[{"intvolume":"        15","scopus_import":"1","date_updated":"2023-05-08T10:58:29Z","article_processing_charge":"No","issue":"2","title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","publication":"DNA Sequence","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1042-5179"]},"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Liao","full_name":"Liao, Zhihua","first_name":"Zhihua"},{"last_name":"Chen","first_name":"Min","full_name":"Chen, Min"},{"last_name":"Gong","full_name":"Gong, Yifu","first_name":"Yifu"},{"first_name":"Liang","full_name":"Guo, Liang","last_name":"Guo"},{"last_name":"Tan","first_name":"Qiumin","full_name":"Tan, Qiumin"},{"first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"first_name":"Xiaofen","full_name":"Sun, Xiaofen","last_name":"Sun"},{"first_name":"Feng","full_name":"Tan, Feng","last_name":"Tan"},{"last_name":"Tang","full_name":"Tang, Kexuan","first_name":"Kexuan"}],"pmid":1,"type":"journal_article","status":"public","acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","year":"2004","citation":{"apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158."},"date_created":"2023-01-16T09:24:50Z","keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"doi":"10.1080/10425170410001667348","article_type":"original","_id":"12203","external_id":{"pmid":["15352294"]},"abstract":[{"text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.","lang":"eng"}],"publication_status":"published","publisher":"Informa UK Limited","date_published":"2004-01-01T00:00:00Z","department":[{"_id":"XiFe"}],"page":"153-158","extern":"1","volume":15,"quality_controlled":"1"},{"scopus_import":"1","intvolume":"       109","date_updated":"2023-02-20T08:40:21Z","issue":"D3","article_processing_charge":"No","title":"Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations","publication":"Journal of Geophysical Research: Atmospheres","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0148-0227"]},"month":"02","oa_version":"None","day":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Strasser","first_name":"Ulrich","full_name":"Strasser, Ulrich"},{"first_name":"Javier","full_name":"Corripio, Javier","last_name":"Corripio"},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"},{"full_name":"Burlando, Paolo","first_name":"Paolo","last_name":"Burlando"},{"first_name":"Ben","full_name":"Brock, Ben","last_name":"Brock"},{"first_name":"Martin","full_name":"Funk, Martin","last_name":"Funk"}],"status":"public","type":"journal_article","article_number":"D03103","year":"2004","date_created":"2023-02-20T08:18:57Z","citation":{"ista":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. Journal of Geophysical Research: Atmospheres. 109(D3), D03103.","mla":"Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>.","chicago":"Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando, Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2004. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>.","ieee":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M. Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3. American Geophysical Union, 2004.","ama":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. 2004;109(D3). doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>","short":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk, Journal of Geophysical Research: Atmospheres 109 (2004).","apa":"Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &#38; Funk, M. (2004). Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>"},"keyword":["Paleontology","Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Earth-Surface Processes","Geochemistry and Petrology","Soil Science","Water Science and Technology","Ecology","Aquatic Science","Forestry","Oceanography","Geophysics"],"doi":"10.1029/2003jd003973","article_type":"original","_id":"12658","abstract":[{"text":"[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community.","lang":"eng"}],"publication_status":"published","publisher":"American Geophysical Union","date_published":"2004-02-16T00:00:00Z","extern":"1","quality_controlled":"1","volume":109},{"publisher":"Wiley","type":"journal_article","date_published":"2004-09-01T00:00:00Z","status":"public","page":"1127-1158","extern":"1","volume":57,"quality_controlled":"1","author":[{"last_name":"Dolgopyat","full_name":"Dolgopyat, Dmitry","first_name":"Dmitry"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"last_name":"Koralov","first_name":"Leonid","full_name":"Koralov, Leonid"}],"publication_status":"published","month":"09","publication_identifier":{"issn":["0010-3640","1097-0312"]},"oa_version":"None","day":"01","abstract":[{"text":"We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","_id":"8517","language":[{"iso":"eng"}],"publication":"Communications on Pure and Applied Mathematics","doi":"10.1002/cpa.20032","date_updated":"2021-01-12T08:19:50Z","article_processing_charge":"No","issue":"9","year":"2004","title":"A limit shape theorem for periodic stochastic dispersion","citation":{"ista":"Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9), 1127–1158.","mla":"Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” <i>Communications on Pure and Applied Mathematics</i>, vol. 57, no. 9, Wiley, 2004, pp. 1127–58, doi:<a href=\"https://doi.org/10.1002/cpa.20032\">10.1002/cpa.20032</a>.","chicago":"Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/cpa.20032\">https://doi.org/10.1002/cpa.20032</a>.","short":"D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied Mathematics 57 (2004) 1127–1158.","ieee":"D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic stochastic dispersion,” <i>Communications on Pure and Applied Mathematics</i>, vol. 57, no. 9. Wiley, pp. 1127–1158, 2004.","ama":"Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic dispersion. <i>Communications on Pure and Applied Mathematics</i>. 2004;57(9):1127-1158. doi:<a href=\"https://doi.org/10.1002/cpa.20032\">10.1002/cpa.20032</a>","apa":"Dolgopyat, D., Kaloshin, V., &#38; Koralov, L. (2004). A limit shape theorem for periodic stochastic dispersion. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.20032\">https://doi.org/10.1002/cpa.20032</a>"},"date_created":"2020-09-18T10:49:12Z","keyword":["Applied Mathematics","General Mathematics"],"intvolume":"        57"},{"type":"journal_article","date_published":"2004-03-04T00:00:00Z","status":"public","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","volume":32,"page":"1-27","extern":"1","author":[{"first_name":"Leonid","full_name":"Koralov, Leonid","last_name":"Koralov"},{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Dolgopyat, Dmitry","first_name":"Dmitry","last_name":"Dolgopyat"}],"publication_status":"published","publication_identifier":{"issn":["0091-1798"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"04","oa_version":"None","_id":"8518","article_type":"original","language":[{"iso":"eng"}],"publication":"The Annals of Probability","doi":"10.1214/aop/1078415827","year":"2004","issue":"1A","article_processing_charge":"No","date_updated":"2021-01-12T08:19:50Z","citation":{"chicago":"Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties of the Stochastic Flows.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2004. <a href=\"https://doi.org/10.1214/aop/1078415827\">https://doi.org/10.1214/aop/1078415827</a>.","mla":"Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” <i>The Annals of Probability</i>, vol. 32, no. 1A, Institute of Mathematical Statistics, 2004, pp. 1–27, doi:<a href=\"https://doi.org/10.1214/aop/1078415827\">10.1214/aop/1078415827</a>.","ista":"Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic flows. The Annals of Probability. 32(1A), 1–27.","short":"L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004) 1–27.","ama":"Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic flows. <i>The Annals of Probability</i>. 2004;32(1A):1-27. doi:<a href=\"https://doi.org/10.1214/aop/1078415827\">10.1214/aop/1078415827</a>","ieee":"L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the stochastic flows,” <i>The Annals of Probability</i>, vol. 32, no. 1A. Institute of Mathematical Statistics, pp. 1–27, 2004.","apa":"Koralov, L., Kaloshin, V., &#38; Dolgopyat, D. (2004). Sample path properties of the stochastic flows. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/aop/1078415827\">https://doi.org/10.1214/aop/1078415827</a>"},"title":"Sample path properties of the stochastic flows","date_created":"2020-09-18T10:49:19Z","intvolume":"        32"},{"intvolume":"        13","citation":{"apa":"Panchenko, A., Kondrashov, F., &#38; Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>","short":"A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.","ama":"Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. 2004;13(4):884-892. doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>","ieee":"A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” <i>Protein Science</i>, vol. 13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.","chicago":"Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>. Wiley-Blackwell, 2004. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>.","ista":"Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.","mla":"Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>."},"publist_id":"6786","title":"Prediction of functional sites by analysis of sequence and structure conservation","date_created":"2018-12-11T11:48:55Z","year":"2004","issue":"4","acknowledgement":"We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport.","date_updated":"2021-01-12T08:20:22Z","doi":"10.1110/ps.03465504","publication":"Protein Science","_id":"864","abstract":[{"text":"We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.","lang":"eng"}],"day":"01","month":"04","author":[{"first_name":"Anna","full_name":"Panchenko, Anna R","last_name":"Panchenko"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"last_name":"Bryant","first_name":"Stephen","full_name":"Bryant, Stephen H"}],"publication_status":"published","quality_controlled":0,"volume":13,"page":"884 - 892","extern":1,"status":"public","type":"journal_article","date_published":"2004-04-01T00:00:00Z","publisher":"Wiley-Blackwell"},{"day":"01","abstract":[{"lang":"eng","text":"Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates."}],"month":"01","publication_status":"published","author":[{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor"},{"last_name":"Ogurtsov","full_name":"Ogurtsov, Aleksey Yu","first_name":"Aleksey"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"}],"page":"1731 - 1737","extern":1,"volume":32,"quality_controlled":0,"publisher":"Oxford University Press","date_published":"2004-01-01T00:00:00Z","status":"public","type":"journal_article","intvolume":"        32","title":"Bioinformatical assay of human gene morbidity","citation":{"apa":"Kondrashov, F., Ogurtsov, A., &#38; Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. 2004;32(5):1731-1737. doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>","ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” <i>Nucleic Acids Research</i>, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.","ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.","mla":"Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>.","chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>."},"date_created":"2018-12-11T11:48:56Z","publist_id":"6780","date_updated":"2021-01-12T08:20:37Z","year":"2004","issue":"5","doi":"10.1093/nar/gkh330","publication":"Nucleic Acids Research","_id":"870"},{"publication_status":"published","author":[{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"last_name":"Koonin","full_name":"Koonin, Eugene V","first_name":"Eugene"}],"month":"07","day":"01","abstract":[{"text":"The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis.","lang":"eng"}],"publisher":"Elsevier","status":"public","date_published":"2004-07-01T00:00:00Z","type":"journal_article","extern":1,"page":"287 - 291","volume":20,"quality_controlled":0,"date_updated":"2021-01-12T08:20:54Z","issue":"7","year":"2004","date_created":"2018-12-11T11:48:58Z","citation":{"apa":"Kondrashov, F., &#38; Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>","ama":"Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. 2004;20(7):287-291. doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>","ieee":"F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” <i>Trends in Genetics</i>, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.","short":"F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.","mla":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>.","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>.","ista":"Kondrashov F, Koonin E. 2004. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics. 20(7), 287–291."},"publist_id":"6775","title":"A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications","intvolume":"        20","_id":"875","publication":"Trends in Genetics","doi":"10.1016/j.tig.2004.05.001"},{"_id":"889","publication":"Nature Genetics","doi":"10.1038/ng1451","acknowledgement":"We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp, S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were supported by a grant from the US National Institutes of Health to S. Nuzhdin, and A.D.K. is a Howard Hughes","date_updated":"2021-01-12T08:21:17Z","issue":"11","year":"2004","citation":{"chicago":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>.","ista":"Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.","mla":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>.","ama":"Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. 2004;36(11):1207-1212. doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>","ieee":"A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” <i>Nature Genetics</i>, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004.","short":"A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.","apa":"Kern, A., &#38; Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>"},"date_created":"2018-12-11T11:49:02Z","title":"Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs","publist_id":"6759","intvolume":"        36","publisher":"Nature Publishing Group","status":"public","date_published":"2004-11-01T00:00:00Z","type":"journal_article","page":"1207 - 1212","extern":1,"quality_controlled":0,"volume":36,"publication_status":"published","author":[{"last_name":"Kern","first_name":"Andrew","full_name":"Kern, Andrew D"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov"}],"month":"11","day":"01","abstract":[{"lang":"eng","text":"The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges."}]},{"volume":429,"quality_controlled":0,"page":"558 - 562","extern":1,"date_published":"2004-06-03T00:00:00Z","type":"journal_article","status":"public","publisher":"Nature Publishing Group","publication_status":"published","author":[{"last_name":"Bazykin","first_name":"Georgii","full_name":"Bazykin, Georgii A"},{"first_name":"Fyodor","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"full_name":"Ogurtsov, Aleksey Yu","first_name":"Aleksey","last_name":"Ogurtsov"},{"first_name":"Shamil","full_name":"Sunyaev, Shamil R","last_name":"Sunyaev"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"}],"abstract":[{"lang":"eng","text":"New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement."}],"day":"03","month":"06","_id":"898","doi":"10.1038/nature02601","publication":"Nature","publist_id":"6746","date_created":"2018-12-11T11:49:05Z","title":"Positive selection at sites of multiple amino acid replacements since rat-mouse divergence","citation":{"apa":"Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., &#38; Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>","ieee":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” <i>Nature</i>, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.","ama":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. 2004;429(6991):558-562. doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>","short":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.","ista":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562.","chicago":"Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>.","mla":"Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>."},"issue":"6991","year":"2004","date_updated":"2021-01-12T08:21:37Z","acknowledgement":"We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.","intvolume":"       429"},{"publication":"Genome Research","doi":"10.1101/gr.2195604","_id":"902","intvolume":"        14","issue":"5","year":"2004","acknowledgement":"We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada.\nThe publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.","date_updated":"2021-01-12T08:21:47Z","citation":{"short":"C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research 14 (2004) 802–811.","ama":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. 2004;14(5):802-811. doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>","ieee":"C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint,” <i>Genome Research</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, pp. 802–811, 2004.","chicago":"Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2004. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>.","mla":"Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.” <i>Genome Research</i>, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004, pp. 802–11, doi:<a href=\"https://doi.org/10.1101/gr.2195604\">10.1101/gr.2195604</a>.","ista":"Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. Genome Research. 14(5), 802–811.","apa":"Castillo Davis, C., Kondrashov, F., Hartl, D., &#38; Kulathinal, R. (2004). The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.2195604\">https://doi.org/10.1101/gr.2195604</a>"},"title":"The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint","date_created":"2018-12-11T11:49:06Z","publist_id":"6750","type":"journal_article","status":"public","date_published":"2004-05-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","volume":14,"quality_controlled":0,"extern":1,"page":"802 - 811","month":"05","abstract":[{"lang":"eng","text":"We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage."}],"day":"01","publication_status":"published","author":[{"full_name":"Castillo-Davis, Cristian I","first_name":"Cristian","last_name":"Castillo Davis"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor"},{"last_name":"Hartl","full_name":"Hartl, Daniel L","first_name":"Daniel"},{"last_name":"Kulathinal","first_name":"Rob","full_name":"Kulathinal, Rob J"}]},{"doi":"10.1002/fuce.200400028","publication":"Fuel Cells","language":[{"iso":"eng"}],"_id":"7333","article_type":"original","intvolume":"         4","date_created":"2020-01-15T12:24:14Z","citation":{"apa":"Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., &#38; Büchi, F. N. (2004). Modular stack-internal air humidification concept-verification in a 1 kW stack. <i>Fuel Cells</i>. Wiley. <a href=\"https://doi.org/10.1002/fuce.200400028\">https://doi.org/10.1002/fuce.200400028</a>","ieee":"M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular stack-internal air humidification concept-verification in a 1 kW stack,” <i>Fuel Cells</i>, vol. 4, no. 3. Wiley, pp. 214–218, 2004.","ama":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal air humidification concept-verification in a 1 kW stack. <i>Fuel Cells</i>. 2004;4(3):214-218. doi:<a href=\"https://doi.org/10.1002/fuce.200400028\">10.1002/fuce.200400028</a>","short":"M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4 (2004) 214–218.","mla":"Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” <i>Fuel Cells</i>, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:<a href=\"https://doi.org/10.1002/fuce.200400028\">10.1002/fuce.200400028</a>.","chicago":"Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N. Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW Stack.” <i>Fuel Cells</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/fuce.200400028\">https://doi.org/10.1002/fuce.200400028</a>.","ista":"Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218."},"title":"Modular stack-internal air humidification concept-verification in a 1 kW stack","article_processing_charge":"No","issue":"3","year":"2004","date_updated":"2021-01-12T08:13:08Z","volume":4,"quality_controlled":"1","page":"214-218","extern":"1","status":"public","type":"journal_article","date_published":"2004-08-01T00:00:00Z","publisher":"Wiley","abstract":[{"lang":"eng","text":"The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"None","publication_identifier":{"issn":["1615-6846","1615-6854"]},"month":"08","author":[{"full_name":"Santis, M.","first_name":"M.","last_name":"Santis"},{"first_name":"D.","full_name":"Schmid, D.","last_name":"Schmid"},{"full_name":"Ruge, M.","first_name":"M.","last_name":"Ruge"},{"last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"first_name":"F.N.","full_name":"Büchi, F.N.","last_name":"Büchi"}],"publication_status":"published"},{"author":[{"full_name":"Mantzaras, John","first_name":"John","last_name":"Mantzaras"},{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319"},{"last_name":"Büchi","full_name":"Büchi, Felix N.","first_name":"Felix N."},{"full_name":"Roos, Markus","first_name":"Markus","last_name":"Roos"},{"full_name":"Brandstätter, Wilhelm","first_name":"Wilhelm","last_name":"Brandstätter"},{"last_name":"Prestat","first_name":"Michel","full_name":"Prestat, Michel"},{"last_name":"Gauckler","first_name":"Ludwig J.","full_name":"Gauckler, Ludwig J."},{"last_name":"Andreaus","full_name":"Andreaus, Bernhard","first_name":"Bernhard"},{"last_name":"Hajbolouri","first_name":"Faegheh","full_name":"Hajbolouri, Faegheh"},{"last_name":"Senn","full_name":"Senn, Stephan M.","first_name":"Stephan M."},{"last_name":"Poulikakos","full_name":"Poulikakos, Dimos","first_name":"Dimos"},{"full_name":"Chaniotis, Andreas K.","first_name":"Andreas K.","last_name":"Chaniotis"},{"last_name":"Larrain","first_name":"Diego","full_name":"Larrain, Diego"},{"last_name":"Autissier","first_name":"Nordahl","full_name":"Autissier, Nordahl"},{"last_name":"Maréchal","full_name":"Maréchal, François","first_name":"François"}],"publication_status":"published","month":"12","publication_identifier":{"issn":["0009-4293"]},"day":"01","oa_version":"None","abstract":[{"text":"Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Swiss Chemical Society","date_published":"2004-12-01T00:00:00Z","type":"journal_article","status":"public","page":"857-868","extern":"1","volume":58,"quality_controlled":"1","date_updated":"2021-01-12T08:13:09Z","issue":"12","year":"2004","article_processing_charge":"No","title":"Fuel cell modeling and simulations","citation":{"apa":"Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W., Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. <i>CHIMIA International Journal for Chemistry</i>. Swiss Chemical Society. <a href=\"https://doi.org/10.2533/000942904777677029\">https://doi.org/10.2533/000942904777677029</a>","ista":"Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M, Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International Journal for Chemistry. 58(12), 857–868.","mla":"Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” <i>CHIMIA International Journal for Chemistry</i>, vol. 58, no. 12, Swiss Chemical Society, 2004, pp. 857–68, doi:<a href=\"https://doi.org/10.2533/000942904777677029\">10.2533/000942904777677029</a>.","chicago":"Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos, Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling and Simulations.” <i>CHIMIA International Journal for Chemistry</i>. Swiss Chemical Society, 2004. <a href=\"https://doi.org/10.2533/000942904777677029\">https://doi.org/10.2533/000942904777677029</a>.","ieee":"J. Mantzaras <i>et al.</i>, “Fuel cell modeling and simulations,” <i>CHIMIA International Journal for Chemistry</i>, vol. 58, no. 12. Swiss Chemical Society, pp. 857–868, 2004.","ama":"Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations. <i>CHIMIA International Journal for Chemistry</i>. 2004;58(12):857-868. doi:<a href=\"https://doi.org/10.2533/000942904777677029\">10.2533/000942904777677029</a>","short":"J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M. Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos, A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal for Chemistry 58 (2004) 857–868."},"date_created":"2020-01-15T12:24:23Z","intvolume":"        58","article_type":"original","_id":"7334","language":[{"iso":"eng"}],"publication":"CHIMIA International Journal for Chemistry","doi":"10.2533/000942904777677029"},{"publication":"Science","doi":"10.1126/science.1094637","_id":"7706","article_type":"original","language":[{"iso":"eng"}],"intvolume":"       303","date_updated":"2024-01-31T10:14:17Z","year":"2004","issue":"5666","article_processing_charge":"No","date_created":"2020-04-30T10:37:41Z","title":"Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase","citation":{"ieee":"A. Brunet <i>et al.</i>, “Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase,” <i>Science</i>, vol. 303, no. 5666. American Association for the Advancement of Science, pp. 2011–2015, 2004.","ama":"Brunet A, Sweeney LB, Sturgill JF, et al. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. <i>Science</i>. 2004;303(5666):2011-2015. doi:<a href=\"https://doi.org/10.1126/science.1094637\">10.1126/science.1094637</a>","short":"A. Brunet, L.B. Sweeney, J.F. Sturgill, K. Chua, P. Greer, Y. Lin, H. Tran, S. Ross, R. Mostoslavsky, H. Cohen, L. Hu, H.-L. Chen, M. Jedrychowski, S. Gygi, D. Sinclair, F. Alt, M. Greenberg, Science 303 (2004) 2011–2015.","mla":"Brunet, Anne, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” <i>Science</i>, vol. 303, no. 5666, American Association for the Advancement of Science, 2004, pp. 2011–15, doi:<a href=\"https://doi.org/10.1126/science.1094637\">10.1126/science.1094637</a>.","chicago":"Brunet, Anne, Lora B. Sweeney, J Fitzhugh  Sturgill, Katrin Chua, Paul Greer, Yingxi Lin, Hien Tran, et al. “Stress-Dependent Regulation of FOXO Transcription Factors by the SIRT1 Deacetylase.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1094637\">https://doi.org/10.1126/science.1094637</a>.","ista":"Brunet A, Sweeney LB, Sturgill JF, Chua K, Greer P, Lin Y, Tran H, Ross S, Mostoslavsky R, Cohen H, Hu L, Chen H-L, Jedrychowski M, Gygi S, Sinclair D, Alt F, Greenberg M. 2004. Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science. 303(5666), 2011–2015.","apa":"Brunet, A., Sweeney, L. B., Sturgill, J. F., Chua, K., Greer, P., Lin, Y., … Greenberg, M. (2004). Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1094637\">https://doi.org/10.1126/science.1094637</a>"},"publisher":"American Association for the Advancement of Science","date_published":"2004-03-26T00:00:00Z","status":"public","type":"journal_article","extern":"1","page":"2011-2015","volume":303,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["0036-8075","1095-9203"]},"day":"26","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.","lang":"eng"}],"publication_status":"published","author":[{"full_name":"Brunet, Anne","first_name":"Anne","last_name":"Brunet"},{"id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","first_name":"Lora Beatrice Jaeger"},{"last_name":"Sturgill","first_name":"J Fitzhugh ","full_name":"Sturgill, J Fitzhugh "},{"last_name":"Chua","first_name":"Katrin","full_name":"Chua, Katrin"},{"last_name":"Greer","first_name":"Paul","full_name":"Greer, Paul"},{"last_name":"Lin","full_name":"Lin, Yingxi","first_name":"Yingxi"},{"last_name":"Tran","full_name":"Tran, Hien","first_name":"Hien"},{"first_name":"Sarah","full_name":"Ross, Sarah","last_name":"Ross"},{"full_name":"Mostoslavsky, Raul","first_name":"Raul","last_name":"Mostoslavsky"},{"last_name":"Cohen","first_name":"Haim","full_name":"Cohen, Haim"},{"last_name":"Hu","first_name":"Linda","full_name":"Hu, Linda"},{"last_name":"Chen","full_name":"Chen, Hwei-Ling","first_name":"Hwei-Ling"},{"first_name":"Mark","full_name":"Jedrychowski, Mark","last_name":"Jedrychowski"},{"full_name":"Gygi, Steven","first_name":"Steven","last_name":"Gygi"},{"full_name":"Sinclair, David","first_name":"David","last_name":"Sinclair"},{"last_name":"Alt","full_name":"Alt, Frederick","first_name":"Frederick"},{"last_name":"Greenberg","first_name":"Michael","full_name":"Greenberg, Michael"}]},{"publication_status":"published","author":[{"first_name":"Aygun","full_name":"Mamedova, Aygun A","last_name":"Mamedova"},{"last_name":"Holt","full_name":"Holt, Peter J","first_name":"Peter"},{"full_name":"Carroll, Joe D","first_name":"Joe","last_name":"Carroll"},{"first_name":"Leonid A","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"abstract":[{"text":"The mechanism coupling electron transfer and proton pumping in respiratory complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has been suggested that it involves conformational changes. Here, the influence of substrates on the conformation of purified complex I from Escherichia coli was studied by cross-linking and electron microscopy. When a zero-length cross-linking reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented the formation of cross-links between the hydrophilic subunits of the complex, including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral arm of the complex adopts a more open conformation, with increased distances between subunits. Single particle analysis showed the nature of this conformational change. The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly more open or expanded structure both in the peripheral arm and, unexpectedly, in the membrane domain also.","lang":"eng"}],"day":"28","month":"05","volume":279,"quality_controlled":0,"extern":1,"page":"23830 - 23836","status":"public","date_published":"2004-05-28T00:00:00Z","type":"journal_article","publisher":"American Society for Biochemistry and Molecular Biology","title":"Substrate-induced conformational change in bacterial complex I","date_created":"2018-12-11T11:54:56Z","publist_id":"5123","citation":{"apa":"Mamedova, A., Holt, P., Carroll, J., &#38; Sazanov, L. A. (2004). Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>","ama":"Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational change in bacterial complex I. <i>Journal of Biological Chemistry</i>. 2004;279(22):23830-23836. doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>","ieee":"A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational change in bacterial complex I,” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836, 2004.","short":"A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry 279 (2004) 23830–23836.","mla":"Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>, vol. 279, no. 22, American Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:<a href=\"https://doi.org/10.1074/jbc.M401539200\">10.1074/jbc.M401539200</a>.","ista":"Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.","chicago":"Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced Conformational Change in Bacterial Complex I.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2004. <a href=\"https://doi.org/10.1074/jbc.M401539200\">https://doi.org/10.1074/jbc.M401539200</a>."},"year":"2004","issue":"22","acknowledgement":"This work was supported by the Medical Research Council and by a Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A. A. M.)","date_updated":"2021-01-12T06:54:22Z","intvolume":"       279","_id":"1963","doi":"10.1074/jbc.M401539200","publication":"Journal of Biological Chemistry"},{"publication":"Advanced Materials","language":[{"iso":"eng"}],"intvolume":"        16","scopus_import":"1","title":"Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts","date_updated":"2023-08-08T12:41:23Z","issue":"21","article_processing_charge":"No","status":"public","type":"journal_article","oa_version":"None","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"author":[{"last_name":"Campbell","full_name":"Campbell, C. J.","first_name":"C. J."},{"full_name":"Fialkowski, M.","first_name":"M.","last_name":"Fialkowski"},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Bensemann, I. T.","first_name":"I. T.","last_name":"Bensemann"},{"last_name":"Grzybowski","full_name":"Grzybowski, B. A.","first_name":"B. A."}],"doi":"10.1002/adma.200400383","article_type":"original","_id":"13434","citation":{"apa":"Campbell, C. J., Fialkowski, M., Klajn, R., Bensemann, I. T., &#38; Grzybowski, B. A. (2004). Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.200400383\">https://doi.org/10.1002/adma.200400383</a>","ista":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. 2004. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced Materials. 16(21), 1912–1917.","mla":"Campbell, C. J., et al. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” <i>Advanced Materials</i>, vol. 16, no. 21, Wiley, 2004, pp. 1912–17, doi:<a href=\"https://doi.org/10.1002/adma.200400383\">10.1002/adma.200400383</a>.","chicago":"Campbell, C. J., M. Fialkowski, Rafal Klajn, I. T. Bensemann, and B. A. Grzybowski. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion Fronts.” <i>Advanced Materials</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/adma.200400383\">https://doi.org/10.1002/adma.200400383</a>.","short":"C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski, Advanced Materials 16 (2004) 1912–1917.","ama":"Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts. <i>Advanced Materials</i>. 2004;16(21):1912-1917. doi:<a href=\"https://doi.org/10.1002/adma.200400383\">10.1002/adma.200400383</a>","ieee":"C. J. Campbell, M. Fialkowski, R. Klajn, I. T. Bensemann, and B. A. Grzybowski, “Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts,” <i>Advanced Materials</i>, vol. 16, no. 21. Wiley, pp. 1912–1917, 2004."},"date_created":"2023-08-01T10:39:09Z","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"year":"2004","page":"1912-1917","extern":"1","quality_controlled":"1","volume":16,"publisher":"Wiley","date_published":"2004-11-14T00:00:00Z","abstract":[{"text":"Thin films of ionically doped gelatin have been color-patterned with submicrometer precision using the wet-stamping technique. Inorganic salts are delivered onto the gelatin surface from an agarose stamp, and diffuse into the gelatine layer, producting deeply colored precipitates. Reaction fronts originating from different features of the stamp cease within < 1 μm of each other, leaving sharp, transparent regions in between.","lang":"eng"}],"publication_status":"published"},{"publisher":"Springer Nature","date_published":"2004-09-19T00:00:00Z","extern":"1","page":"729-735","quality_controlled":"1","volume":3,"external_id":{"pmid":["15378052"]},"abstract":[{"lang":"eng","text":"Micropatterning of surfaces with several chemicals at different spatial locations usually requires multiple stamping and registration steps. Here, we describe an experimental method based on reaction–diffusion phenomena that allows for simultaneous micropatterning of a substrate with several coloured chemicals. In this method, called wet stamping (WETS), aqueous solutions of two or more inorganic salts are delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned in bas relief. Once in conformal contact, these salts diffuse into the gelatin, where they react to give deeply coloured precipitates. Separation of colours in the plane of the surface is the consequence of the differences in the diffusion coefficients, the solubility products, and the amounts of different salts delivered from the stamp, and is faithfully reproduced by a theoretical model based on a system of reaction–diffusion partial differential equations. The multicolour micropatterns are useful as non-binary optical elements, and could potentially form the basis of new applications in microseparations and in controlled delivery."}],"publication_status":"published","doi":"10.1038/nmat1231","_id":"13435","article_type":"original","year":"2004","date_created":"2023-08-01T10:39:23Z","citation":{"short":"R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop, S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735.","ama":"Klajn R, Fialkowski M, Bensemann IT, et al. Multicolour micropatterning of thin films of dry gels. <i>Nature Materials</i>. 2004;3:729-735. doi:<a href=\"https://doi.org/10.1038/nmat1231\">10.1038/nmat1231</a>","ieee":"R. Klajn <i>et al.</i>, “Multicolour micropatterning of thin films of dry gels,” <i>Nature Materials</i>, vol. 3. Springer Nature, pp. 729–735, 2004.","mla":"Klajn, Rafal, et al. “Multicolour Micropatterning of Thin Films of Dry Gels.” <i>Nature Materials</i>, vol. 3, Springer Nature, 2004, pp. 729–35, doi:<a href=\"https://doi.org/10.1038/nmat1231\">10.1038/nmat1231</a>.","ista":"Klajn R, Fialkowski M, Bensemann IT, Bitner A, Campbell CJ, Bishop K, Smoukov S, Grzybowski BA. 2004. Multicolour micropatterning of thin films of dry gels. Nature Materials. 3, 729–735.","chicago":"Klajn, Rafal, Marcin Fialkowski, Igor T. Bensemann, Agnieszka Bitner, C. J. Campbell, Kyle Bishop, Stoyan Smoukov, and Bartosz A. Grzybowski. “Multicolour Micropatterning of Thin Films of Dry Gels.” <i>Nature Materials</i>. Springer Nature, 2004. <a href=\"https://doi.org/10.1038/nmat1231\">https://doi.org/10.1038/nmat1231</a>.","apa":"Klajn, R., Fialkowski, M., Bensemann, I. T., Bitner, A., Campbell, C. J., Bishop, K., … Grzybowski, B. A. (2004). Multicolour micropatterning of thin films of dry gels. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat1231\">https://doi.org/10.1038/nmat1231</a>"},"keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science","General Chemistry"],"pmid":1,"status":"public","type":"journal_article","month":"09","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"oa_version":"None","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"first_name":"Marcin","full_name":"Fialkowski, Marcin","last_name":"Fialkowski"},{"last_name":"Bensemann","first_name":"Igor T.","full_name":"Bensemann, Igor T."},{"last_name":"Bitner","full_name":"Bitner, Agnieszka","first_name":"Agnieszka"},{"last_name":"Campbell","first_name":"C. J.","full_name":"Campbell, C. J."},{"last_name":"Bishop","first_name":"Kyle","full_name":"Bishop, Kyle"},{"full_name":"Smoukov, Stoyan","first_name":"Stoyan","last_name":"Smoukov"},{"last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A."}],"publication":"Nature Materials","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"         3","date_updated":"2023-08-08T12:42:51Z","article_processing_charge":"No","title":"Multicolour micropatterning of thin films of dry gels"},{"doi":"10.1215/S0012-7094-04-12233-X","publication":"Duke Mathematical Journal","_id":"1456","intvolume":"       122","citation":{"mla":"Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548, doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>.","ista":"Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons. Duke Mathematical Journal. 122(3), 485–548.","chicago":"Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of Gravitational Instantons.” <i>Duke Mathematical Journal</i>. Duke University Press, 2004. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>.","ama":"Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. 2004;122(3):485-548. doi:<a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">10.1215/S0012-7094-04-12233-X</a>","ieee":"T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational instantons,” <i>Duke Mathematical Journal</i>, vol. 122, no. 3. Duke University Press, pp. 485–548, 2004.","short":"T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004) 485–548.","apa":"Hausel, T., Hunsicker, E., &#38; Mazzeo, R. (2004). Hodge cohomology of gravitational instantons. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/S0012-7094-04-12233-X\">https://doi.org/10.1215/S0012-7094-04-12233-X</a>"},"date_created":"2018-12-11T11:52:08Z","title":"Hodge cohomology of gravitational instantons","publist_id":"5737","date_updated":"2021-01-12T06:50:52Z","oa":1,"acknowledgement":"Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.\nHunsicker’s work partially supported by Stanford University.\nMazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and\nby the Mathematical Sciences Research Institute.","year":"2004","issue":"3","page":"485 - 548","extern":1,"quality_controlled":0,"volume":122,"publisher":"Duke University Press","date_published":"2004-04-15T00:00:00Z","type":"journal_article","status":"public","day":"15","main_file_link":[{"url":"http://arxiv.org/abs/math/0207169","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory."}],"month":"04","publication_status":"published","author":[{"first_name":"Tamas","full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"last_name":"Hunsicker","full_name":"Hunsicker, Eugénie","first_name":"Eugénie"},{"last_name":"Mazzeo","first_name":"Rafe","full_name":"Mazzeo, Rafe R"}]},{"type":"journal_article","status":"public","date_published":"2004-05-01T00:00:00Z","publisher":"Oxford University Press","volume":88,"quality_controlled":0,"page":"632 - 658","extern":1,"author":[{"first_name":"Tamas","full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"},{"first_name":"Michael","full_name":"Thaddeus, Michael","last_name":"Thaddeus"}],"publication_status":"published","month":"05","abstract":[{"text":"The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle.\n\nThis paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes.\n\nThe spaces of Higgs bundles with values in K(n) for n &gt; 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). ","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/math/0003093"}],"day":"01","_id":"1464","publication":"Proceedings of the London Mathematical Society","doi":"10.1112/S0024611503014618","year":"2004","issue":"3","oa":1,"date_updated":"2021-01-12T06:50:55Z","date_created":"2018-12-11T11:52:10Z","citation":{"ieee":"T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli space of rank 2 higgs bundles,” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.","ama":"Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. 2004;88(3):632-658. doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>","short":"T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88 (2004) 632–658.","ista":"Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical Society. 88(3), 632–658.","mla":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:<a href=\"https://doi.org/10.1112/S0024611503014618\">10.1112/S0024611503014618</a>.","chicago":"Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of the Moduli Space of Rank 2 Higgs Bundles.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>.","apa":"Hausel, T., &#38; Thaddeus, M. (2004). Generators for the cohomology ring of the moduli space of rank 2 higgs bundles. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/S0024611503014618\">https://doi.org/10.1112/S0024611503014618</a>"},"title":"Generators for the cohomology ring of the moduli space of rank 2 higgs bundles","publist_id":"5736","intvolume":"        88"},{"oa_version":"None","day":"22","external_id":{"pmid":["15203005"]},"abstract":[{"text":"The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","publication_identifier":{"issn":["0960-9822"]},"author":[{"last_name":"Cheung","first_name":"Benny H.H","full_name":"Cheung, Benny H.H"},{"last_name":"Arellano-Carbajal","first_name":"Fausto","full_name":"Arellano-Carbajal, Fausto"},{"last_name":"Rybicki","full_name":"Rybicki, Irene","first_name":"Irene"},{"full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","orcid":"0000-0001-8347-0443"}],"publication_status":"published","page":"1105-1111","extern":"1","volume":14,"quality_controlled":"1","publisher":"Elsevier","pmid":1,"type":"journal_article","date_published":"2004-06-22T00:00:00Z","status":"public","intvolume":"        14","date_created":"2019-03-21T09:42:01Z","title":"Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior","citation":{"mla":"Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” <i>Current Biology</i>, vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">10.1016/j.cub.2004.06.027</a>.","ista":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. Current Biology. 14(12), 1105–1111.","chicago":"Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to Promote C. Elegans Aggregation Behavior.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">https://doi.org/10.1016/j.cub.2004.06.027</a>.","short":"B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology 14 (2004) 1105–1111.","ieee":"B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior,” <i>Current Biology</i>, vol. 14, no. 12. Elsevier, pp. 1105–1111, 2004.","ama":"Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. <i>Current Biology</i>. 2004;14(12):1105-1111. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">10.1016/j.cub.2004.06.027</a>","apa":"Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., &#38; de Bono, M. (2004). Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.027\">https://doi.org/10.1016/j.cub.2004.06.027</a>"},"date_updated":"2021-01-12T08:06:25Z","issue":"12","year":"2004","doi":"10.1016/j.cub.2004.06.027","publication":"Current Biology","language":[{"iso":"eng"}],"_id":"6155"},{"publication_status":"published","external_id":{"pmid":["14988555"]},"publisher":"American Association for the Advancement of Science","date_published":"2004-02-27T00:00:00Z","page":"1336","department":[{"_id":"DaZi"}],"extern":"1","quality_controlled":"1","volume":303,"year":"2004","date_created":"2021-06-04T11:12:35Z","citation":{"ama":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. <i>Science</i>. 2004;303(5662):1336. doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>","ieee":"S. W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” <i>Science</i>, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.","short":"S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.","ista":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.","chicago":"Chan, Simon W.-L., Daniel Zilberman,  Zhixin Xie,  Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>.","mla":"Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>.","apa":"Chan, S. W.-L., Zilberman, D., Xie,  Zhixin, Johansen,  Lisa K., Carrington, J. C., &#38; Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>"},"keyword":["Multidisciplinary"],"_id":"9454","article_type":"original","doi":"10.1126/science.1095989","author":[{"full_name":"Chan, Simon W.-L.","first_name":"Simon W.-L.","last_name":"Chan"},{"full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":" Zhixin","full_name":"Xie,  Zhixin","last_name":"Xie"},{"last_name":"Johansen","full_name":"Johansen,  Lisa K.","first_name":" Lisa K."},{"last_name":"Carrington","first_name":"James C.","full_name":"Carrington, James C."},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"}],"month":"02","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"day":"27","oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"type":"journal_article","status":"public","date_updated":"2021-12-14T09:13:53Z","issue":"5662","article_processing_charge":"No","title":"RNA silencing genes control de novo DNA methylation","intvolume":"       303","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Science"}]