshin, D. DOLGOPYAT, and L. KORALOV, “Long time behaviour of periodic stochastic flows,” in XIVth International Congress on Mathematical Physics, Lisbon, Portugal, 2006, pp. 290–295. ista: Kaloshin V, DOLGOPYAT D, KORALOV L. 2006. Long time behaviour of periodic stochastic flows. XIVth International Congress on Mathematical Physics. International Congress on Mathematical Physics, 290–295. mla: Kaloshin, Vadim, et al. “Long Time Behaviour of Periodic Stochastic Flows.” XIVth International Congress on Mathematical Physics, World Scientific, 2006, pp. 290–95, doi:10.1142/9789812704016_0026. short: V. Kaloshin, D. DOLGOPYAT, L. KORALOV, in:, XIVth International Congress on Mathematical Physics, World Scientific, 2006, pp. 290–295. conference: end_date: 2003-08-02 location: Lisbon, Portugal name: International Congress on Mathematical Physics start_date: 2003-07-28 date_created: 2020-09-18T10:48:59Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T08:19:49Z day: '01' doi: 10.1142/9789812704016_0026 extern: '1' language: - iso: eng month: '03' oa_version: None page: 290-295 publication: XIVth International Congress on Mathematical Physics publication_identifier: isbn: - '9789812562012' - '9789812704016' publication_status: published publisher: World Scientific quality_controlled: '1' status: public title: Long time behaviour of periodic stochastic flows type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2006' ... --- _id: '8513' article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Maria full_name: Saprykina, Maria last_name: Saprykina citation: ama: Kaloshin V, Saprykina M. Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. Discrete & Continuous Dynamical Systems - A. 2006;15(2):611-640. doi:10.3934/dcds.2006.15.611 apa: Kaloshin, V., & Saprykina, M. (2006). Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. Discrete & Continuous Dynamical Systems - A. American Institute of Mathematical Sciences (AIMS). https://doi.org/10.3934/dcds.2006.15.611 chicago: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete & Continuous Dynamical Systems - A. American Institute of Mathematical Sciences (AIMS), 2006. https://doi.org/10.3934/dcds.2006.15.611. ieee: V. Kaloshin and M. Saprykina, “Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits,” Discrete & Continuous Dynamical Systems - A, vol. 15, no. 2. American Institute of Mathematical Sciences (AIMS), pp. 611–640, 2006. ista: Kaloshin V, Saprykina M. 2006. Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits. Discrete & Continuous Dynamical Systems - A. 15(2), 611–640. mla: Kaloshin, Vadim, and Maria Saprykina. “Generic 3-Dimensional Volume-Preserving Diffeomorphisms with Superexponential Growth of Number of Periodic Orbits.” Discrete & Continuous Dynamical Systems - A, vol. 15, no. 2, American Institute of Mathematical Sciences (AIMS), 2006, pp. 611–40, doi:10.3934/dcds.2006.15.611. short: V. Kaloshin, M. Saprykina, Discrete & Continuous Dynamical Systems - A 15 (2006) 611–640. date_created: 2020-09-18T10:48:43Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T08:19:48Z day: '01' doi: 10.3934/dcds.2006.15.611 extern: '1' intvolume: ' 15' issue: '2' language: - iso: eng month: '05' oa_version: None page: 611-640 publication: Discrete & Continuous Dynamical Systems - A publication_identifier: issn: - 1553-5231 publication_status: published publisher: American Institute of Mathematical Sciences (AIMS) quality_controlled: '1' status: public title: Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2006' ... --- _id: '869' abstract: - lang: eng text: The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them. acknowledgement: This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Aleksey full_name: Ogurtsov, Aleksey Yu last_name: Ogurtsov - first_name: Alexey full_name: Kondrashov, Alexey S last_name: Kondrashov citation: ama: Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 2006;240(4):616-626. doi:10.1016/j.jtbi.2005.10.020 apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.10.020 chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.10.020. ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp. 616–626, 2006. ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626. mla: Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal of Theoretical Biology, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020. short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626. date_created: 2018-12-11T11:48:56Z date_published: 2006-06-21T00:00:00Z date_updated: 2021-01-12T08:20:33Z day: '21' doi: 10.1016/j.jtbi.2005.10.020 extern: 1 intvolume: ' 240' issue: '4' month: '06' page: 616 - 626 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '6779' quality_controlled: 0 status: public title: Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites type: journal_article volume: 240 year: '2006' ... --- _id: '903' abstract: - lang: eng text: 'Background: Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. Methods: A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. Results: We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. Conclusion: The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during tumorigenic somatic evolution.' acknowledgement: This work was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health/DHHS. FAK is an NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions. author: - first_name: Vladimir full_name: Babenko, Vladimir N last_name: Babenko - first_name: Malay full_name: Basu, Malay K last_name: Basu - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Igor full_name: Rogozin, Igor B last_name: Rogozin - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 2006;6. doi:10.1186/1471-2407-6-36 apa: Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., & Koonin, E. (2006). Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. BioMed Central. https://doi.org/10.1186/1471-2407-6-36 chicago: Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer. BioMed Central, 2006. https://doi.org/10.1186/1471-2407-6-36. ieee: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis,” BMC Cancer, vol. 6. BioMed Central, 2006. ista: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC Cancer. 6. mla: Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6, BioMed Central, 2006, doi:10.1186/1471-2407-6-36. short: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006). date_created: 2018-12-11T11:49:07Z date_published: 2006-02-09T00:00:00Z date_updated: 2021-01-12T08:21:47Z day: '09' doi: 10.1186/1471-2407-6-36 extern: 1 intvolume: ' 6' month: '02' publication: BMC Cancer publication_status: published publisher: BioMed Central publist_id: '6744' quality_controlled: 0 status: public title: Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 6 year: '2006' ... --- _id: '9505' abstract: - lang: eng text: 'Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.' article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Mary full_name: Gehring, Mary last_name: Gehring - first_name: Robert K. full_name: Tran, Robert K. last_name: Tran - first_name: Tracy full_name: Ballinger, Tracy last_name: Ballinger - first_name: Steven full_name: Henikoff, Steven last_name: Henikoff citation: ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929 apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., & Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng1929 chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” Nature Genetics. Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929. ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006. ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69. mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” Nature Genetics, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:10.1038/ng1929. short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69. date_created: 2021-06-07T12:19:31Z date_published: 2006-11-26T00:00:00Z date_updated: 2021-12-14T09:02:51Z day: '26' department: - _id: DaZi doi: 10.1038/ng1929 extern: '1' external_id: pmid: - '17128275' intvolume: ' 39' issue: '1' language: - iso: eng month: '11' oa_version: None page: 61-69 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - 1546-1718 issn: - 1061-4036 publication_status: published publisher: Nature Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 39 year: '2006' ... --- _id: '13430' abstract: - lang: eng text: Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed. article_processing_charge: No article_type: original author: - first_name: Marcin full_name: Fialkowski, Marcin last_name: Fialkowski - first_name: Kyle J. M. full_name: Bishop, Kyle J. M. last_name: Bishop - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Stoyan K. full_name: Smoukov, Stoyan K. last_name: Smoukov - first_name: Christopher J. full_name: Campbell, Christopher J. last_name: Campbell - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA. Principles and implementations of dissipative (dynamic) self-assembly. The Journal of Physical Chemistry B. 2006;110(6):2482-2496. doi:10.1021/jp054153q apa: Fialkowski, M., Bishop, K. J. M., Klajn, R., Smoukov, S. K., Campbell, C. J., & Grzybowski, B. A. (2006). Principles and implementations of dissipative (dynamic) self-assembly. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/jp054153q chicago: Fialkowski, Marcin, Kyle J. M. Bishop, Rafal Klajn, Stoyan K. Smoukov, Christopher J. Campbell, and Bartosz A. Grzybowski. “Principles and Implementations of Dissipative (Dynamic) Self-Assembly.” The Journal of Physical Chemistry B. American Chemical Society, 2006. https://doi.org/10.1021/jp054153q. ieee: M. Fialkowski, K. J. M. Bishop, R. Klajn, S. K. Smoukov, C. J. Campbell, and B. A. Grzybowski, “Principles and implementations of dissipative (dynamic) self-assembly,” The Journal of Physical Chemistry B, vol. 110, no. 6. American Chemical Society, pp. 2482–2496, 2006. ista: Fialkowski M, Bishop KJM, Klajn R, Smoukov SK, Campbell CJ, Grzybowski BA. 2006. Principles and implementations of dissipative (dynamic) self-assembly. The Journal of Physical Chemistry B. 110(6), 2482–2496. mla: Fialkowski, Marcin, et al. “Principles and Implementations of Dissipative (Dynamic) Self-Assembly.” The Journal of Physical Chemistry B, vol. 110, no. 6, American Chemical Society, 2006, pp. 2482–96, doi:10.1021/jp054153q. short: M. Fialkowski, K.J.M. Bishop, R. Klajn, S.K. Smoukov, C.J. Campbell, B.A. Grzybowski, The Journal of Physical Chemistry B 110 (2006) 2482–2496. date_created: 2023-08-01T10:37:35Z date_published: 2006-01-25T00:00:00Z date_updated: 2023-08-08T11:33:08Z day: '25' doi: 10.1021/jp054153q extern: '1' external_id: pmid: - '16471845' intvolume: ' 110' issue: '6' keyword: - Materials Chemistry - Surfaces - Coatings and Films - Physical and Theoretical Chemistry language: - iso: eng month: '01' oa_version: None page: 2482-2496 pmid: 1 publication: The Journal of Physical Chemistry B publication_identifier: issn: - 1520-6106 - 1520-5207 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Principles and implementations of dissipative (dynamic) self-assembly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2006' ... --- _id: '13428' abstract: - lang: eng text: Mixtures of oppositely charged nanoparticles of various sizes and charge ratios precipitate only at the point of electroneutrality. This phenomenonspecific to the nanoscale and reminiscent of threshold precipitation of ionsis a consequence of the formation of core-and-shell nanoparticle aggregates, in which the shells are composed of like-charged particles and are stabilized by efficient electrostatic screening. article_processing_charge: No article_type: original author: - first_name: Alexander M. full_name: Kalsin, Alexander M. last_name: Kalsin - first_name: Bartlomiej full_name: Kowalczyk, Bartlomiej last_name: Kowalczyk - first_name: Stoyan K. full_name: Smoukov, Stoyan K. last_name: Smoukov - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. Ionic-like behavior of oppositely charged nanoparticles. Journal of the American Chemical Society. 2006;128(47):15046-15047. doi:10.1021/ja0642966 apa: Kalsin, A. M., Kowalczyk, B., Smoukov, S. K., Klajn, R., & Grzybowski, B. A. (2006). Ionic-like behavior of oppositely charged nanoparticles. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja0642966 chicago: Kalsin, Alexander M., Bartlomiej Kowalczyk, Stoyan K. Smoukov, Rafal Klajn, and Bartosz A. Grzybowski. “Ionic-like Behavior of Oppositely Charged Nanoparticles.” Journal of the American Chemical Society. American Chemical Society, 2006. https://doi.org/10.1021/ja0642966. ieee: A. M. Kalsin, B. Kowalczyk, S. K. Smoukov, R. Klajn, and B. A. Grzybowski, “Ionic-like behavior of oppositely charged nanoparticles,” Journal of the American Chemical Society, vol. 128, no. 47. American Chemical Society, pp. 15046–15047, 2006. ista: Kalsin AM, Kowalczyk B, Smoukov SK, Klajn R, Grzybowski BA. 2006. Ionic-like behavior of oppositely charged nanoparticles. Journal of the American Chemical Society. 128(47), 15046–15047. mla: Kalsin, Alexander M., et al. “Ionic-like Behavior of Oppositely Charged Nanoparticles.” Journal of the American Chemical Society, vol. 128, no. 47, American Chemical Society, 2006, pp. 15046–47, doi:10.1021/ja0642966. short: A.M. Kalsin, B. Kowalczyk, S.K. Smoukov, R. Klajn, B.A. Grzybowski, Journal of the American Chemical Society 128 (2006) 15046–15047. date_created: 2023-08-01T10:36:27Z date_published: 2006-11-29T00:00:00Z date_updated: 2023-08-08T11:30:06Z day: '29' doi: 10.1021/ja0642966 extern: '1' external_id: pmid: - '17117829' intvolume: ' 128' issue: '47' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '11' oa_version: None page: 15046-15047 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Ionic-like behavior of oppositely charged nanoparticles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2006' ... --- _id: '13429' abstract: - lang: eng text: 'The fruitful core: Organic syntheses reported in the literature from 1850 to 2004 are analyzed with mathematical tools from network theory and statistical physics. There is a set of substances (the core) from which the majority of other organic compounds can be made (see picture; red: core, blue: periphery, green: islands). Search algorithms are used to identify small optimal sets of maximally useful chemicals.' article_processing_charge: No article_type: original author: - first_name: Kyle J. M. full_name: Bishop, Kyle J. M. last_name: Bishop - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Bartosz A. full_name: Grzybowski, Bartosz A. last_name: Grzybowski citation: ama: Bishop KJM, Klajn R, Grzybowski BA. The core and most useful molecules in organic chemistry. Angewandte Chemie International Edition. 2006;45(32):5348-5354. doi:10.1002/anie.200600881 apa: Bishop, K. J. M., Klajn, R., & Grzybowski, B. A. (2006). The core and most useful molecules in organic chemistry. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.200600881 chicago: Bishop, Kyle J. M., Rafal Klajn, and Bartosz A. Grzybowski. “The Core and Most Useful Molecules in Organic Chemistry.” Angewandte Chemie International Edition. Wiley, 2006. https://doi.org/10.1002/anie.200600881. ieee: K. J. M. Bishop, R. Klajn, and B. A. Grzybowski, “The core and most useful molecules in organic chemistry,” Angewandte Chemie International Edition, vol. 45, no. 32. Wiley, pp. 5348–5354, 2006. ista: Bishop KJM, Klajn R, Grzybowski BA. 2006. The core and most useful molecules in organic chemistry. Angewandte Chemie International Edition. 45(32), 5348–5354. mla: Bishop, Kyle J. M., et al. “The Core and Most Useful Molecules in Organic Chemistry.” Angewandte Chemie International Edition, vol. 45, no. 32, Wiley, 2006, pp. 5348–54, doi:10.1002/anie.200600881. short: K.J.M. Bishop, R. Klajn, B.A. Grzybowski, Angewandte Chemie International Edition 45 (2006) 5348–5354. date_created: 2023-08-01T10:37:16Z date_published: 2006-08-11T00:00:00Z date_updated: 2023-08-08T11:31:27Z day: '11' doi: 10.1002/anie.200600881 extern: '1' external_id: pmid: - '16835857' intvolume: ' 45' issue: '32' keyword: - General Chemistry - Catalysis language: - iso: eng month: '08' oa_version: None page: 5348-5354 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: The core and most useful molecules in organic chemistry type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2006' ...