[{"type":"journal_article","extern":1,"publist_id":"2192","issue":"Pt 7","abstract":[{"lang":"eng","text":"T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla."}],"intvolume":" 119","publisher":"Company of Biologists","title":"Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules","publication_status":"published","status":"public","_id":"3934","year":"2006","volume":119,"date_created":"2018-12-11T12:05:58Z","date_updated":"2021-01-12T07:53:18Z","author":[{"full_name":"Drumea-Mirancea, Mihaela","last_name":"Drumea Mirancea","first_name":"Mihaela"},{"full_name":"Wessels, Johannes T","last_name":"Wessels","first_name":"Johannes"},{"full_name":"Müller, Claudia A","first_name":"Claudia","last_name":"Müller"},{"last_name":"Essl","first_name":"Mike","full_name":"Essl, Mike"},{"full_name":"Eble, Johannes A","last_name":"Eble","first_name":"Johannes"},{"full_name":"Tolosa, Eva","last_name":"Tolosa","first_name":"Eva"},{"full_name":"Koch, Manuel","last_name":"Koch","first_name":"Manuel"},{"full_name":"Reinhardt, Dieter P","last_name":"Reinhardt","first_name":"Dieter"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Michael Sixt"},{"last_name":"Sorokin","first_name":"Lydia","full_name":"Sorokin, Lydia"},{"full_name":"Stierhof, York-Dieter","last_name":"Stierhof","first_name":"York"},{"last_name":"Schwarz","first_name":"Heinz","full_name":"Schwarz, Heinz"},{"first_name":"Gerd","last_name":"Klein","full_name":"Klein, Gerd"}],"month":"04","day":"01","page":"1396 - 1405","quality_controlled":0,"citation":{"chicago":"Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl, Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02840.","short":"M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M. Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein, Journal of Cell Science 119 (2006) 1396–1405.","mla":"Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.” Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006, pp. 1396–405, doi:10.1242/jcs.02840.","apa":"Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa, E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02840","ieee":"M. Drumea Mirancea et al., “Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules,” Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp. 1396–1405, 2006.","ista":"Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M, Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.","ama":"Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405. doi:10.1242/jcs.02840"},"publication":"Journal of Cell Science","date_published":"2006-04-01T00:00:00Z","doi":"10.1242/jcs.02840"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis."}],"publist_id":"2193","issue":"5","extern":1,"year":"2006","_id":"3935","publication_status":"published","title":"γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response","status":"public","intvolume":" 26","publisher":"American Society for Microbiology","author":[{"full_name":"Chu, Haiyan","last_name":"Chu","first_name":"Haiyan"},{"first_name":"Ingo","last_name":"Thievessen","full_name":"Thievessen, Ingo"},{"full_name":"Michael Sixt","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lämmermann, Tim","first_name":"Tim","last_name":"Lämmermann"},{"full_name":"Waisman, Ari","last_name":"Waisman","first_name":"Ari"},{"first_name":"Attila","last_name":"Braun","full_name":"Braun, Attila"},{"full_name":"Noegel, Angelika A","first_name":"Angelika","last_name":"Noegel"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"}],"date_created":"2018-12-11T12:05:58Z","date_updated":"2021-01-12T07:53:18Z","volume":26,"day":"01","month":"03","publication":"Molecular and Cellular Biology","citation":{"mla":"Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology, vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006.","short":"H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A. Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825.","chicago":"Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman, Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology. American Society for Microbiology, 2006. https://doi.org/10.1128/MCB.26.5.1817-1825.2006.","ama":"Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006","ista":"Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A, Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5), 1817–1825.","apa":"Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A., … Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response. Molecular and Cellular Biology. American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006","ieee":"H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response,” Molecular and Cellular Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825, 2006."},"quality_controlled":0,"page":"1817 - 1825","doi":"10.1128/MCB.26.5.1817-1825.2006","date_published":"2006-03-01T00:00:00Z"},{"month":"10","day":"01","date_published":"2006-10-01T00:00:00Z","doi":"10.1016/j.ceb.2006.08.007","publication":"Current Opinion in Cell Biology","citation":{"short":"M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology 18 (2006) 482–490.","mla":"Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier, 2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.","chicago":"Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler. “Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.","ama":"Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490. doi:10.1016/j.ceb.2006.08.007","ieee":"M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes and signaling relay for blood cells,” Current Opinion in Cell Biology, vol. 18, no. 5. Elsevier, pp. 482–490, 2006.","apa":"Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007","ista":"Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490."},"quality_controlled":0,"page":"482 - 490","abstract":[{"lang":"eng","text":"At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials."}],"issue":"5","publist_id":"2191","extern":1,"type":"journal_article","author":[{"full_name":"Michael Sixt","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Bauer","first_name":"Martina","full_name":"Bauer, Martina"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"},{"full_name":"Fässler, Reinhard","last_name":"Fässler","first_name":"Reinhard"}],"date_created":"2018-12-11T12:05:59Z","date_updated":"2021-01-12T07:53:19Z","volume":18,"year":"2006","_id":"3936","publication_status":"published","title":"β1 integrins: zip codes and signaling relay for blood cells","status":"public","intvolume":" 18","publisher":"Elsevier"},{"month":"12","day":"04","article_processing_charge":"No","publication":"Journal of Cell Biology","citation":{"mla":"Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175, no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017.","short":"S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg, Journal of Cell Biology 175 (2006) 791–802.","chicago":"Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada, and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology. Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017.","ama":"Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017","ista":"Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. 175(5), 791–802.","ieee":"S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg, “Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller University Press, pp. 791–802, 2006.","apa":"Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg, C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200606017"},"page":"791 - 802","date_published":"2006-12-04T00:00:00Z","doi":"10.1083/jcb.200606017","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Wnt11 is a key signal, determining cell polarization and migration during vertebrate gastrulation. It is known that Wnt11 functionally interacts with several signaling components, the homologues of which control planar cell polarity in Drosophila melanogaster. Although in D. melanogaster these components are thought to polarize cells by asymmetrically localizing at the plasma membrane, it is not yet clear whether their subcellular localization plays a similarly important role in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase cell contact persistence. This increase in cell contact persistence is mediated by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo at the plasma membrane, and it does not require the activity of further downstream effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence to coordinate cell movements during gastrulation."}],"publist_id":"1980","issue":"5","extern":"1","_id":"4140","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane","status":"public","intvolume":" 175","publisher":"Rockefeller University Press","author":[{"full_name":"Witzel, Sabine","first_name":"Sabine","last_name":"Witzel"},{"last_name":"Zimyanin","first_name":"Vitaly","full_name":"Zimyanin, Vitaly"},{"full_name":"Carreira Barbosa, Filipa","last_name":"Carreira Barbosa","first_name":"Filipa"},{"full_name":"Tada, Masazumi","last_name":"Tada","first_name":"Masazumi"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"date_updated":"2021-01-12T07:54:48Z","date_created":"2018-12-11T12:07:11Z","volume":175,"oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4145","year":"2006","title":"Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid","status":"public","publication_status":"published","publisher":"Informa Healthcare","intvolume":" 41","author":[{"full_name":"Tonelli, Davide","first_name":"Davide","last_name":"Tonelli"},{"full_name":"Calegari, Frederico","last_name":"Calegari","first_name":"Frederico"},{"full_name":"Fei, Ji","first_name":"Ji","last_name":"Fei"},{"full_name":"Nomura, Tadashi","last_name":"Nomura","first_name":"Tadashi"},{"last_name":"Osumi","first_name":"Noriko","full_name":"Osumi, Noriko"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Huttner, Wieland","first_name":"Wieland","last_name":"Huttner"}],"date_updated":"2021-01-12T07:54:50Z","date_created":"2018-12-11T12:07:12Z","volume":41,"oa_version":"None","type":"journal_article","abstract":[{"text":"The detection of microRNAs (miRNAs) at single-cell resolution is important for studying the role of these posttranscriptional regulators. Here, we use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics of specific miRNAs in individual live cells. This approach reveals, for example, that in the developing mouse central nervous system,, miR-124a is expressed not only in postmitotic neurons but also in neuronal progenitor cells. Collectively, our results demonstrate that acute administration of DFRS plasmids.offers an alternative to previous in situ hybridization and transgenic approaches and allows the monitoring of miRNA appearance and disappearance in defined cell lineages during vertebrate development.","lang":"eng"}],"issue":"6","publist_id":"1974","extern":"1","publication":"Biotechniques","citation":{"ieee":"D. Tonelli et al., “Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732, 2006.","apa":"Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P. J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296","ista":"Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 41(6), 727–732.","ama":"Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in developing vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296","chicago":"Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi, Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296.","short":"D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg, W. Huttner, Biotechniques 41 (2006) 727–732.","mla":"Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.” Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296."},"page":"727 - 732","doi":"10.2144/000112296","date_published":"2006-12-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","month":"12","article_processing_charge":"No"},{"citation":{"short":"V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J. Heisenberg, Journal of Cell Science 119 (2006) 2073–2083.","mla":"Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no. 10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928.","chicago":"Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928.","ama":"Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928","ieee":"V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P. J. Heisenberg, “Identification of regulators of germ layer morphogenesis using proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company of Biologists, pp. 2073–2083, 2006.","apa":"Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02928","ista":"Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ. 2006. Identification of regulators of germ layer morphogenesis using proteomics in zebrafish. Journal of Cell Science. 119(10), 2073–2083."},"publication":"Journal of Cell Science","page":"2073 - 2083","date_published":"2006-05-15T00:00:00Z","doi":"10.1242/jcs.02928","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"05","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4176","year":"2006","intvolume":" 119","publisher":"Company of Biologists","publication_status":"published","status":"public","title":"Identification of regulators of germ layer morphogenesis using proteomics in zebrafish","author":[{"first_name":"Vinzenz","last_name":"Link","full_name":"Link, Vinzenz"},{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"full_name":"Castanon, Irinka","last_name":"Castanon","first_name":"Irinka"},{"full_name":"Stockinger, Petra","last_name":"Stockinger","first_name":"Petra"},{"full_name":"Shevchenko, Andrej","first_name":"Andrej","last_name":"Shevchenko"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"volume":119,"oa_version":"None","date_updated":"2021-01-12T07:55:04Z","date_created":"2018-12-11T12:07:24Z","type":"journal_article","issue":"10","publist_id":"1944","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, a well-orchestrated series of morphogenetic changes leads to the formation of the three germ layers: the ectoderm, mesoderm and endoderm. The analysis of gene expression patterns during gastrulation has been central to the identification of genes involved in germ layer formation. However, many proteins are regulated on a translational or post-translational level and are thus undetectable by gene expression analysis. Therefore, we developed a 2D-gel-based comparative proteomic approach to target proteins involved in germ layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and mesendodermal progenitor cells were compared and 35 significantly regulated proteins were identified by mass spectrometry, including several proteins with predicted functions in cytoskeletal organization. A comparison of our proteomic results with data obtained in an accompanying microarray-based gene expression analysis revealed no significant overlap, confirming the complementary nature of proteomics and transcriptomics. The regulation of ezrin2, which was identified based on a reduction in spot intensity in mesendodermal cells, was independently validated. Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal cells and is required for proper germ layer morphogenesis. We demonstrate the feasibility of proteomics in zebrafish, concluding that proteomics is a valuable tool for analysis of early development."}],"extern":"1"},{"publication_status":"published","status":"public","title":"Proteomics of early zebrafish embryos","publisher":"BioMed Central","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4173","year":"2006","date_updated":"2021-01-12T07:55:02Z","date_created":"2018-12-11T12:07:23Z","oa_version":"None","volume":6,"author":[{"full_name":"Link, Vinzenz","first_name":"Vinzenz","last_name":"Link"},{"full_name":"Shevchenko, Andrej","last_name":"Shevchenko","first_name":"Andrej"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Background: Zebrafish (D. rerio) has become a powerful and widely used model system for the analysis of vertebrate embryogenesis and organ development. While genetic methods are readily available in zebrafish, protocols for two dimensional (2D) gel electrophoresis and proteomics have yet to be developed. Results: As a prerequisite to carry out proteomic experiments with early zebrafish embryos, we developed a method to efficiently remove the yolk from large batches of embryos. This method enabled high resolution 2D gel electrophoresis and improved Western blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish from sample preparation to mass spectrometry (MS), including a comparison of databases for MS identification of zebrafish proteins. Conclusion: The provided protocols for proteomic analysis of early embryos enable research to be taken in novel directions in embryogenesis."}],"publist_id":"1945","page":"1 - 9","publication":"BMC Developmental Biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos. BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1","apa":"Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1","ieee":"V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006.","ista":"Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish embryos. BMC Developmental Biology. 6, 1–9.","short":"V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006) 1–9.","mla":"Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1.","chicago":"Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central, 2006. https://doi.org/10.1186/1471-213X-6-1."},"main_file_link":[{"url":"http://www.biomedcentral.com/1471-213X/6/1","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/1471-213X-6-1","date_published":"2006-01-13T00:00:00Z","day":"13","month":"01","article_processing_charge":"No"},{"article_processing_charge":"No","day":"01","month":"04","language":[{"iso":"eng"}],"doi":"10.1002/dvdy.20692","date_published":"2006-04-01T00:00:00Z","page":"928 - 933","citation":{"ieee":"T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis and visualization of cell movement in the developing zebrafish brain,” Developmental Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006.","apa":"Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M. (2006). Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692","ista":"Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 235(4), 928–933.","ama":"Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization of cell movement in the developing zebrafish brain. Developmental Dynamics. 2006;235(4):928-933. doi:10.1002/dvdy.20692","chicago":"Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg, and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692.","short":"T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental Dynamics 235 (2006) 928–933.","mla":"Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no. 4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692."},"publication":"Developmental Dynamics","extern":"1","publist_id":"1940","issue":"4","abstract":[{"text":"Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":235,"date_updated":"2021-01-12T07:55:04Z","date_created":"2018-12-11T12:07:25Z","author":[{"first_name":"Tobias","last_name":"Langenberg","full_name":"Langenberg, Tobias"},{"full_name":"Dracz, Tadeusz","last_name":"Dracz","first_name":"Tadeusz"},{"first_name":"Andrew","last_name":"Oates","full_name":"Oates, Andrew"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Michael","last_name":"Brand","full_name":"Brand, Michael"}],"publisher":"Wiley-Blackwell","intvolume":" 235","publication_status":"published","status":"public","title":"Analysis and visualization of cell movement in the developing zebrafish brain","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4178","year":"2006"},{"author":[{"full_name":"Köppen, Mathias","last_name":"Köppen","first_name":"Mathias"},{"full_name":"Fernández, Beatriz","last_name":"Fernández","first_name":"Beatriz"},{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"full_name":"Jacinto, António","first_name":"António","last_name":"Jacinto"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2018-12-11T12:07:27Z","date_updated":"2021-01-12T07:55:08Z","volume":133,"oa_version":"None","year":"2006","_id":"4184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila","publisher":"Company of Biologists","intvolume":" 133","abstract":[{"lang":"eng","text":"Epithelial morphogenesis depends on coordinated changes in cell shape, a process that is still poorly understood. During zebrafish epiboly and Drosophila dorsal closure, cell-shape changes at the epithelial margin are of critical importance. Here evidence is provided for a conserved mechanism of local actin and myosin 2 recruitment during theses events. It was found that during epiboly of the zebrafish embryo, the movement of the outer epithelium (enveloping layer) over the yolk cell surface involves the constriction of marginal cells. This process depends on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly, in Drosophila, actin and myosin 2 localization and cell constriction at the margin of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus, this study has characterized a conserved mechanism underlying coordinated cell-shape changes during epithelial morphogenesis."}],"issue":"14","publist_id":"1935","extern":"1","type":"journal_article","doi":"doi: 10.1242/dev.02439","date_published":"2006-07-15T00:00:00Z","language":[{"iso":"eng"}],"publication":"Development","citation":{"ieee":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,” Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006.","apa":"Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P. J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439","ista":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 133(14), 2671–2681.","ama":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila. Development. 2006;133(14):2671-2681. doi:doi: 10.1242/dev.02439","chicago":"Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development. Company of Biologists, 2006. https://doi.org/doi: 10.1242/dev.02439.","short":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development 133 (2006) 2671–2681.","mla":"Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company of Biologists, 2006, pp. 2671–81, doi:doi: 10.1242/dev.02439."},"page":"2671 - 2681","month":"07","day":"15","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2006.09.023","date_published":"2006-11-06T00:00:00Z","page":"613 - 627","citation":{"chicago":"Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei, Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg, and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006. https://doi.org/10.1016/j.devcel.2006.09.023.","mla":"Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol. 11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.","short":"H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami, L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627.","ista":"Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K, Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 11(5), 613–627.","apa":"Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami, K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2006.09.023","ieee":"H. Blaser et al., “Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow,” Developmental Cell, vol. 11, no. 5. Cell Press, pp. 613–627, 2006.","ama":"Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow. Developmental Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023"},"publication":"Developmental Cell","article_processing_charge":"No","day":"06","month":"11","volume":11,"oa_version":"None","date_updated":"2021-01-12T07:55:23Z","date_created":"2018-12-11T12:07:39Z","author":[{"first_name":"Heiko","last_name":"Blaser","full_name":"Blaser, Heiko"},{"full_name":"Reichman Fried, Michal","last_name":"Reichman Fried","first_name":"Michal"},{"full_name":"Castanon, Irinka","first_name":"Irinka","last_name":"Castanon"},{"last_name":"Dumstrei","first_name":"Karin","full_name":"Dumstrei, Karin"},{"full_name":"Marlow, Florence","first_name":"Florence","last_name":"Marlow"},{"first_name":"Koichi","last_name":"Kawakami","full_name":"Kawakami, Koichi"},{"first_name":"Lilianna","last_name":"Solnica Krezel","full_name":"Solnica Krezel, Lilianna"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"publisher":"Cell Press","intvolume":" 11","publication_status":"published","title":"Migration of zebrafish primordial germ cells: A role for myosin contraction and cytoplasmic flow","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"4218","year":"2006","extern":"1","issue":"5","publist_id":"1898","abstract":[{"text":"The molecular and cellular mechanisms governing cell motility and directed migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate that zebrafish primordial germ cells whose migration is guided by SDF-1 generate bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed at sites of higher levels of free calcium where activation of myosin contraction occurs. Separation of the acto-myosin cortex from the plasma membrane at these sites is followed by a flow of cytoplasm into the forming bleb. We propose that polarized activation of the receptor CXCR4 leads to a rise in free calcium that in turn activates myosin contraction in the part of the cell responding to higher levels of the ligand SDF-1. The biased formation of new protrusions in a particular region of the cell in response to SDF-1 defines the leading edge and the direction of cell migration.","lang":"eng"}],"type":"journal_article"},{"month":"01","day":"01","article_processing_charge":"No","page":"245 - 256","publication":"Journal of Theoretical Biology","citation":{"chicago":"Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802.","short":"H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256.","mla":"de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.” Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56, doi:3802.","ieee":"H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,” Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256, 2006.","apa":"de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. Elsevier. https://doi.org/3802","ista":"de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 238(2), 245–256.","ama":"de Vladar H. Density-dependence as a size-independent regulatory mechanism. Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802"},"language":[{"iso":"eng"}],"date_published":"2006-01-01T00:00:00Z","doi":"3802","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the Population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population. (c) 2005 Elsevier Ltd. All rights reserved."}],"issue":"2","publist_id":"1878","status":"public","title":"Density-dependence as a size-independent regulatory mechanism","publication_status":"published","intvolume":" 238","publisher":"Elsevier","year":"2006","_id":"4237","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:55:31Z","date_created":"2018-12-11T12:07:46Z","volume":238,"oa_version":"None","author":[{"full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar"}]},{"author":[{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold","full_name":"Harold Vladar"},{"last_name":"González","first_name":"J.","full_name":"González,J. A"}],"date_created":"2018-12-11T12:07:45Z","date_updated":"2021-01-12T07:55:30Z","year":"2006","_id":"4235","status":"public","title":"Dynamic response of cancer under the influence of immunological activity and therapy","publication_status":"published","publisher":"Elsevier","publist_id":"1879","extern":1,"type":"journal_article","date_published":"2006-01-01T00:00:00Z","publication":"Journal of Theoretical Biology","citation":{"short":"H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109.","mla":"de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, Elsevier, 2006, pp. 91–109.","chicago":"Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2006.","ama":"de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109.","ieee":"H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology. Elsevier, pp. 91–109, 2006.","apa":"de Vladar, H., & González, J. (2006). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier.","ista":"de Vladar H, González J. 2006. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology., 91–109."},"quality_controlled":0,"page":"91 - 109","day":"01","month":"01"},{"day":"01","month":"07","doi":"10.1534/genetics.106.058586 ","date_published":"2006-07-01T00:00:00Z","publication":"Genetics","citation":{"chicago":"Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics. Genetics Society of America, 2006. https://doi.org/10.1534/genetics.106.058586 .","short":"D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811.","mla":"Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America, 2006, pp. 1793–811, doi:10.1534/genetics.106.058586 .","apa":"Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586 ","ieee":"D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of recombination,” Genetics, vol. 173, no. 3. Genetics Society of America, pp. 1793–1811, 2006.","ista":"Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination. Genetics. 173(3), 1793–1811.","ama":"Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination. Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586 "},"quality_controlled":0,"page":"1793 - 1811","abstract":[{"text":"In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.","lang":"eng"}],"publist_id":"1854","issue":"3","extern":1,"type":"journal_article","author":[{"last_name":"Roze","first_name":"Denis","full_name":"Roze, Denis"},{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_updated":"2021-01-12T07:55:36Z","date_created":"2018-12-11T12:07:50Z","volume":173,"year":"2006","_id":"4248","publication_status":"published","title":"The Hill-Robertson effect and the evolution of recombination","status":"public","intvolume":" 173","publisher":"Genetics Society of America"},{"month":"08","day":"22","doi":"10.1016/j.cub.2006.07.032","date_published":"2006-08-22T00:00:00Z","citation":{"chicago":"Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.","mla":"Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?” Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.","short":"N.H. Barton, Current Biology 16 (2006) 647–650.","ista":"Barton NH. 2006. Evolutionary Biology: How did the human species form? Current Biology. 16(16), 647–650.","apa":"Barton, N. H. (2006). Evolutionary Biology: How did the human species form? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032","ieee":"N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.","ama":"Barton NH. Evolutionary Biology: How did the human species form? Current Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032"},"publication":"Current Biology","page":"647 - 650","quality_controlled":0,"publist_id":"1850","issue":"16","abstract":[{"text":"A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation.","lang":"eng"}],"extern":1,"type":"review","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton"}],"volume":16,"date_created":"2018-12-11T12:07:51Z","date_updated":"2019-04-26T07:22:41Z","year":"2006","_id":"4250","intvolume":" 16","publisher":"Cell Press","publication_status":"published","title":"Evolutionary Biology: How did the human species form?","status":"public"},{"publist_id":"1097","extern":1,"type":"conference","alternative_title":["LNCS 3855"],"author":[{"first_name":"Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Wies"},{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"},{"last_name":"Lam","first_name":"Patrick","full_name":"Lam,Patrick"},{"full_name":"Podelski,Andreas","first_name":"Andreas","last_name":"Podelski"},{"full_name":"Rinard,Martin","first_name":"Martin","last_name":"Rinard"}],"date_updated":"2021-01-12T07:56:23Z","date_created":"2018-12-11T12:08:27Z","_id":"4359","year":"2006","status":"public","publication_status":"published","title":"Field Constraint Analysis","publisher":"Springer","day":"01","month":"01","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"date_published":"2006-01-01T00:00:00Z","doi":"1551","citation":{"ieee":"T. Wies, V. Kuncak, P. Lam, A. Podelski, and M. Rinard, “Field Constraint Analysis,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, 2006, pp. 157–173.","apa":"Wies, T., Kuncak, V., Lam, P., Podelski, A., & Rinard, M. (2006). Field Constraint Analysis (pp. 157–173). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Springer. https://doi.org/1551","ista":"Wies T, Kuncak V, Lam P, Podelski A, Rinard M. 2006. Field Constraint Analysis. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS 3855, , 157–173.","ama":"Wies T, Kuncak V, Lam P, Podelski A, Rinard M. Field Constraint Analysis. In: Springer; 2006:157-173. doi:1551","chicago":"Wies, Thomas, Viktor Kuncak, Patrick Lam, Andreas Podelski, and Martin Rinard. “Field Constraint Analysis,” 157–73. Springer, 2006. https://doi.org/1551.","short":"T. Wies, V. Kuncak, P. Lam, A. Podelski, M. Rinard, in:, Springer, 2006, pp. 157–173.","mla":"Wies, Thomas, et al. Field Constraint Analysis. Springer, 2006, pp. 157–73, doi:1551."},"quality_controlled":0,"page":"157 - 173"},{"author":[{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"full_name":"Dejan Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","last_name":"Nickovic"},{"last_name":"Pnueli","first_name":"Amir","full_name":"Pnueli,Amir"}],"date_updated":"2021-01-12T07:56:29Z","date_created":"2018-12-11T12:08:31Z","_id":"4373","year":"2006","publisher":"Springer","title":"Real Time Temporal Logic: Past, Present, Future","status":"public","publication_status":"published","publist_id":"1084","extern":1,"type":"conference","alternative_title":["LNCS"],"doi":"1571","date_published":"2006-01-23T00:00:00Z","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"citation":{"chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Real Time Temporal Logic: Past, Present, Future,” 2–16. Springer, 2006. https://doi.org/1571.","mla":"Maler, Oded, et al. Real Time Temporal Logic: Past, Present, Future. Springer, 2006, pp. 2–16, doi:1571.","short":"O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 2–16.","ista":"Maler O, Nickovic D, Pnueli A. 2006. Real Time Temporal Logic: Past, Present, Future. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 2–16.","apa":"Maler, O., Nickovic, D., & Pnueli, A. (2006). Real Time Temporal Logic: Past, Present, Future (pp. 2–16). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1571","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “Real Time Temporal Logic: Past, Present, Future,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 2–16.","ama":"Maler O, Nickovic D, Pnueli A. Real Time Temporal Logic: Past, Present, Future. In: Springer; 2006:2-16. doi:1571"},"page":"2 - 16","quality_controlled":0,"month":"01","day":"23"},{"publist_id":"1085","extern":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"full_name":"Dejan Nickovic","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir","last_name":"Pnueli","full_name":"Pnueli,Amir"}],"date_created":"2018-12-11T12:08:31Z","date_updated":"2021-01-12T07:56:30Z","_id":"4374","year":"2006","publication_status":"published","title":"From MITL to Timed Automata","status":"public","publisher":"Springer","day":"19","month":"10","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"date_published":"2006-10-19T00:00:00Z","doi":"1570","citation":{"ista":"Maler O, Nickovic D, Pnueli A. 2006. From MITL to Timed Automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 274–289.","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “From MITL to Timed Automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, pp. 274–289.","apa":"Maler, O., Nickovic, D., & Pnueli, A. (2006). From MITL to Timed Automata (pp. 274–289). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1570","ama":"Maler O, Nickovic D, Pnueli A. From MITL to Timed Automata. In: Springer; 2006:274-289. doi:1570","chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “From MITL to Timed Automata,” 274–89. Springer, 2006. https://doi.org/1570.","mla":"Maler, Oded, et al. From MITL to Timed Automata. Springer, 2006, pp. 274–89, doi:1570.","short":"O. Maler, D. Nickovic, A. Pnueli, in:, Springer, 2006, pp. 274–289."},"quality_controlled":0,"page":"274 - 289"},{"intvolume":" 4144","publisher":"Springer","title":"Antichains: A new algorithm for checking universality of finite automata","status":"public","publication_status":"published","acknowledgement":"This research was supported in part by the NSF grants CCR-0234690 and CCR-0225610, and the Belgian FNRS grant 2.4530.02 of the FRFC project “Centre Fédéré en Vérification.”","_id":"4406","year":"2006","volume":4144,"date_updated":"2021-01-12T07:56:45Z","date_created":"2018-12-11T12:08:41Z","author":[{"last_name":"De Wulf","first_name":"Martin","full_name":"De Wulf, Martin"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean-François"}],"alternative_title":["LNCS"],"type":"conference","extern":1,"publist_id":"326","abstract":[{"lang":"eng","text":"We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata."}],"page":"17 - 30","quality_controlled":0,"citation":{"ista":"De Wulf M, Doyen L, Henzinger TA, Raskin J. 2006. Antichains: A new algorithm for checking universality of finite automata. CAV: Computer Aided Verification, LNCS, vol. 4144, 17–30.","apa":"De Wulf, M., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Antichains: A new algorithm for checking universality of finite automata (Vol. 4144, pp. 17–30). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_5","ieee":"M. De Wulf, L. Doyen, T. A. Henzinger, and J. Raskin, “Antichains: A new algorithm for checking universality of finite automata,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 17–30.","ama":"De Wulf M, Doyen L, Henzinger TA, Raskin J. Antichains: A new algorithm for checking universality of finite automata. In: Vol 4144. Springer; 2006:17-30. doi:10.1007/11817963_5","chicago":"De Wulf, Martin, Laurent Doyen, Thomas A Henzinger, and Jean Raskin. “Antichains: A New Algorithm for Checking Universality of Finite Automata,” 4144:17–30. Springer, 2006. https://doi.org/10.1007/11817963_5.","mla":"De Wulf, Martin, et al. Antichains: A New Algorithm for Checking Universality of Finite Automata. Vol. 4144, Springer, 2006, pp. 17–30, doi:10.1007/11817963_5.","short":"M. De Wulf, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006, pp. 17–30."},"date_published":"2006-08-08T00:00:00Z","doi":"10.1007/11817963_5","conference":{"name":"CAV: Computer Aided Verification"},"day":"08","month":"08"},{"day":"01","month":"01","conference":{"name":"ICALP: Automata, Languages and Programming"},"date_published":"2006-01-01T00:00:00Z","doi":"1543","citation":{"mla":"Alur, Rajeev, et al. Preserving Secrecy Under Refinement. Springer, 2006, pp. 107–18, doi:1543.","short":"R. Alur, P. Cerny, S. Zdancewic, in:, Springer, 2006, pp. 107–118.","chicago":"Alur, Rajeev, Pavol Cerny, and Steve Zdancewic. “Preserving Secrecy Under Refinement,” 107–18. Springer, 2006. https://doi.org/1543.","ama":"Alur R, Cerny P, Zdancewic S. Preserving Secrecy Under Refinement. In: Springer; 2006:107-118. doi:1543","ista":"Alur R, Cerny P, Zdancewic S. 2006. Preserving Secrecy Under Refinement. ICALP: Automata, Languages and Programming, LNCS, , 107–118.","ieee":"R. Alur, P. Cerny, and S. Zdancewic, “Preserving Secrecy Under Refinement,” presented at the ICALP: Automata, Languages and Programming, 2006, pp. 107–118.","apa":"Alur, R., Cerny, P., & Zdancewic, S. (2006). Preserving Secrecy Under Refinement (pp. 107–118). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/1543"},"quality_controlled":0,"page":"107 - 118","publist_id":"1054","extern":1,"type":"conference","alternative_title":["LNCS"],"author":[{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"},{"full_name":"Pavol Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol"},{"last_name":"Zdancewic","first_name":"Steve","full_name":"Zdancewic,Steve"}],"date_updated":"2021-01-12T07:56:42Z","date_created":"2018-12-11T12:08:40Z","year":"2006","_id":"4401","title":"Preserving Secrecy Under Refinement","status":"public","publication_status":"published","publisher":"Springer"},{"type":"conference","alternative_title":["LNCS"],"publist_id":"295","abstract":[{"text":"The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies.","lang":"eng"}],"extern":1,"_id":"4437","year":"2006","acknowledgement":"This research was supported in part by the Swiss National Science Foundation.","publisher":"Springer","intvolume":" 4207","publication_status":"published","status":"public","title":"Solving games without determinization","author":[{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"}],"volume":4207,"date_updated":"2021-01-12T07:56:58Z","date_created":"2018-12-11T12:08:51Z","month":"09","day":"20","citation":{"chicago":"Henzinger, Thomas A, and Nir Piterman. “Solving Games without Determinization,” 4207:395–410. Springer, 2006. https://doi.org/10.1007/11874683_26.","mla":"Henzinger, Thomas A., and Nir Piterman. Solving Games without Determinization. Vol. 4207, Springer, 2006, pp. 395–410, doi:10.1007/11874683_26.","short":"T.A. Henzinger, N. Piterman, in:, Springer, 2006, pp. 395–410.","ista":"Henzinger TA, Piterman N. 2006. Solving games without determinization. CSL: Computer Science Logic, LNCS, vol. 4207, 395–410.","apa":"Henzinger, T. A., & Piterman, N. (2006). Solving games without determinization (Vol. 4207, pp. 395–410). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_26","ieee":"T. A. Henzinger and N. Piterman, “Solving games without determinization,” presented at the CSL: Computer Science Logic, 2006, vol. 4207, pp. 395–410.","ama":"Henzinger TA, Piterman N. Solving games without determinization. In: Vol 4207. Springer; 2006:395-410. doi:10.1007/11874683_26"},"page":"395 - 410","quality_controlled":0,"date_published":"2006-09-20T00:00:00Z","doi":"10.1007/11874683_26","conference":{"name":"CSL: Computer Science Logic"}},{"type":"conference","publist_id":"294","abstract":[{"text":"We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments.","lang":"eng"}],"extern":1,"year":"2006","_id":"4436","publisher":"IEEE","title":"An interface algebra for real-time components","status":"public","publication_status":"published","author":[{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Slobodan","last_name":"Matic","full_name":"Matic, Slobodan"}],"date_updated":"2021-01-12T07:56:57Z","date_created":"2018-12-11T12:08:50Z","month":"04","day":"24","citation":{"ama":"Henzinger TA, Matic S. An interface algebra for real-time components. In: IEEE; 2006:253-266. doi:10.1109/RTAS.2006.11","apa":"Henzinger, T. A., & Matic, S. (2006). An interface algebra for real-time components (pp. 253–266). Presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, IEEE. https://doi.org/10.1109/RTAS.2006.11","ieee":"T. A. Henzinger and S. Matic, “An interface algebra for real-time components,” presented at the RTAS: Real-time and Embedded Technology and Applications Symposium, 2006, pp. 253–266.","ista":"Henzinger TA, Matic S. 2006. An interface algebra for real-time components. RTAS: Real-time and Embedded Technology and Applications Symposium, 253–266.","short":"T.A. Henzinger, S. Matic, in:, IEEE, 2006, pp. 253–266.","mla":"Henzinger, Thomas A., and Slobodan Matic. An Interface Algebra for Real-Time Components. IEEE, 2006, pp. 253–66, doi:10.1109/RTAS.2006.11.","chicago":"Henzinger, Thomas A, and Slobodan Matic. “An Interface Algebra for Real-Time Components,” 253–66. IEEE, 2006. https://doi.org/10.1109/RTAS.2006.11."},"page":"253 - 266","quality_controlled":0,"date_published":"2006-04-24T00:00:00Z","doi":"10.1109/RTAS.2006.11","conference":{"name":"RTAS: Real-time and Embedded Technology and Applications Symposium"}},{"month":"09","day":"19","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"date_published":"2006-09-19T00:00:00Z","doi":"10.1007/11867340_1","quality_controlled":0,"page":"1 - 17","citation":{"ama":"Henzinger TA, Prabhu V. Timed alternating-time temporal logic. In: Vol 4202. Springer; 2006:1-17. doi:10.1007/11867340_1","ieee":"T. A. Henzinger and V. Prabhu, “Timed alternating-time temporal logic,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2006, vol. 4202, pp. 1–17.","apa":"Henzinger, T. A., & Prabhu, V. (2006). Timed alternating-time temporal logic (Vol. 4202, pp. 1–17). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/11867340_1","ista":"Henzinger TA, Prabhu V. 2006. Timed alternating-time temporal logic. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 4202, 1–17.","short":"T.A. Henzinger, V. Prabhu, in:, Springer, 2006, pp. 1–17.","mla":"Henzinger, Thomas A., and Vinayak Prabhu. Timed Alternating-Time Temporal Logic. Vol. 4202, Springer, 2006, pp. 1–17, doi:10.1007/11867340_1.","chicago":"Henzinger, Thomas A, and Vinayak Prabhu. “Timed Alternating-Time Temporal Logic,” 4202:1–17. Springer, 2006. https://doi.org/10.1007/11867340_1."},"extern":1,"abstract":[{"lang":"eng","text":"We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision."}],"publist_id":"296","alternative_title":["LNCS"],"type":"conference","date_updated":"2021-01-12T07:56:56Z","date_created":"2018-12-11T12:08:49Z","volume":4202,"author":[{"full_name":"Thomas Henzinger","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prabhu, Vinayak S","first_name":"Vinayak","last_name":"Prabhu"}],"title":"Timed alternating-time temporal logic","publication_status":"published","status":"public","intvolume":" 4202","publisher":"Springer","acknowledgement":"This research was supported in part by the NSF grants CCR-0208875, CCR-0225610, and CCR-0234690.","_id":"4432","year":"2006"},{"author":[{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Sifakis","first_name":"Joseph","full_name":"Sifakis, Joseph"}],"volume":4085,"date_updated":"2021-01-12T07:56:55Z","date_created":"2018-12-11T12:08:49Z","_id":"4431","acknowledgement":"Supported in part by the ARTIST2 European Network of Excellence on Embedded Systems Design, by the NSF ITR Center on Hybrid and Embedded Software Systems (CHESS), and by the SNSF NCCR on Mobile Information and Communication Systems (MICS).","year":"2006","publisher":"Springer","intvolume":" 4085","status":"public","publication_status":"published","title":"The embedded systems design challenge","publist_id":"301","abstract":[{"lang":"eng","text":"We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science."}],"extern":1,"type":"conference","alternative_title":["LNCS"],"date_published":"2006-08-10T00:00:00Z","doi":"10.1007/11813040_1","conference":{"name":"FM: Formal Methods"},"citation":{"chicago":"Henzinger, Thomas A, and Joseph Sifakis. “The Embedded Systems Design Challenge,” 4085:1–15. Springer, 2006. https://doi.org/10.1007/11813040_1.","short":"T.A. Henzinger, J. Sifakis, in:, Springer, 2006, pp. 1–15.","mla":"Henzinger, Thomas A., and Joseph Sifakis. The Embedded Systems Design Challenge. Vol. 4085, Springer, 2006, pp. 1–15, doi:10.1007/11813040_1.","ieee":"T. A. Henzinger and J. Sifakis, “The embedded systems design challenge,” presented at the FM: Formal Methods, 2006, vol. 4085, pp. 1–15.","apa":"Henzinger, T. A., & Sifakis, J. (2006). The embedded systems design challenge (Vol. 4085, pp. 1–15). Presented at the FM: Formal Methods, Springer. https://doi.org/10.1007/11813040_1","ista":"Henzinger TA, Sifakis J. 2006. The embedded systems design challenge. FM: Formal Methods, LNCS, vol. 4085, 1–15.","ama":"Henzinger TA, Sifakis J. The embedded systems design challenge. In: Vol 4085. Springer; 2006:1-15. doi:10.1007/11813040_1"},"page":"1 - 15","quality_controlled":0,"month":"08","day":"10"},{"day":"28","month":"03","doi":"10.1016/j.tcs.2005.11.015","date_published":"2006-03-28T00:00:00Z","citation":{"chicago":"Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2005.11.015.","mla":"Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of the Mu-Calculus.” Theoretical Computer Science, vol. 354, no. 2, Elsevier, 2006, pp. 173–86, doi:10.1016/j.tcs.2005.11.015.","short":"T.A. Henzinger, O. Kupferman, R. Majumdar, Theoretical Computer Science 354 (2006) 173–186.","ista":"Henzinger TA, Kupferman O, Majumdar R. 2006. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 354(2), 173–186.","apa":"Henzinger, T. A., Kupferman, O., & Majumdar, R. (2006). On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2005.11.015","ieee":"T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential fragments of the mu-calculus,” Theoretical Computer Science, vol. 354, no. 2. Elsevier, pp. 173–186, 2006.","ama":"Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments of the mu-calculus. Theoretical Computer Science. 2006;354(2):173-186. doi:10.1016/j.tcs.2005.11.015"},"publication":"Theoretical Computer Science","page":"173 - 186","quality_controlled":0,"issue":"2","publist_id":"276","abstract":[{"lang":"eng","text":"One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternation-free fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment."}],"extern":1,"type":"journal_article","author":[{"full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"},{"full_name":"Majumdar, Ritankar S","first_name":"Ritankar","last_name":"Majumdar"}],"volume":354,"date_created":"2018-12-11T12:08:55Z","date_updated":"2021-01-12T07:57:04Z","_id":"4451","year":"2006","publisher":"Elsevier","intvolume":" 354","status":"public","publication_status":"published","title":"On the universal and existential fragments of the mu-calculus"},{"extern":1,"abstract":[{"lang":"eng","text":"We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi."}],"publist_id":"206","type":"conference","date_created":"2018-12-11T12:09:18Z","date_updated":"2021-01-12T07:59:26Z","author":[{"first_name":"Bhargav","last_name":"Gulavani","full_name":"Gulavani, Bhargav S"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger"},{"full_name":"Kannan, Yamini","last_name":"Kannan","first_name":"Yamini"},{"full_name":"Nori, Aditya V","last_name":"Nori","first_name":"Aditya"},{"last_name":"Rajamani","first_name":"Sriram","full_name":"Rajamani, Sriram K"}],"title":"Synergy: A new algorithm for property checking","publication_status":"published","status":"public","publisher":"ACM","_id":"4523","year":"2006","day":"01","month":"01","conference":{"name":"FSE: Foundations of Software Engineering"},"date_published":"2006-01-01T00:00:00Z","doi":"10.1145/1181775.1181790","quality_controlled":0,"page":"117 - 127","citation":{"ama":"Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. Synergy: A new algorithm for property checking. In: ACM; 2006:117-127. doi:10.1145/1181775.1181790","ieee":"B. Gulavani, T. A. Henzinger, Y. Kannan, A. Nori, and S. Rajamani, “Synergy: A new algorithm for property checking,” presented at the FSE: Foundations of Software Engineering, 2006, pp. 117–127.","apa":"Gulavani, B., Henzinger, T. A., Kannan, Y., Nori, A., & Rajamani, S. (2006). Synergy: A new algorithm for property checking (pp. 117–127). Presented at the FSE: Foundations of Software Engineering, ACM. https://doi.org/10.1145/1181775.1181790","ista":"Gulavani B, Henzinger TA, Kannan Y, Nori A, Rajamani S. 2006. Synergy: A new algorithm for property checking. FSE: Foundations of Software Engineering, 117–127.","short":"B. Gulavani, T.A. Henzinger, Y. Kannan, A. Nori, S. Rajamani, in:, ACM, 2006, pp. 117–127.","mla":"Gulavani, Bhargav, et al. Synergy: A New Algorithm for Property Checking. ACM, 2006, pp. 117–27, doi:10.1145/1181775.1181790.","chicago":"Gulavani, Bhargav, Thomas A Henzinger, Yamini Kannan, Aditya Nori, and Sriram Rajamani. “Synergy: A New Algorithm for Property Checking,” 117–27. ACM, 2006. https://doi.org/10.1145/1181775.1181790."}},{"author":[{"last_name":"Ghosal","first_name":"Arkadeb","full_name":"Ghosal, Arkadeb"},{"full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Daniel","last_name":"Iercan","full_name":"Iercan, Daniel"},{"full_name":"Kirsch, Christoph M","last_name":"Kirsch","first_name":"Christoph"},{"full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni Vincentelli","first_name":"Alberto"}],"date_updated":"2021-01-12T07:59:27Z","date_created":"2018-12-11T12:09:18Z","_id":"4526","year":"2006","publisher":"ACM","publication_status":"published","status":"public","title":"A hierarchical coordination language for interacting real-time tasks","publist_id":"201","abstract":[{"lang":"eng","text":"We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller."}],"extern":1,"type":"conference","date_published":"2006-01-01T00:00:00Z","doi":"10.1145/1176887.1176907","conference":{"name":"EMSOFT: Embedded Software "},"citation":{"chicago":"Ghosal, Arkadeb, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, and Alberto Sangiovanni Vincentelli. “A Hierarchical Coordination Language for Interacting Real-Time Tasks,” 132–41. ACM, 2006. https://doi.org/10.1145/1176887.1176907.","short":"A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, A. Sangiovanni Vincentelli, in:, ACM, 2006, pp. 132–141.","mla":"Ghosal, Arkadeb, et al. A Hierarchical Coordination Language for Interacting Real-Time Tasks. ACM, 2006, pp. 132–41, doi:10.1145/1176887.1176907.","ieee":"A. Ghosal, T. A. Henzinger, D. Iercan, C. Kirsch, and A. Sangiovanni Vincentelli, “A hierarchical coordination language for interacting real-time tasks,” presented at the EMSOFT: Embedded Software , 2006, pp. 132–141.","apa":"Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., & Sangiovanni Vincentelli, A. (2006). A hierarchical coordination language for interacting real-time tasks (pp. 132–141). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1176887.1176907","ista":"Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. 2006. A hierarchical coordination language for interacting real-time tasks. EMSOFT: Embedded Software , 132–141.","ama":"Ghosal A, Henzinger TA, Iercan D, Kirsch C, Sangiovanni Vincentelli A. A hierarchical coordination language for interacting real-time tasks. In: ACM; 2006:132-141. doi:10.1145/1176887.1176907"},"page":"132 - 141","quality_controlled":0,"month":"01","day":"01"},{"quality_controlled":0,"page":"1675 - 1682","citation":{"apa":"Fisher, J., & Henzinger, T. A. (2006). Executable biology (pp. 1675–1682). Presented at the WSC: Winter Simulation Conference, IEEE. https://doi.org/10.1109/WSC.2006.322942","ieee":"J. Fisher and T. A. Henzinger, “Executable biology,” presented at the WSC: Winter Simulation Conference, 2006, pp. 1675–1682.","ista":"Fisher J, Henzinger TA. 2006. Executable biology. WSC: Winter Simulation Conference, 1675–1682.","ama":"Fisher J, Henzinger TA. Executable biology. In: IEEE; 2006:1675-1682. doi:10.1109/WSC.2006.322942","chicago":"Fisher, Jasmin, and Thomas A Henzinger. “Executable Biology,” 1675–82. IEEE, 2006. https://doi.org/10.1109/WSC.2006.322942.","short":"J. Fisher, T.A. Henzinger, in:, IEEE, 2006, pp. 1675–1682.","mla":"Fisher, Jasmin, and Thomas A. Henzinger. Executable Biology. IEEE, 2006, pp. 1675–82, doi:10.1109/WSC.2006.322942."},"conference":{"name":"WSC: Winter Simulation Conference"},"doi":"10.1109/WSC.2006.322942","date_published":"2006-12-03T00:00:00Z","month":"12","day":"03","title":"Executable biology","status":"public","publication_status":"published","publisher":"IEEE","_id":"4528","year":"2006","date_created":"2018-12-11T12:09:19Z","date_updated":"2021-01-12T07:59:28Z","author":[{"full_name":"Fisher, Jasmin","first_name":"Jasmin","last_name":"Fisher"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"type":"conference","extern":1,"abstract":[{"text":"Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models mathematical and computational - according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems executable biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.","lang":"eng"}],"publist_id":"197"},{"publication_status":"published","status":"public","title":"Finitary winning in omega-regular games","publisher":"Springer","intvolume":" 3920","_id":"4539","year":"2006","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF ITR grant CCR-0225610.","date_created":"2018-12-11T12:09:22Z","date_updated":"2021-01-12T07:59:32Z","volume":3920,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Krishnendu Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"}],"alternative_title":["LNCS"],"type":"conference","extern":1,"abstract":[{"lang":"eng","text":"Games on graphs with ω-regular objectives provide a model for the control and synthesis of reactive systems. Every ω-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Büchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett (fairness) objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound."}],"publist_id":"183","quality_controlled":0,"page":"257 - 271","citation":{"chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Finitary Winning in Omega-Regular Games,” 3920:257–71. Springer, 2006. https://doi.org/10.1007/11691372_17.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. Finitary Winning in Omega-Regular Games. Vol. 3920, Springer, 2006, pp. 257–71, doi:10.1007/11691372_17.","short":"K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 257–271.","ista":"Chatterjee K, Henzinger TA. 2006. Finitary winning in omega-regular games. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 3920, 257–271.","apa":"Chatterjee, K., & Henzinger, T. A. (2006). Finitary winning in omega-regular games (Vol. 3920, pp. 257–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. https://doi.org/10.1007/11691372_17","ieee":"K. Chatterjee and T. A. Henzinger, “Finitary winning in omega-regular games,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2006, vol. 3920, pp. 257–271.","ama":"Chatterjee K, Henzinger TA. Finitary winning in omega-regular games. In: Vol 3920. Springer; 2006:257-271. doi:10.1007/11691372_17"},"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"date_published":"2006-03-15T00:00:00Z","doi":"10.1007/11691372_17","day":"15","month":"03"},{"extern":1,"abstract":[{"lang":"eng","text":"A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives. These games lie in NP ∩ coNP. We present a strategy improvement algorithm for stochastic parity games; this is the first non-brute-force algorithm for solving these games. From the strategy improvement algorithm we obtain a randomized subexponential-time algorithm to solve such games."}],"publist_id":"184","alternative_title":["LNCS"],"type":"conference","date_updated":"2021-01-12T07:59:32Z","date_created":"2018-12-11T12:09:22Z","volume":3884,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"title":"Strategy improvement and randomized subexponential algorithms for stochastic parity games","publication_status":"published","status":"public","publisher":"Springer","intvolume":" 3884","_id":"4538","year":"2006","day":"14","month":"02","conference":{"name":"STACS: Theoretical Aspects of Computer Science"},"doi":"10.1007/11672142_42","date_published":"2006-02-14T00:00:00Z","quality_controlled":0,"page":"512 - 523","citation":{"chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games,” 3884:512–23. Springer, 2006. https://doi.org/10.1007/11672142_42.","short":"K. Chatterjee, T.A. Henzinger, in:, Springer, 2006, pp. 512–523.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement and Randomized Subexponential Algorithms for Stochastic Parity Games. Vol. 3884, Springer, 2006, pp. 512–23, doi:10.1007/11672142_42.","ieee":"K. Chatterjee and T. A. Henzinger, “Strategy improvement and randomized subexponential algorithms for stochastic parity games,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 512–523.","apa":"Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement and randomized subexponential algorithms for stochastic parity games (Vol. 3884, pp. 512–523). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_42","ista":"Chatterjee K, Henzinger TA. 2006. Strategy improvement and randomized subexponential algorithms for stochastic parity games. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 512–523.","ama":"Chatterjee K, Henzinger TA. Strategy improvement and randomized subexponential algorithms for stochastic parity games. In: Vol 3884. Springer; 2006:512-523. doi:10.1007/11672142_42"}},{"alternative_title":["LNCS"],"type":"conference","extern":1,"publist_id":"161","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple discounted reward objectives. Such MDPs occur in design problems where one wishes to simultaneously optimize several criteria, for example, latency and power. The possible trade-offs between the different objectives are characterized by the Pareto curve. We show that every Pareto-optimal point can be achieved by a memoryless strategy; however, unlike in the single-objective case, the memoryless strategy may require randomization. Moreover, we show that the Pareto curve can be approximated in polynomial time in the size of the MDP. Additionally, we study the problem if a given value vector is realizable by any strategy, and show that it can be decided in polynomial time; but the question whether it is realizable by a deterministic memoryless strategy is NP-complete. These results provide efficient algorithms for design exploration in MDP models with multiple objectives.\nThis research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202. ","lang":"eng"}],"publisher":"Springer","intvolume":" 3884","title":"Markov decision processes with multiple objectives","publication_status":"published","status":"public","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, and the NSF grants CCR-0225610, CCR-0234690, and CCR-0427202.","_id":"4551","year":"2006","volume":3884,"date_updated":"2021-01-12T07:59:38Z","date_created":"2018-12-11T12:09:26Z","author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger"}],"day":"14","month":"02","page":"325 - 336","quality_controlled":0,"citation":{"ista":"Chatterjee K, Majumdar R, Henzinger TA. 2006. Markov decision processes with multiple objectives. STACS: Theoretical Aspects of Computer Science, LNCS, vol. 3884, 325–336.","ieee":"K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Markov decision processes with multiple objectives,” presented at the STACS: Theoretical Aspects of Computer Science, 2006, vol. 3884, pp. 325–336.","apa":"Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2006). Markov decision processes with multiple objectives (Vol. 3884, pp. 325–336). Presented at the STACS: Theoretical Aspects of Computer Science, Springer. https://doi.org/10.1007/11672142_26","ama":"Chatterjee K, Majumdar R, Henzinger TA. Markov decision processes with multiple objectives. In: Vol 3884. Springer; 2006:325-336. doi:10.1007/11672142_26","chicago":"Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Markov Decision Processes with Multiple Objectives,” 3884:325–36. Springer, 2006. https://doi.org/10.1007/11672142_26.","mla":"Chatterjee, Krishnendu, et al. Markov Decision Processes with Multiple Objectives. Vol. 3884, Springer, 2006, pp. 325–36, doi:10.1007/11672142_26.","short":"K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2006, pp. 325–336."},"doi":"10.1007/11672142_26","date_published":"2006-02-14T00:00:00Z","conference":{"name":"STACS: Theoretical Aspects of Computer Science"}},{"extern":1,"issue":"1-2","publist_id":"164","abstract":[{"lang":"eng","text":"In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it sometimes suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of ω-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium."}],"type":"journal_article","volume":365,"date_updated":"2021-01-12T07:59:38Z","date_created":"2018-12-11T12:09:26Z","author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"first_name":"Marcin","last_name":"Jurdziński","full_name":"Jurdziński, Marcin"}],"publisher":"Elsevier","intvolume":" 365","status":"public","title":"Games with secure equilibria","publication_status":"published","year":"2006","_id":"4550","day":"07","month":"08","date_published":"2006-08-07T00:00:00Z","doi":"10.1016/j.tcs.2006.07.032","page":"67 - 82","quality_controlled":0,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria.” Theoretical Computer Science. Elsevier, 2006. https://doi.org/10.1016/j.tcs.2006.07.032.","mla":"Chatterjee, Krishnendu, et al. “Games with Secure Equilibria.” Theoretical Computer Science, vol. 365, no. 1–2, Elsevier, 2006, pp. 67–82, doi:10.1016/j.tcs.2006.07.032.","short":"K. Chatterjee, T.A. Henzinger, M. Jurdziński, Theoretical Computer Science 365 (2006) 67–82.","ista":"Chatterjee K, Henzinger TA, Jurdziński M. 2006. Games with secure equilibria. Theoretical Computer Science. 365(1–2), 67–82.","apa":"Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2006). Games with secure equilibria. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2006.07.032","ieee":"K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” Theoretical Computer Science, vol. 365, no. 1–2. Elsevier, pp. 67–82, 2006.","ama":"Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. Theoretical Computer Science. 2006;365(1-2):67-82. doi:10.1016/j.tcs.2006.07.032"},"publication":"Theoretical Computer Science"},{"month":"09","day":"01","citation":{"short":"K. Chatterjee, L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, IEEE, 2006, pp. 179–188.","mla":"Chatterjee, Krishnendu, et al. Compositional Quantitative Reasoning. IEEE, 2006, pp. 179–88, doi:10.1109/QEST.2006.11.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Compositional Quantitative Reasoning,” 179–88. IEEE, 2006. https://doi.org/10.1109/QEST.2006.11.","ama":"Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Compositional quantitative reasoning. In: IEEE; 2006:179-188. doi:10.1109/QEST.2006.11","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Compositional quantitative reasoning,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 179–188.","apa":"Chatterjee, K., De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2006). Compositional quantitative reasoning (pp. 179–188). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.11","ista":"Chatterjee K, De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2006. Compositional quantitative reasoning. QEST: Quantitative Evaluation of Systems, 179–188."},"page":"179 - 188","quality_controlled":0,"date_published":"2006-09-01T00:00:00Z","doi":"10.1109/QEST.2006.11","conference":{"name":"QEST: Quantitative Evaluation of Systems"},"type":"conference","publist_id":"163","abstract":[{"lang":"eng","text":"We present a compositional theory of system verification, where specifications assign real-numbered costs to systems. These costs can express a wide variety of quantitative system properties, such as resource consumption, price, or a measure of how well a system satisfies its specification. The theory supports the composition of systems and specifications, and the hiding of variables. Boolean refinement relations are replaced by real-numbered distances between descriptions of a system at different levels of detail. We show that the classical Boolean rules for compositional reasoning have quantitative counterparts in our setting. While our general theory allows costs to be specified by arbitrary cost functions, we also consider a class of linear cost functions, which give rise to an instance of our framework where all operations are computable in polynomial time."}],"extern":1,"_id":"4549","acknowledgement":"Supported in part by the NSF grants CCR-0234690, CCR-0208875, and CCR-0225610; by the NSF grant CCR-0132780 and ARP grant SC20051123.","year":"2006","publisher":"IEEE","status":"public","publication_status":"published","title":"Compositional quantitative reasoning","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee"},{"first_name":"Luca","last_name":"De Alfaro","full_name":"de Alfaro, Luca"},{"full_name":"Faella, Marco","last_name":"Faella","first_name":"Marco"},{"full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Majumdar, Ritankar S","first_name":"Ritankar","last_name":"Majumdar"},{"full_name":"Stoelinga, Mariëlle","last_name":"Stoelinga","first_name":"Mariëlle"}],"date_updated":"2021-01-12T07:59:37Z","date_created":"2018-12-11T12:09:26Z"},{"publist_id":"162","abstract":[{"text":"A concurrent reachability game is a two-player game played on a graph: at each state, the players simultaneously and independently select moves; the two moves determine jointly a probability distribution over the successor states. The objective for player 1 consists in reaching a set of target states; the objective for player 2 is to prevent this, so that the game is zero-sum. Our contributions are two-fold. First, we present a simple proof of the fact that in concurrent reachability games, for all epsilon > 0, memoryless epsilon-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an epsilon-optimal strategy achieves the objective with probability within epsilon of the value of the game. In contrast to previous proofs of this fact, which rely on the limit behavior of discounted games using advanced Puisieux series analysis, our proof is elementary and combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives.","lang":"eng"}],"extern":1,"type":"conference","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Krishnendu Chatterjee"},{"last_name":"De Alfaro","first_name":"Luca","full_name":"de Alfaro, Luca"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"}],"date_created":"2018-12-11T12:09:26Z","date_updated":"2021-01-12T07:59:39Z","year":"2006","_id":"4552","publisher":"IEEE","status":"public","title":"Strategy improvement for concurrent reachability games","publication_status":"published","day":"01","month":"01","date_published":"2006-01-01T00:00:00Z","doi":"10.1109/QEST.2006.48","conference":{"name":"QEST: Quantitative Evaluation of Systems"},"citation":{"chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability Games,” 291–300. IEEE, 2006. https://doi.org/10.1109/QEST.2006.48.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2006, pp. 291–300.","mla":"Chatterjee, Krishnendu, et al. Strategy Improvement for Concurrent Reachability Games. IEEE, 2006, pp. 291–300, doi:10.1109/QEST.2006.48.","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability games,” presented at the QEST: Quantitative Evaluation of Systems, 2006, pp. 291–300.","apa":"Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). Strategy improvement for concurrent reachability games (pp. 291–300). Presented at the QEST: Quantitative Evaluation of Systems, IEEE. https://doi.org/10.1109/QEST.2006.48","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2006. Strategy improvement for concurrent reachability games. QEST: Quantitative Evaluation of Systems, 291–300.","ama":"Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability games. In: IEEE; 2006:291-300. doi:10.1109/QEST.2006.48"},"page":"291 - 300","quality_controlled":0},{"day":"08","month":"08","page":"532 - 546","quality_controlled":0,"citation":{"ama":"Beyer D, Henzinger TA, Théoduloz G. Lazy shape analysis. In: Vol 4144. Springer; 2006:532-546. doi:10.1007/11817963_48","ista":"Beyer D, Henzinger TA, Théoduloz G. 2006. Lazy shape analysis. CAV: Computer Aided Verification, LNCS, vol. 4144, 532–546.","apa":"Beyer, D., Henzinger, T. A., & Théoduloz, G. (2006). Lazy shape analysis (Vol. 4144, pp. 532–546). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/11817963_48","ieee":"D. Beyer, T. A. Henzinger, and G. Théoduloz, “Lazy shape analysis,” presented at the CAV: Computer Aided Verification, 2006, vol. 4144, pp. 532–546.","mla":"Beyer, Dirk, et al. Lazy Shape Analysis. Vol. 4144, Springer, 2006, pp. 532–46, doi:10.1007/11817963_48.","short":"D. Beyer, T.A. Henzinger, G. Théoduloz, in:, Springer, 2006, pp. 532–546.","chicago":"Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Lazy Shape Analysis,” 4144:532–46. Springer, 2006. https://doi.org/10.1007/11817963_48."},"doi":"10.1007/11817963_48","date_published":"2006-08-08T00:00:00Z","conference":{"name":"CAV: Computer Aided Verification"},"alternative_title":["LNCS"],"type":"conference","extern":1,"publist_id":"133","abstract":[{"text":"Many software model checkers are based on predicate abstraction. If the verification goal depends on pointer structures, the approach does not work well, because it is difficult to find adequate predicate abstractions for the heap. In contrast, shape analysis, which uses graph-based heap abstractions, can provide a compact representation of recursive data structures. We integrate shape analysis into the software model checker Blast. Because shape analysis is expensive, we do not apply it globally. Instead, we ensure that, like predicates, shape graphs are computed and stored locally, only where necessary for proving the verification goal. To achieve this, we extend lazy abstraction refinement, which so far has been used only for predicate abstractions, to three-valued logical structures. This approach does not only increase the precision of model checking, but it also increases the efficiency of shape analysis. We implemented the technique by extending Blast with calls to Tvla.","lang":"eng"}],"publisher":"Springer","intvolume":" 4144","title":"Lazy shape analysis","publication_status":"published","status":"public","year":"2006","_id":"4574","volume":4144,"date_created":"2018-12-11T12:09:33Z","date_updated":"2021-01-12T07:59:49Z","author":[{"full_name":"Beyer, Dirk","last_name":"Beyer","first_name":"Dirk"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Grégory","last_name":"Théoduloz","full_name":"Théoduloz, Grégory"}]},{"month":"08","day":"06","article_processing_charge":"No","page":"12","external_id":{"arxiv":["0607101"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/quant-ph/0607101"}],"citation":{"short":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, (2006).","mla":"Hosten, Onur, et al. Counterfactual Computation Revisited. ArXiv, 2006.","chicago":"Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Computation Revisited.” ArXiv, 2006.","ama":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual computation revisited. 2006.","ieee":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual computation revisited.” ArXiv, 2006.","apa":"Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual computation revisited. ArXiv.","ista":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual computation revisited."},"language":[{"iso":"eng"}],"date_published":"2006-08-06T00:00:00Z","type":"preprint","extern":"1","abstract":[{"lang":"eng","text":"Mitchison and Jozsa recently suggested that the "chained-Zeno" counterfactual computation protocol recently proposed by Hosten et al. is counterfactual for only one output of the computer. This claim was based on the existing abstract algebraic definition of counterfactual computation, and indeed according to this definition, their argument is correct. However, a more general definition (physically adequate) for counterfactual computation is implicitly assumed by Hosten et. al. Here we explain in detail why the protocol is counterfactual and how the "history tracking" method of the existing description inadequately represents the physics underlying the protocol. Consequently, we propose a modified definition of counterfactual computation. Finally, we comment on one of the most interesting aspects of the error-correcting protocol. "}],"publist_id":"7241","publication_status":"published","title":"Counterfactual computation revisited","status":"public","publisher":"ArXiv","_id":"573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","date_updated":"2020-05-12T08:23:52Z","date_created":"2018-12-11T11:47:16Z","oa_version":"Preprint","author":[{"full_name":"Hosten, Onur","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"full_name":"Rakher, Matthew","first_name":"Matthew","last_name":"Rakher"},{"full_name":"Barreiro, Julio","last_name":"Barreiro","first_name":"Julio"},{"last_name":"Peters","first_name":"Nicholas","full_name":"Peters, Nicholas"},{"full_name":"Kwiat, Paul","first_name":"Paul","last_name":"Kwiat"}]},{"title":"Weak measurements and counterfactual computation","publication_status":"published","status":"public","publisher":"ArXiv","year":"2006","_id":"574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2020-05-12T08:18:01Z","date_created":"2018-12-11T11:47:16Z","oa_version":"Preprint","author":[{"full_name":"Hosten, Onur","last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","last_name":"Kwiat","full_name":"Kwiat, Paul"}],"type":"preprint","extern":"1","abstract":[{"lang":"eng","text":"Vaidman, in a recent article adopts the method of 'quantum weak measurements in pre- and postselected ensembles' to ascertain whether or not the chained-Zeno counterfactual computation scheme proposed by Hosten et al. is counterfactual; which has been the topic of a debate on the definition of counterfactuality. We disagree with his conclusion, which brings up some interesting aspects of quantum weak measurements and some concerns about the way they are interpreted. "}],"publist_id":"7240","page":"2","citation":{"ama":"Hosten O, Kwiat P. Weak measurements and counterfactual computation. 2006.","apa":"Hosten, O., & Kwiat, P. (2006). Weak measurements and counterfactual computation. ArXiv.","ieee":"O. Hosten and P. Kwiat, “Weak measurements and counterfactual computation.” ArXiv, 2006.","ista":"Hosten O, Kwiat P. 2006. Weak measurements and counterfactual computation.","short":"O. Hosten, P. Kwiat, (2006).","mla":"Hosten, Onur, and Paul Kwiat. Weak Measurements and Counterfactual Computation. ArXiv, 2006.","chicago":"Hosten, Onur, and Paul Kwiat. “Weak Measurements and Counterfactual Computation.” ArXiv, 2006."},"oa":1,"external_id":{"arxiv":["0612159"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/quant-ph/0612159"}],"language":[{"iso":"eng"}],"date_published":"2006-12-19T00:00:00Z","month":"12","day":"19","article_processing_charge":"No"},{"day":"01","month":"01","date_published":"2006-01-01T00:00:00Z","doi":"10.1117/12.684702","conference":{"name":"Quantum Communications and Quantum Imaging"},"quality_controlled":0,"citation":{"short":"N. Peters, K. Arnold, A. Vandevender, E. Jeffrey, R. Rangarajan, O. Hosten, J. Barreiro, J. Altepeter, P. Kwiat, in:, SPIE, 2006.","mla":"Peters, Nicholas, et al. Towards a Quasi-Deterministic Single-Photon Source. Vol. 6305, SPIE, 2006, doi:10.1117/12.684702.","chicago":"Peters, Nicholas, Keith Arnold, Aaron Vandevender, Evan Jeffrey, Radhika Rangarajan, Onur Hosten, Julio Barreiro, Joseph Altepeter, and Paul Kwiat. “Towards a Quasi-Deterministic Single-Photon Source,” Vol. 6305. SPIE, 2006. https://doi.org/10.1117/12.684702.","ama":"Peters N, Arnold K, Vandevender A, et al. Towards a quasi-deterministic single-photon source. In: Vol 6305. SPIE; 2006. doi:10.1117/12.684702","apa":"Peters, N., Arnold, K., Vandevender, A., Jeffrey, E., Rangarajan, R., Hosten, O., … Kwiat, P. (2006). Towards a quasi-deterministic single-photon source (Vol. 6305). Presented at the Quantum Communications and Quantum Imaging, SPIE. https://doi.org/10.1117/12.684702","ieee":"N. Peters et al., “Towards a quasi-deterministic single-photon source,” presented at the Quantum Communications and Quantum Imaging, 2006, vol. 6305.","ista":"Peters N, Arnold K, Vandevender A, Jeffrey E, Rangarajan R, Hosten O, Barreiro J, Altepeter J, Kwiat P. 2006. Towards a quasi-deterministic single-photon source. Quantum Communications and Quantum Imaging, Proc. SPIE, vol. 6305."},"extern":1,"publist_id":"7234","abstract":[{"lang":"eng","text":"A source of single photons allows secure quantum key distribution, in addition, to being a critical resource for linear optics quantum computing. We describe our progress on deterministically creating single photons from spontaneous parametric downconversion, an extension of the Pittman, Jacobs and Franson scheme [Phys. Rev A, v66, 042303 (2002)]. Their idea was to conditionally prepare single photons by measuring one member of a spontaneously emitted photon pair and storing the remaining conditionally prepared photon until a predetermined time, when it would be "deterministically" released from storage. Our approach attempts to improve upon this by recycling the pump pulse in order to decrease the possibility of multiple-pair generation, while maintaining a high probability of producing a single pair. Many of the challenges we discuss are central to other quantum information technologies, including the need for low-loss optical storage, switching and detection, and fast feed-forward control."}],"alternative_title":["Proc. SPIE"],"type":"conference","volume":6305,"date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-11T11:47:17Z","author":[{"last_name":"Peters","first_name":"Nicholas","full_name":"Peters, Nicholas A"},{"last_name":"Arnold","first_name":"Keith","full_name":"Arnold, Keith J"},{"first_name":"Aaron","last_name":"Vandevender","full_name":"VanDevender, Aaron P"},{"full_name":"Jeffrey, Evan R","last_name":"Jeffrey","first_name":"Evan"},{"full_name":"Rangarajan, Radhika","last_name":"Rangarajan","first_name":"Radhika"},{"first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"full_name":"Barreiro, Julio T","first_name":"Julio","last_name":"Barreiro"},{"full_name":"Altepeter, Joseph B","last_name":"Altepeter","first_name":"Joseph"},{"full_name":"Kwiat, Paul G","first_name":"Paul","last_name":"Kwiat"}],"intvolume":" 6305","publisher":"SPIE","title":"Towards a quasi-deterministic single-photon source","publication_status":"published","status":"public","year":"2006","_id":"578"},{"author":[{"full_name":"Rangarajan, Radhika","first_name":"Radhika","last_name":"Rangarajan"},{"full_name":"Altepeter, Joseph B","last_name":"Altepeter","first_name":"Joseph"},{"first_name":"Evan","last_name":"Jeffrey","full_name":"Jeffrey, Evan R"},{"last_name":"Stoutimore","first_name":"Micah","full_name":"Stoutimore, Micah J"},{"first_name":"Nicholas","last_name":"Peters","full_name":"Peters, Nicholas A"},{"last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten"},{"last_name":"Kwiat","first_name":"Paul","full_name":"Kwiat, Paul G"}],"date_created":"2018-12-11T11:47:17Z","date_updated":"2020-07-14T12:47:11Z","volume":6372,"_id":"577","year":"2006","status":"public","publication_status":"published","title":"High-efficiency single-photon detectors","intvolume":" 6372","publisher":"SPIE","abstract":[{"text":"Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) are high-efficiency single-photon detectors which have multi-photon counting capability. While both the VLPCs and the SSPMs have inferred internal quantum efficiencies above 93%, the actual measured values for both the detectors were in fact limited to less than 88%, attributed to in-coupling losses. We are currently improving this overall detection efficiency via a) custom anti-reflection coating the detectors and the in-coupling fibers, b) implementing a novel cryogenic design to reduce transmission losses and, c) using low-noise electronics to obtain a better signal-to-noise ratio.","lang":"eng"}],"publist_id":"7233","extern":1,"type":"conference","alternative_title":["Proceedings of SPIE"],"conference":{"name":"Unknown (978-081946470-5)"},"date_published":"2006-01-01T00:00:00Z","doi":"10.1117/12.686117","citation":{"chicago":"Rangarajan, Radhika, Joseph Altepeter, Evan Jeffrey, Micah Stoutimore, Nicholas Peters, Onur Hosten, and Paul Kwiat. “High-Efficiency Single-Photon Detectors,” Vol. 6372. SPIE, 2006. https://doi.org/10.1117/12.686117.","short":"R. Rangarajan, J. Altepeter, E. Jeffrey, M. Stoutimore, N. Peters, O. Hosten, P. Kwiat, in:, SPIE, 2006.","mla":"Rangarajan, Radhika, et al. High-Efficiency Single-Photon Detectors. Vol. 6372, SPIE, 2006, doi:10.1117/12.686117.","ieee":"R. Rangarajan et al., “High-efficiency single-photon detectors,” presented at the Unknown (978-081946470-5), 2006, vol. 6372.","apa":"Rangarajan, R., Altepeter, J., Jeffrey, E., Stoutimore, M., Peters, N., Hosten, O., & Kwiat, P. (2006). High-efficiency single-photon detectors (Vol. 6372). Presented at the Unknown (978-081946470-5), SPIE. https://doi.org/10.1117/12.686117","ista":"Rangarajan R, Altepeter J, Jeffrey E, Stoutimore M, Peters N, Hosten O, Kwiat P. 2006. High-efficiency single-photon detectors. Unknown (978-081946470-5), Proceedings of SPIE, vol. 6372.","ama":"Rangarajan R, Altepeter J, Jeffrey E, et al. High-efficiency single-photon detectors. In: Vol 6372. SPIE; 2006. doi:10.1117/12.686117"},"quality_controlled":0,"day":"01","month":"01"},{"extern":1,"publist_id":"7235","issue":"7079","abstract":[{"text":"The logic underlying the coherent nature of quantum information processing often deviates from intuitive reasoning, leading to surprising effects. Counterfactual computation constitutes a striking example: the potential outcome of a quantum computation can be inferred, even if the computer is not run 1. Relying on similar arguments to interaction-free measurements 2 (or quantum interrogation3), counterfactual computation is accomplished by putting the computer in a superposition of 'running' and 'not running' states, and then interfering the two histories. Conditional on the as-yet-unknown outcome of the computation, it is sometimes possible to counterfactually infer information about the solution. Here we demonstrate counterfactual computation, implementing Grover's search algorithm with an all-optical approach4. It was believed that the overall probability of such counterfactual inference is intrinsically limited1,5, so that it could not perform better on average than random guesses. However, using a novel 'chained' version of the quantum Zeno effect6, we show how to boost the counterfactual inference probability to unity, thereby beating the random guessing limit. Our methods are general and apply to any physical system, as illustrated by a discussion of trapped-ion systems. Finally, we briefly show that, in certain circumstances, counterfactual computation can eliminate errors induced by decoherence. ","lang":"eng"}],"type":"journal_article","volume":439,"date_updated":"2021-01-12T08:03:29Z","date_created":"2018-12-11T11:47:18Z","author":[{"last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten"},{"last_name":"Rakher","first_name":"Matthew","full_name":"Rakher, Matthew T"},{"full_name":"Barreiro, Julio T","first_name":"Julio","last_name":"Barreiro"},{"first_name":"Nicholas","last_name":"Peters","full_name":"Peters, Nicholas A"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"intvolume":" 439","publisher":"Nature Publishing Group","publication_status":"published","status":"public","title":"Counterfactual quantum computation through quantum interrogation","year":"2006","_id":"579","day":"23","month":"02","doi":"10.1038/nature04523","date_published":"2006-02-23T00:00:00Z","page":"949 - 952","quality_controlled":0,"citation":{"ista":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2006. Counterfactual quantum computation through quantum interrogation. Nature. 439(7079), 949–952.","ieee":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation through quantum interrogation,” Nature, vol. 439, no. 7079. Nature Publishing Group, pp. 949–952, 2006.","apa":"Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2006). Counterfactual quantum computation through quantum interrogation. Nature. Nature Publishing Group. https://doi.org/10.1038/nature04523","ama":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation through quantum interrogation. Nature. 2006;439(7079):949-952. doi:10.1038/nature04523","chicago":"Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature. Nature Publishing Group, 2006. https://doi.org/10.1038/nature04523.","mla":"Hosten, Onur, et al. “Counterfactual Quantum Computation through Quantum Interrogation.” Nature, vol. 439, no. 7079, Nature Publishing Group, 2006, pp. 949–52, doi:10.1038/nature04523.","short":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, Nature 439 (2006) 949–952."},"publication":"Nature"},{"quality_controlled":0,"citation":{"short":"R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, P. Kwiat, in:, IEEE, 2006.","mla":"Rangarajan, Radhika, et al. Improved Single-Photon Detection. IEEE, 2006, doi:10.1109/CLEO.2006.4628641.","chicago":"Rangarajan, Radhika, Nicholas Peters, Onur Hosten, Joseph Altepeter, Evan Jeffrey, and Paul Kwiat. “Improved Single-Photon Detection.” IEEE, 2006. https://doi.org/10.1109/CLEO.2006.4628641.","ama":"Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. Improved single-photon detection. In: IEEE; 2006. doi:10.1109/CLEO.2006.4628641","apa":"Rangarajan, R., Peters, N., Hosten, O., Altepeter, J., Jeffrey, E., & Kwiat, P. (2006). Improved single-photon detection. Presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, IEEE. https://doi.org/10.1109/CLEO.2006.4628641","ieee":"R. Rangarajan, N. Peters, O. Hosten, J. Altepeter, E. Jeffrey, and P. Kwiat, “Improved single-photon detection,” presented at the CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference, 2006.","ista":"Rangarajan R, Peters N, Hosten O, Altepeter J, Jeffrey E, Kwiat P. 2006. Improved single-photon detection. CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference."},"doi":"10.1109/CLEO.2006.4628641","date_published":"2006-01-01T00:00:00Z","conference":{"name":"CLEO/QELS: Conference on Lasers and Electro-Optics / Quantum Electronics and Laser Science Conference"},"day":"01","month":"01","publisher":"IEEE","publication_status":"published","status":"public","title":"Improved single-photon detection","_id":"583","year":"2006","date_created":"2018-12-11T11:47:19Z","date_updated":"2021-01-12T08:03:43Z","author":[{"last_name":"Rangarajan","first_name":"Radhika","full_name":"Rangarajan, Radhika"},{"last_name":"Peters","first_name":"Nicholas","full_name":"Peters, Nicholas A"},{"full_name":"Onur Hosten","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"first_name":"Joseph","last_name":"Altepeter","full_name":"Altepeter, Joseph B"},{"full_name":"Jeffrey, Evan R","first_name":"Evan","last_name":"Jeffrey"},{"last_name":"Kwiat","first_name":"Paul","full_name":"Kwiat, Paul G"}],"type":"conference","extern":1,"publist_id":"7232","abstract":[{"lang":"eng","text":"Visible light photon counters (VLPCs) and solid-state photomultipliers (SSPMs) facilitate efficient single-photon detection. We are attempting to improve their efficiency, previously limited to < 88% by coupling losses, via anti-reflection coatings, better electronics and cryogenics."}]},{"publication_identifier":{"issn":["1469-221X","1469-3178"]},"day":"01","month":"06","date_published":"2006-06-01T00:00:00Z","doi":"10.1038/sj.embor.7400713","language":[{"iso":"eng"}],"external_id":{"pmid":["16729018"]},"oa":1,"citation":{"apa":"Salecker, I., Häusser, M., & de Bono, M. (2006). On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO Reports. Wiley. https://doi.org/10.1038/sj.embor.7400713","ieee":"I. Salecker, M. Häusser, and M. de Bono, “On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits,” EMBO reports, vol. 7, no. 6. Wiley, pp. 585–589, 2006.","ista":"Salecker I, Häusser M, de Bono M. 2006. On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO reports. 7(6), 585–589.","ama":"Salecker I, Häusser M, de Bono M. On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits. EMBO reports. 2006;7(6):585-589. doi:10.1038/sj.embor.7400713","chicago":"Salecker, Iris, Michael Häusser, and Mario de Bono. “On the Axonal Road to Circuit Function and Behaviour: Workshop on the Assembly and Function of Neuronal Circuits.” EMBO Reports. Wiley, 2006. https://doi.org/10.1038/sj.embor.7400713.","short":"I. Salecker, M. Häusser, M. de Bono, EMBO Reports 7 (2006) 585–589.","mla":"Salecker, Iris, et al. “On the Axonal Road to Circuit Function and Behaviour: Workshop on the Assembly and Function of Neuronal Circuits.” EMBO Reports, vol. 7, no. 6, Wiley, 2006, pp. 585–89, doi:10.1038/sj.embor.7400713."},"main_file_link":[{"open_access":"1","url":"https://europepmc.org/articles/pmc1479602"}],"publication":"EMBO reports","page":"585-589","quality_controlled":"1","issue":"6","extern":"1","type":"journal_article","author":[{"full_name":"Salecker, Iris","last_name":"Salecker","first_name":"Iris"},{"full_name":"Häusser, Michael","last_name":"Häusser","first_name":"Michael"},{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"volume":7,"oa_version":"Published Version","date_updated":"2021-01-12T08:06:23Z","date_created":"2019-03-21T08:50:43Z","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6151","year":"2006","publisher":"Wiley","intvolume":" 7","title":"On the axonal road to circuit function and behaviour: Workshop on the assembly and function of neuronal circuits","status":"public","publication_status":"published"},{"language":[{"iso":"eng"}],"date_published":"2006-04-04T00:00:00Z","doi":"10.1016/j.cub.2006.03.023","quality_controlled":"1","page":"649-659","publication":"Current Biology","external_id":{"pmid":["16581509"]},"citation":{"ama":"Rogers C, Persson A, Cheung B, de Bono M. Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. 2006;16(7):649-659. doi:10.1016/j.cub.2006.03.023","ieee":"C. Rogers, A. Persson, B. Cheung, and M. de Bono, “Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans,” Current Biology, vol. 16, no. 7. Elsevier, pp. 649–659, 2006.","apa":"Rogers, C., Persson, A., Cheung, B., & de Bono, M. (2006). Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2006.03.023","ista":"Rogers C, Persson A, Cheung B, de Bono M. 2006. Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans. Current Biology. 16(7), 649–659.","short":"C. Rogers, A. Persson, B. Cheung, M. de Bono, Current Biology 16 (2006) 649–659.","mla":"Rogers, Candida, et al. “Behavioral Motifs and Neural Pathways Coordinating O2 Responses and Aggregation in C. Elegans.” Current Biology, vol. 16, no. 7, Elsevier, 2006, pp. 649–59, doi:10.1016/j.cub.2006.03.023.","chicago":"Rogers, Candida, Annelie Persson, Benny Cheung, and Mario de Bono. “Behavioral Motifs and Neural Pathways Coordinating O2 Responses and Aggregation in C. Elegans.” Current Biology. Elsevier, 2006. https://doi.org/10.1016/j.cub.2006.03.023."},"month":"04","day":"04","publication_identifier":{"issn":["0960-9822"]},"date_created":"2019-03-21T09:15:27Z","date_updated":"2021-01-12T08:06:23Z","oa_version":"None","volume":16,"author":[{"first_name":"Candida","last_name":"Rogers","full_name":"Rogers, Candida"},{"full_name":"Persson, Annelie","last_name":"Persson","first_name":"Annelie"},{"full_name":"Cheung, Benny","first_name":"Benny","last_name":"Cheung"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"}],"status":"public","publication_status":"published","title":"Behavioral motifs and neural pathways coordinating O2 responses and aggregation in C. elegans","publisher":"Elsevier","intvolume":" 16","_id":"6152","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2006","pmid":1,"extern":"1","issue":"7","type":"journal_article"},{"publication":"Journal of The Electrochemical Society","citation":{"chicago":"Freunberger, Stefan Alexander, Mathias Reum, Jörg Evertz, Alexander Wokaun, and Felix N. Büchi. “Measuring the Current Distribution in PEFCs with Sub-Millimeter Resolution.” Journal of The Electrochemical Society. The Electrochemical Society, 2006. https://doi.org/10.1149/1.2345591.","short":"S.A. Freunberger, M. Reum, J. Evertz, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006).","mla":"Freunberger, Stefan Alexander, et al. “Measuring the Current Distribution in PEFCs with Sub-Millimeter Resolution.” Journal of The Electrochemical Society, vol. 153, no. 11, A2158, The Electrochemical Society, 2006, doi:10.1149/1.2345591.","ieee":"S. A. Freunberger, M. Reum, J. Evertz, A. Wokaun, and F. N. Büchi, “Measuring the current distribution in PEFCs with sub-millimeter resolution,” Journal of The Electrochemical Society, vol. 153, no. 11. The Electrochemical Society, 2006.","apa":"Freunberger, S. A., Reum, M., Evertz, J., Wokaun, A., & Büchi, F. N. (2006). Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. The Electrochemical Society. https://doi.org/10.1149/1.2345591","ista":"Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. 2006. Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. 153(11), A2158.","ama":"Freunberger SA, Reum M, Evertz J, Wokaun A, Büchi FN. Measuring the current distribution in PEFCs with sub-millimeter resolution. Journal of The Electrochemical Society. 2006;153(11). doi:10.1149/1.2345591"},"quality_controlled":"1","article_type":"original","date_published":"2006-09-20T00:00:00Z","doi":"10.1149/1.2345591","language":[{"iso":"eng"}],"month":"09","day":"20","publication_identifier":{"issn":["0013-4651"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7328","year":"2006","publication_status":"published","status":"public","title":"Measuring the current distribution in PEFCs with sub-millimeter resolution","intvolume":" 153","publisher":"The Electrochemical Society","author":[{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Reum","first_name":"Mathias","full_name":"Reum, Mathias"},{"last_name":"Evertz","first_name":"Jörg","full_name":"Evertz, Jörg"},{"full_name":"Wokaun, Alexander","last_name":"Wokaun","first_name":"Alexander"},{"full_name":"Büchi, Felix N.","last_name":"Büchi","first_name":"Felix N."}],"date_created":"2020-01-15T12:23:12Z","date_updated":"2021-01-12T08:13:06Z","volume":153,"oa_version":"None","article_number":"A2158","type":"journal_article","abstract":[{"text":"An experimental technique for measuring the current density distribution with a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular to the channel direction are considered as two-dimensional resistors. Hence, the current density is obtained from the solution of Laplace's equation with the potentials at current collector and reaction layer as boundary conditions. Using ohmic drop for calculating the local current, detailed knowledge of all resistances involved is of prime importance. In particular, the contact resistance between the gas diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are strongly dependent on clamping pressure. They represent a substantial amount of the total ohmic drop and therefore require careful consideration. The detailed experimental setup as well as the concise procedure for quantitative data evaluation is described. Finally, the method is applied successfully to a cell operated on pure oxygen and air up to high current densities. The results show that electrical and ionic resistances seem to govern the current distribution at low current regimes, whereas mass transport limitations locally hamper the current production at high loads.","lang":"eng"}],"issue":"11","extern":"1"},{"author":[{"full_name":"Santis, Marco","last_name":"Santis","first_name":"Marco"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"full_name":"Papra, Matthias","first_name":"Matthias","last_name":"Papra"},{"full_name":"Wokaun, Alexander","last_name":"Wokaun","first_name":"Alexander"},{"full_name":"Büchi, Felix N.","last_name":"Büchi","first_name":"Felix N."}],"volume":161,"oa_version":"None","date_created":"2020-01-15T12:22:56Z","date_updated":"2021-01-12T08:13:06Z","_id":"7327","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","intvolume":" 161","publisher":"Elsevier","status":"public","publication_status":"published","title":"Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks","issue":"2","abstract":[{"text":"Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.\r\nTwo anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells.","lang":"eng"}],"extern":"1","type":"journal_article","doi":"10.1016/j.jpowsour.2006.06.007","date_published":"2006-10-27T00:00:00Z","language":[{"iso":"eng"}],"citation":{"short":"M. Santis, S.A. Freunberger, M. Papra, A. Wokaun, F.N. Büchi, Journal of Power Sources 161 (2006) 1076–1083.","mla":"Santis, Marco, et al. “Experimental Investigation of Coupling Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources, vol. 161, no. 2, Elsevier, 2006, pp. 1076–83, doi:10.1016/j.jpowsour.2006.06.007.","chicago":"Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, Alexander Wokaun, and Felix N. Büchi. “Experimental Investigation of Coupling Phenomena in Polymer Electrolyte Fuel Cell Stacks.” Journal of Power Sources. Elsevier, 2006. https://doi.org/10.1016/j.jpowsour.2006.06.007.","ama":"Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. 2006;161(2):1076-1083. doi:10.1016/j.jpowsour.2006.06.007","ieee":"M. Santis, S. A. Freunberger, M. Papra, A. Wokaun, and F. N. Büchi, “Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks,” Journal of Power Sources, vol. 161, no. 2. Elsevier, pp. 1076–1083, 2006.","apa":"Santis, M., Freunberger, S. A., Papra, M., Wokaun, A., & Büchi, F. N. (2006). Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. Elsevier. https://doi.org/10.1016/j.jpowsour.2006.06.007","ista":"Santis M, Freunberger SA, Papra M, Wokaun A, Büchi FN. 2006. Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks. Journal of Power Sources. 161(2), 1076–1083."},"publication":"Journal of Power Sources","page":"1076-1083","article_type":"original","publication_identifier":{"issn":["0378-7753"]},"article_processing_charge":"No","month":"10","day":"27"},{"quality_controlled":"1","page":"963-968","publication":"ECS Transactions","citation":{"ieee":"F. N. Büchi, S. A. Freunberger, and M. Santis, “What is learned beyond the scale of single cells?,” in ECS Transactions, Cancun, Mexico, 2006, vol. 3, no. 1, pp. 963–968.","apa":"Büchi, F. N., Freunberger, S. A., & Santis, M. (2006). What is learned beyond the scale of single cells? In ECS Transactions (Vol. 3, pp. 963–968). Cancun, Mexico: ECS. https://doi.org/10.1149/1.2356215","ista":"Büchi FN, Freunberger SA, Santis M. 2006. What is learned beyond the scale of single cells? ECS Transactions. ECS Meeting vol. 3, 963–968.","ama":"Büchi FN, Freunberger SA, Santis M. What is learned beyond the scale of single cells? In: ECS Transactions. Vol 3. ECS; 2006:963-968. doi:10.1149/1.2356215","chicago":"Büchi, Felix N., Stefan Alexander Freunberger, and Marco Santis. “What Is Learned beyond the Scale of Single Cells?” In ECS Transactions, 3:963–68. ECS, 2006. https://doi.org/10.1149/1.2356215.","short":"F.N. Büchi, S.A. Freunberger, M. Santis, in:, ECS Transactions, ECS, 2006, pp. 963–968.","mla":"Büchi, Felix N., et al. “What Is Learned beyond the Scale of Single Cells?” ECS Transactions, vol. 3, no. 1, ECS, 2006, pp. 963–68, doi:10.1149/1.2356215."},"language":[{"iso":"eng"}],"conference":{"name":"ECS Meeting","start_date":"2006-10-29","location":"Cancun, Mexico","end_date":"2006-11-03"},"date_published":"2006-11-03T00:00:00Z","doi":"10.1149/1.2356215","day":"03","month":"11","article_processing_charge":"No","status":"public","publication_status":"published","title":"What is learned beyond the scale of single cells?","intvolume":" 3","publisher":"ECS","year":"2006","_id":"7326","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-01-15T12:22:44Z","date_updated":"2021-01-12T08:13:05Z","oa_version":"None","volume":3,"author":[{"full_name":"Büchi, Felix N.","first_name":"Felix N.","last_name":"Büchi"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"},{"last_name":"Santis","first_name":"Marco","full_name":"Santis, Marco"}],"type":"conference","extern":"1","abstract":[{"lang":"eng","text":"Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified. "}],"issue":"1"},{"_id":"7329","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","publisher":"Elsevier","status":"public","publication_status":"published","title":"Expanding current distribution measurement in PEFCs to sub-millimeter resolution","author":[{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Reum, Mathias","last_name":"Reum","first_name":"Mathias"},{"full_name":"Wokaun, Alexander","first_name":"Alexander","last_name":"Wokaun"},{"full_name":"Büchi, Felix N.","first_name":"Felix N.","last_name":"Büchi"}],"volume":8,"oa_version":"None","date_updated":"2021-01-12T08:13:06Z","date_created":"2020-01-15T12:23:22Z","type":"journal_article","issue":"9","abstract":[{"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.","lang":"eng"}],"extern":"1","citation":{"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.","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","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.","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","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.","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."},"publication":"Electrochemistry Communications","page":"1435-1438","quality_controlled":"1","article_type":"original","doi":"10.1016/j.elecom.2006.05.032","date_published":"2006-09-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1388-2481"]},"month":"09","day":"01"},{"type":"journal_article","extern":"1","abstract":[{"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.","lang":"eng"}],"issue":"25","publication_status":"published","title":"Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients","status":"public","intvolume":" 51","publisher":"Elsevier","_id":"7330","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","date_created":"2020-01-15T12:23:34Z","date_updated":"2021-01-12T08:13:07Z","volume":51,"oa_version":"None","author":[{"full_name":"Santis, M.","first_name":"M.","last_name":"Santis"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander"},{"first_name":"A.","last_name":"Reiner","full_name":"Reiner, A."},{"full_name":"Büchi, F.N.","first_name":"F.N.","last_name":"Büchi"}],"month":"07","day":"01","publication_identifier":{"issn":["0013-4686"]},"article_processing_charge":"No","quality_controlled":"1","article_type":"original","page":"5383-5393","publication":"Electrochimica Acta","citation":{"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.","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.","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.","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","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.","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"},"language":[{"iso":"eng"}],"doi":"10.1016/j.electacta.2006.02.008","date_published":"2006-07-01T00:00:00Z"},{"language":[{"iso":"eng"}],"date_published":"2006-01-04T00:00:00Z","doi":"10.1149/1.2150150","article_type":"original","quality_controlled":"1","citation":{"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.","short":"S.A. Freunberger, M. Santis, I.A. Schneider, A. Wokaun, F.N. Büchi, Journal of The Electrochemical Society 153 (2006).","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.","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.","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","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.","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"},"publication":"Journal of The Electrochemical Society","publication_identifier":{"issn":["0013-4651"]},"article_processing_charge":"No","month":"01","day":"04","volume":153,"oa_version":"None","date_created":"2020-01-15T12:24:00Z","date_updated":"2021-01-12T08:13:08Z","author":[{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Marco","last_name":"Santis","full_name":"Santis, Marco"},{"full_name":"Schneider, Ingo A.","last_name":"Schneider","first_name":"Ingo A."},{"last_name":"Wokaun","first_name":"Alexander","full_name":"Wokaun, Alexander"},{"last_name":"Büchi","first_name":"Felix N.","full_name":"Büchi, Felix N."}],"intvolume":" 153","publisher":"The Electrochemical Society","title":"In-plane effects in large-scale PEMFCs","publication_status":"published","status":"public","year":"2006","_id":"7332","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"2","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."}],"type":"journal_article","article_number":"A396"},{"article_number":"A909","type":"journal_article","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."}],"issue":"5","extern":"1","_id":"7331","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance","publication_status":"published","publisher":"The Electrochemical Society","intvolume":" 153","author":[{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"},{"full_name":"Wokaun, Alexander","first_name":"Alexander","last_name":"Wokaun"},{"full_name":"Büchi, Felix N.","last_name":"Büchi","first_name":"Felix N."}],"date_created":"2020-01-15T12:23:46Z","date_updated":"2021-01-12T08:13:08Z","oa_version":"None","volume":153,"day":"27","month":"03","article_processing_charge":"No","publication_identifier":{"issn":["0013-4651"]},"publication":"Journal of The Electrochemical Society","citation":{"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.","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.","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","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","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.","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)."},"quality_controlled":"1","article_type":"original","date_published":"2006-03-27T00:00:00Z","doi":"10.1149/1.2185282","language":[{"iso":"eng"}]},{"page":"0403 - 0410","quality_controlled":0,"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","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.","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","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.","short":"E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov, A. Grigorenko, PLoS Biology 4 (2006) 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.","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."},"publication":"PLoS Biology","doi":"10.1371/journal.pbio.0040073","date_published":"2006-03-01T00:00:00Z","month":"03","day":"01","publisher":"Public Library of Science","intvolume":" 4","publication_status":"published","title":"Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius","status":"public","_id":"854","acknowledgement":"FAK is supported by the NSF Graduate Research Fellowship.\nWe 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.","year":"2006","volume":4,"date_created":"2018-12-11T11:48:51Z","date_updated":"2021-01-12T08:19:58Z","author":[{"first_name":"Evgeny","last_name":"Rogaev","full_name":"Rogaev, Evgeny I"},{"last_name":"Moliaka","first_name":"Yuri","full_name":"Moliaka, Yuri K"},{"first_name":"Boris","last_name":"Malyarchuk","full_name":"Malyarchuk, Boris A"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"},{"first_name":"Miroslava","last_name":"Derenko","full_name":"Derenko, Miroslava V"},{"full_name":"Chumakov, Ilya M","last_name":"Chumakov","first_name":"Ilya"},{"full_name":"Grigorenko, Anastasia P","last_name":"Grigorenko","first_name":"Anastasia"}],"type":"journal_article","extern":1,"issue":"3","publist_id":"6794","abstract":[{"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.","lang":"eng"}]},{"type":"journal_article","extern":1,"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."}],"publist_id":"6778","publication_status":"published","status":"public","title":"Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer events and pseudogene formation","intvolume":" 1","publisher":"BioMed Central","_id":"868","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.","year":"2006","date_created":"2018-12-11T11:48:56Z","date_updated":"2021-01-12T08:20:31Z","volume":1,"author":[{"full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene V"},{"last_name":"Morgunov","first_name":"Igor","full_name":"Morgunov, Igor G"},{"last_name":"Finogenova","first_name":"Tatiana","full_name":"Finogenova, Tatiana V"},{"full_name":"Kondrashova, Marie N","first_name":"Marie","last_name":"Kondrashova"}],"day":"23","month":"10","quality_controlled":0,"publication":"Biology Direct","citation":{"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).","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.","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","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.","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.","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"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2006-10-23T00:00:00Z","doi":"10.1186/1745-6150-1-31"},{"status":"public","title":"Role of selection in fixation of gene duplications","publication_status":"published","intvolume":" 239","publisher":"Elsevier","_id":"873","year":"2006","date_created":"2018-12-11T11:48:57Z","date_updated":"2021-01-12T08:20:47Z","volume":239,"author":[{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"type":"journal_article","extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"2","publist_id":"6773","quality_controlled":0,"page":"141 - 151","publication":"Journal of Theoretical Biology","citation":{"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","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.","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","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.","short":"F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 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."},"doi":"10.1016/j.jtbi.2005.08.033","date_published":"2006-03-21T00:00:00Z","day":"21","month":"03"},{"date_published":"2006-07-06T00:00:00Z","doi":"10.1002/mrc.1825","language":[{"iso":"eng"}],"publication":"Magnetic Resonance in Chemistry","citation":{"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.","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.","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","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.","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.","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"},"article_type":"original","quality_controlled":"1","page":"S177-S184","month":"07","day":"06","article_processing_charge":"No","publication_identifier":{"issn":["0749-1581","1097-458X"]},"author":[{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"last_name":"Forge","first_name":"Vincent","full_name":"Forge, Vincent"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"date_created":"2020-09-18T10:13:42Z","date_updated":"2021-01-12T08:19:37Z","volume":44,"oa_version":"None","_id":"8489","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"HET-SOFAST NMR for fast detection of structural compactness and heterogeneity along polypeptide chains","publication_status":"published","intvolume":" 44","publisher":"Wiley","abstract":[{"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.","lang":"eng"}],"issue":"S1","extern":"1","type":"journal_article"},{"article_processing_charge":"No","publication_identifier":{"issn":["0002-7863","1520-5126"]},"day":"21","month":"06","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"doi":"10.1021/ja062025p","date_published":"2006-06-21T00:00:00Z","page":"9042-9043","quality_controlled":"1","article_type":"original","citation":{"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.","short":"P. Schanda, H. Van Melckebeke, B. Brutscher, Journal of the American Chemical Society 128 (2006) 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.","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","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.","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"},"publication":"Journal of the American Chemical Society","extern":"1","issue":"28","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."}],"type":"journal_article","oa_version":"None","volume":128,"date_created":"2020-09-18T10:13:36Z","date_updated":"2021-01-12T08:19:37Z","author":[{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"full_name":"Van Melckebeke, Hélène","first_name":"Hélène","last_name":"Van Melckebeke"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"intvolume":" 128","publisher":"American Chemical Society","publication_status":"published","title":"Speeding up three-dimensional protein NMR experiments to a few minutes","status":"public","year":"2006","_id":"8488","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"334-339","article_type":"original","citation":{"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.","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.","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","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.","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.","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"},"publication":"Journal of Magnetic Resonance","language":[{"iso":"eng"}],"doi":"10.1016/j.jmr.2005.10.007","date_published":"2006-02-01T00:00:00Z","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"article_processing_charge":"No","publication_identifier":{"issn":["1090-7807"]},"month":"02","day":"01","intvolume":" 178","publisher":"Elsevier","publication_status":"published","status":"public","title":"Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR","_id":"8490","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2006","oa_version":"None","volume":178,"date_updated":"2021-01-12T08:19:38Z","date_created":"2020-09-18T10:13:51Z","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"type":"journal_article","extern":"1","issue":"2","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."}]},{"author":[{"full_name":"OTT, WILLIAM","last_name":"OTT","first_name":"WILLIAM"},{"full_name":"HUNT, BRIAN","first_name":"BRIAN","last_name":"HUNT"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"}],"volume":26,"oa_version":"None","date_created":"2020-09-18T10:48:52Z","date_updated":"2021-01-12T08:19:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8514","year":"2006","intvolume":" 26","publisher":"Cambridge University Press","title":"The effect of projections on fractal sets and measures in Banach spaces","publication_status":"published","status":"public","issue":"3","abstract":[{"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 $\\tau > 0$.","lang":"eng"}],"extern":"1","type":"journal_article","doi":"10.1017/s0143385705000714","date_published":"2006-06-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"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.","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","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.","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","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.","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."},"publication":"Ergodic Theory and Dynamical Systems","page":"869-891","quality_controlled":"1","article_type":"original","article_processing_charge":"No","publication_identifier":{"issn":["0143-3857","1469-4417"]},"day":"01","month":"06"},{"language":[{"iso":"eng"}],"conference":{"name":"International Congress on Mathematical Physics","location":"Lisbon, Portugal","start_date":"2003-07-28","end_date":"2003-08-02"},"doi":"10.1142/9789812704016_0026","date_published":"2006-03-01T00:00:00Z","quality_controlled":"1","page":"290-295","publication":"XIVth International Congress on Mathematical Physics","citation":{"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.","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.","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","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","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.","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."},"month":"03","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9789812562012","9789812704016"]},"date_created":"2020-09-18T10:48:59Z","date_updated":"2021-01-12T08:19:49Z","oa_version":"None","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"},{"full_name":"DOLGOPYAT, D.","first_name":"D.","last_name":"DOLGOPYAT"},{"last_name":"KORALOV","first_name":"L.","full_name":"KORALOV, L."}],"publication_status":"published","status":"public","title":"Long time behaviour of periodic stochastic flows","publisher":"World Scientific","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8515","year":"2006","extern":"1","abstract":[{"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.","lang":"eng"}],"type":"conference"},{"_id":"8513","year":"2006","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","publisher":"American Institute of Mathematical Sciences (AIMS)","title":"Generic 3-dimensional volume-preserving diffeomorphisms with superexponential growth of number of periodic orbits","status":"public","publication_status":"published","author":[{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Maria","last_name":"Saprykina","full_name":"Saprykina, Maria"}],"oa_version":"None","volume":15,"date_created":"2020-09-18T10:48:43Z","date_updated":"2021-01-12T08:19:48Z","type":"journal_article","issue":"2","extern":"1","citation":{"short":"V. Kaloshin, M. Saprykina, Discrete & Continuous Dynamical Systems - A 15 (2006) 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.","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.","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","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."},"publication":"Discrete & Continuous Dynamical Systems - A","page":"611-640","quality_controlled":"1","article_type":"original","date_published":"2006-05-01T00:00:00Z","doi":"10.3934/dcds.2006.15.611","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1553-5231"]},"day":"01","month":"05"},{"day":"21","month":"06","quality_controlled":0,"page":"616 - 626","publication":"Journal of Theoretical Biology","citation":{"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.","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","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.","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","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.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 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."},"date_published":"2006-06-21T00:00:00Z","doi":"10.1016/j.jtbi.2005.10.020","type":"journal_article","extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"4","publist_id":"6779","publication_status":"published","status":"public","title":"Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites","publisher":"Elsevier","intvolume":" 240","_id":"869","year":"2006","acknowledgement":"This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine.","date_created":"2018-12-11T11:48:56Z","date_updated":"2021-01-12T08:20:33Z","volume":240,"author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov"},{"full_name":"Ogurtsov, Aleksey Yu","first_name":"Aleksey","last_name":"Ogurtsov"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"}]},{"month":"02","day":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"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).","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.","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","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.","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.","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"},"publication":"BMC Cancer","quality_controlled":0,"doi":"10.1186/1471-2407-6-36","date_published":"2006-02-09T00:00:00Z","type":"journal_article","publist_id":"6744","abstract":[{"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.","lang":"eng"}],"extern":1,"_id":"903","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.","year":"2006","publisher":"BioMed Central","intvolume":" 6","status":"public","publication_status":"published","title":"Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis","author":[{"first_name":"Vladimir","last_name":"Babenko","full_name":"Babenko, Vladimir N"},{"full_name":"Basu, Malay K","last_name":"Basu","first_name":"Malay"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"},{"last_name":"Rogozin","first_name":"Igor","full_name":"Rogozin, Igor B"},{"first_name":"Eugene","last_name":"Koonin","full_name":"Koonin, Eugene V"}],"volume":6,"date_updated":"2021-01-12T08:21:47Z","date_created":"2018-12-11T11:49:07Z"},{"article_processing_charge":"No","day":"26","scopus_import":"1","date_published":"2006-11-26T00:00:00Z","citation":{"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","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.","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","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.","short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 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."},"publication":"Nature Genetics","page":"61-69","article_type":"original","issue":"1","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."}],"type":"journal_article","oa_version":"None","_id":"9505","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 39","title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","status":"public","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"month":"11","doi":"10.1038/ng1929","language":[{"iso":"eng"}],"external_id":{"pmid":["17128275"]},"quality_controlled":"1","extern":"1","author":[{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Gehring, Mary","last_name":"Gehring","first_name":"Mary"},{"first_name":"Robert K.","last_name":"Tran","full_name":"Tran, Robert K."},{"full_name":"Ballinger, Tracy","last_name":"Ballinger","first_name":"Tracy"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"volume":39,"date_updated":"2021-12-14T09:02:51Z","date_created":"2021-06-07T12:19:31Z","pmid":1,"year":"2006","department":[{"_id":"DaZi"}],"publisher":"Nature Publishing Group","publication_status":"published"},{"scopus_import":"1","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"day":"25","article_processing_charge":"No","publication":"The Journal of Physical Chemistry B","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","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.","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.","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","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.","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."},"article_type":"original","page":"2482-2496","date_published":"2006-01-25T00:00:00Z","type":"journal_article","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."}],"issue":"6","_id":"13430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Principles and implementations of dissipative (dynamic) self-assembly","intvolume":" 110","oa_version":"None","month":"01","publication_identifier":{"issn":["1520-6106","1520-5207"]},"external_id":{"pmid":["16471845"]},"quality_controlled":"1","doi":"10.1021/jp054153q","language":[{"iso":"eng"}],"extern":"1","year":"2006","pmid":1,"publication_status":"published","publisher":"American Chemical Society","author":[{"full_name":"Fialkowski, Marcin","last_name":"Fialkowski","first_name":"Marcin"},{"full_name":"Bishop, Kyle J. M.","last_name":"Bishop","first_name":"Kyle J. M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal"},{"full_name":"Smoukov, Stoyan K.","last_name":"Smoukov","first_name":"Stoyan K."},{"last_name":"Campbell","first_name":"Christopher J.","full_name":"Campbell, Christopher J."},{"last_name":"Grzybowski","first_name":"Bartosz A.","full_name":"Grzybowski, Bartosz A."}],"date_created":"2023-08-01T10:37:35Z","date_updated":"2023-08-08T11:33:08Z","volume":110},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13428","status":"public","title":"Ionic-like behavior of oppositely charged nanoparticles","intvolume":" 128","abstract":[{"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.","lang":"eng"}],"issue":"47","type":"journal_article","date_published":"2006-11-29T00:00:00Z","publication":"Journal of the American Chemical Society","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","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.","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","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.","short":"A.M. Kalsin, B. Kowalczyk, S.K. Smoukov, R. Klajn, B.A. Grzybowski, Journal of the American Chemical Society 128 (2006) 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.","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."},"article_type":"original","page":"15046-15047","day":"29","article_processing_charge":"No","scopus_import":"1","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"author":[{"full_name":"Kalsin, Alexander M.","last_name":"Kalsin","first_name":"Alexander M."},{"full_name":"Kowalczyk, Bartlomiej","first_name":"Bartlomiej","last_name":"Kowalczyk"},{"last_name":"Smoukov","first_name":"Stoyan K.","full_name":"Smoukov, Stoyan K."},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A.","last_name":"Grzybowski"}],"date_updated":"2023-08-08T11:30:06Z","date_created":"2023-08-01T10:36:27Z","volume":128,"year":"2006","pmid":1,"publication_status":"published","publisher":"American Chemical Society","extern":"1","doi":"10.1021/ja0642966","language":[{"iso":"eng"}],"external_id":{"pmid":["17117829"]},"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"type":"journal_article","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."}],"issue":"32","title":"The core and most useful molecules in organic chemistry","status":"public","intvolume":" 45","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13429","oa_version":"None","keyword":["General Chemistry","Catalysis"],"scopus_import":"1","day":"11","article_processing_charge":"No","article_type":"original","page":"5348-5354","publication":"Angewandte Chemie International Edition","citation":{"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.","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.","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","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.","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.","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"},"date_published":"2006-08-11T00:00:00Z","extern":"1","publication_status":"published","publisher":"Wiley","year":"2006","pmid":1,"date_updated":"2023-08-08T11:31:27Z","date_created":"2023-08-01T10:37:16Z","volume":45,"author":[{"last_name":"Bishop","first_name":"Kyle J. M.","full_name":"Bishop, Kyle J. M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"first_name":"Bartosz A.","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A."}],"month":"08","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"quality_controlled":"1","external_id":{"pmid":["16835857"]},"language":[{"iso":"eng"}],"doi":"10.1002/anie.200600881"}]