[{"day":"01","pmid":1,"language":[{"iso":"eng"}],"month":"09","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59373/","open_access":"1"}],"intvolume":" 121","doi":"10.1104/pp.121.1.245","date_updated":"2022-09-07T13:56:12Z","article_processing_charge":"No","author":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Witters, Erwin","first_name":"Erwin","last_name":"Witters"},{"full_name":"Van Dongen, Walter","last_name":"Van Dongen","first_name":"Walter"},{"last_name":"Kolář","first_name":"Jan","full_name":"Kolář, Jan"},{"full_name":"Motyka, Václav","last_name":"Motyka","first_name":"Václav"},{"full_name":"Brzobohatý, Břetislav","last_name":"Brzobohatý","first_name":"Břetislav"},{"last_name":"Van Onckelen","first_name":"Henri","full_name":"Van Onckelen, Henri"},{"full_name":"Macháčková, Ivana","last_name":"Macháčková","first_name":"Ivana"}],"date_published":"1999-09-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","external_id":{"pmid":["10482680"]},"article_type":"original","issue":"1","acknowledgement":"The authors thank Prof. Dennis Baker (Wye College, London) and Dr. Laura Zonia (Institute of Experimental Botany, Prague) for language correction of the manuscript and Prof. Miroslav Kamínek (Institute of Experimental Botany, Prague) for critical reading of the manuscript.","oa":1,"status":"public","publication_identifier":{"issn":["0032-0889"]},"citation":{"chicago":"Benková, Eva, Erwin Witters, Walter Van Dongen, Jan Kolář, Václav Motyka, Břetislav Brzobohatý, Henri Van Onckelen, and Ivana Macháčková. “Cytokinins in Tobacco and Wheat Chloroplasts. Occurrence and Changes Due to Light/Dark Treatment.” Plant Physiology. American Society of Plant Biologists, 1999. https://doi.org/10.1104/pp.121.1.245.","ieee":"E. Benková et al., “Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment,” Plant Physiology, vol. 121, no. 1. American Society of Plant Biologists, pp. 245–251, 1999.","apa":"Benková, E., Witters, E., Van Dongen, W., Kolář, J., Motyka, V., Brzobohatý, B., … Macháčková, I. (1999). Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.121.1.245","ama":"Benková E, Witters E, Van Dongen W, et al. Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment. Plant Physiology. 1999;121(1):245-251. doi:10.1104/pp.121.1.245","short":"E. Benková, E. Witters, W. Van Dongen, J. Kolář, V. Motyka, B. Brzobohatý, H. Van Onckelen, I. Macháčková, Plant Physiology 121 (1999) 245–251.","ista":"Benková E, Witters E, Van Dongen W, Kolář J, Motyka V, Brzobohatý B, Van Onckelen H, Macháčková I. 1999. Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment. Plant Physiology. 121(1), 245–251.","mla":"Benková, Eva, et al. “Cytokinins in Tobacco and Wheat Chloroplasts. Occurrence and Changes Due to Light/Dark Treatment.” Plant Physiology, vol. 121, no. 1, American Society of Plant Biologists, 1999, pp. 245–51, doi:10.1104/pp.121.1.245."},"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"245 - 251","volume":121,"year":"1999","_id":"2865","extern":"1","abstract":[{"text":"Although cytokinins (CKs) affect a number of processes connected with chloroplasts, it has never been rigorously proven that chloroplasts contain CKs. We isolated intact chloroplasts from tobacco (Nicotiana tabacum L. cv SR1) and wheat (Triticum aestivum L. cv Ritmo) leaves and determined their CKs by liquid chromatography/tandem mass spectroscopy. Chloroplasts from both species contained a whole spectrum of CKs, including free bases (zeatin and isopentenyladenine), ribosides (zeatin riboside, and isopentenyladenosine), ribotides (isopentenyladenosine-5′-monophosphate, zeatin riboside-5′-monophosphate, and dihydrozeatin riboside-5′-monophosphate), and N-glucosides (zeatin-N 9-glucoside, dihydrozeatin-N 9-glucoside, zeatin-N 7-glucoside, and isopentenyladenine-N-glucosides). In chloroplasts there was a moderately higher relative amount of bases, ribosides, and ribotides than in leaves, and a significantly increased level ofN 9-glucosides of zeatin and dihydrozeatin. Tobacco and wheat chloroplasts were prepared from leaves at the end of either a dark or light period. After a dark period, chloroplasts accumulated more CKs than after a light period. The differences were moderate for free bases and ribosides, but highly significant for glucosides. Tobacco chloroplasts from dark-treated leaves contained zeatin riboside-O-glucoside and dihydrozeatin riboside-O-glucoside, as well as a relatively high CK oxidase activity. These data show that chloroplasts contain a whole spectrum of CKs and the enzymatic activity necessary for their metabolism. ","lang":"eng"}],"publisher":"American Society of Plant Biologists","title":"Cytokinins in tobacco and wheat chloroplasts. Occurrence and changes due to light/dark treatment","publication":"Plant Physiology","publist_id":"3924","oa_version":"Published Version","date_created":"2018-12-11T12:00:00Z"},{"publication_identifier":{"issn":["0270-6474"]},"citation":{"apa":"Siekhaus, D. E., & Fuller, R. (1999). A role for amontillado the Drosophila homolog of the neuropeptide precursor processing protease PC2 in triggering hatching behavior. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.19-16-06942.1999","ieee":"D. E. Siekhaus and R. Fuller, “A role for amontillado the Drosophila homolog of the neuropeptide precursor processing protease PC2 in triggering hatching behavior,” Journal of Neuroscience, vol. 19, no. 16. Society for Neuroscience, pp. 6942–6954, 1999.","chicago":"Siekhaus, Daria E, and Robert Fuller. “A Role for Amontillado the Drosophila Homolog of the Neuropeptide Precursor Processing Protease PC2 in Triggering Hatching Behavior.” Journal of Neuroscience. Society for Neuroscience, 1999. https://doi.org/10.1523/jneurosci.19-16-06942.1999.","ista":"Siekhaus DE, Fuller R. 1999. A role for amontillado the Drosophila homolog of the neuropeptide precursor processing protease PC2 in triggering hatching behavior. Journal of Neuroscience. 19(16), 6942–6954.","short":"D.E. Siekhaus, R. Fuller, Journal of Neuroscience 19 (1999) 6942–6954.","mla":"Siekhaus, Daria E., and Robert Fuller. “A Role for Amontillado the Drosophila Homolog of the Neuropeptide Precursor Processing Protease PC2 in Triggering Hatching Behavior.” Journal of Neuroscience, vol. 19, no. 16, Society for Neuroscience, 1999, pp. 6942–54, doi:10.1523/jneurosci.19-16-06942.1999.","ama":"Siekhaus DE, Fuller R. A role for amontillado the Drosophila homolog of the neuropeptide precursor processing protease PC2 in triggering hatching behavior. Journal of Neuroscience. 1999;19(16):6942-6954. doi:10.1523/jneurosci.19-16-06942.1999"},"article_type":"original","external_id":{"pmid":["10436051 "]},"issue":"16","status":"public","acknowledgement":"This research was supported by National Institutes of Health Grant GM39697 to R.S.F. D.S. was supported in part by National Institutes of Health training Grant 2T32GM07599. We thank M. A. Krasnow and members of his laboratory, particularly J. Jarecki, for technical guidance, encouragement, and stimulating scientific discussions. We thank A. Maghbouleh and the Stanford Statistics Department Consulting Service for help with statistical analysis. We thank G. Beitel, S. Dietrich, K. Guillemin, D. Micklem, Y. Nakajima, and members of the Fuller and Krasnow laboratories for comments on this manuscript. We thank M. Palazzolo for the use of theDrosophila head cDNA library, D. Kiehart for the use of a Drosophila myosin antibody, and D. Casso, F.-A. Ramirez-Weber, and T. B. Kornberg for use of the D/TM3SbKrGFP flies. We thank A. R. Kidd, D. Tolla, and M. Bender and D. Casso, F.-A. Ramirez-Weber and T. B. Kornberg for communication of results before publication","oa":1,"year":"1999","_id":"3148","type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"6942 - 6954","volume":19,"extern":"1","abstract":[{"text":"Accurate proteolytic processing of neuropeptide and peptide hormone precursors by members of the kexin/furin family of proteases is key to determining both the identities and activities of signaling peptides. Here we identify amontillado (amon), the Drosophila melanogaster homolog of the mammalian neuropeptide processing protease PC2, and show that in contrast to vertebrate PC2, amontillado expression undergoes extensive regulation in the nervous system during development. In situ hybridization reveals that expression of amontillado is restricted to the final stages of embryogenesis when it is found in anterior sensory structures and in only 168 cells in the brain and ventral nerve cord. After larvae hatch from their egg shells, the sensory structures and most cells in the CNS turn off or substantially reduce amontillado expression, suggesting that amontillado plays a specific role late in embryogenesis. Larvae lacking the chromosomal region containing amontillado show no gross anatomical defects and respond to touch. However, such larvae show a greatly reduced frequency of a hatching behavior of wild- type Drosophila in which larvae swing their heads, scraping through the eggshell with their mouth hooks. Ubiquitous expression of amontillado can restore near wild-type levels of this behavior, whereas expression of amontillado with an alanine substitution for the catalytic histidine cannot. These results suggest that amontillado expression is regulated as part of a programmed modulation of neural signaling that controls hatching behavior by producing specific neuropeptides in particular neurons at an appropriate developmental time.","lang":"eng"}],"publist_id":"3547","oa_version":"Published Version","date_created":"2018-12-11T12:01:40Z","publisher":"Society for Neuroscience","title":"A role for amontillado the Drosophila homolog of the neuropeptide precursor processing protease PC2 in triggering hatching behavior","publication":"Journal of Neuroscience","language":[{"iso":"eng"}],"month":"08","day":"15","pmid":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782853/"}],"intvolume":" 19","quality_controlled":"1","scopus_import":"1","date_updated":"2022-09-07T13:48:41Z","doi":"10.1523/jneurosci.19-16-06942.1999","article_processing_charge":"No","author":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E"},{"last_name":"Fuller","first_name":"Robert","full_name":"Fuller, Robert"}],"date_published":"1999-08-15T00:00:00Z"},{"date_created":"2022-08-17T08:53:02Z","oa_version":"Published Version","publisher":"Association for Computing Machinery","publication":"ACM SIGIR Forum","title":"Analysis of a very large web search engine query log","extern":"1","abstract":[{"lang":"eng","text":"In this paper we present an analysis of an AltaVista Search Engine query log consisting of approximately 1 billion entries for search requests over a period of six weeks. This represents almost 285 million user sessions, each an attempt to fill a single information need. We present an analysis of individual queries, query duplication, and query sessions. We also present results of a correlation analysis of the log entries, studying the interaction of terms within queries. Our data supports the conjecture that web users differ significantly from the user assumed in the standard information retrieval literature. Specifically, we show that web users type in short queries, mostly look at the first 10 results only, and seldom modify the query. This suggests that traditional information retrieval techniques may not work well for answering web search requests. The correlation analysis showed that the most highly correlated items are constituents of phrases. This result indicates it may be useful for search engines to consider search terms as parts of phrases even if the user did not explicitly specify them as such."}],"year":"1999","_id":"11895","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":33,"page":"6-12","publication_identifier":{"issn":["0163-5840"]},"citation":{"apa":"Silverstein, C., Marais, H., Henzinger, M. H., & Moricz, M. (1999). Analysis of a very large web search engine query log. ACM SIGIR Forum. Association for Computing Machinery. https://doi.org/10.1145/331403.331405","chicago":"Silverstein, Craig, Hannes Marais, Monika H Henzinger, and Michael Moricz. “Analysis of a Very Large Web Search Engine Query Log.” ACM SIGIR Forum. Association for Computing Machinery, 1999. https://doi.org/10.1145/331403.331405.","ieee":"C. Silverstein, H. Marais, M. H. Henzinger, and M. Moricz, “Analysis of a very large web search engine query log,” ACM SIGIR Forum, vol. 33, no. 1. Association for Computing Machinery, pp. 6–12, 1999.","short":"C. Silverstein, H. Marais, M.H. Henzinger, M. Moricz, ACM SIGIR Forum 33 (1999) 6–12.","ista":"Silverstein C, Marais H, Henzinger MH, Moricz M. 1999. Analysis of a very large web search engine query log. ACM SIGIR Forum. 33(1), 6–12.","mla":"Silverstein, Craig, et al. “Analysis of a Very Large Web Search Engine Query Log.” ACM SIGIR Forum, vol. 33, no. 1, Association for Computing Machinery, 1999, pp. 6–12, doi:10.1145/331403.331405.","ama":"Silverstein C, Marais H, Henzinger MH, Moricz M. Analysis of a very large web search engine query log. ACM SIGIR Forum. 1999;33(1):6-12. doi:10.1145/331403.331405"},"issue":"1","article_type":"original","status":"public","oa":1,"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-02-17T14:46:04Z","doi":"10.1145/331403.331405","date_published":"1999-01-01T00:00:00Z","author":[{"full_name":"Silverstein, Craig","last_name":"Silverstein","first_name":"Craig"},{"full_name":"Marais, Hannes","last_name":"Marais","first_name":"Hannes"},{"first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Moricz","first_name":"Michael","full_name":"Moricz, Michael"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/331403.331405"}],"intvolume":" 33","month":"01","language":[{"iso":"eng"}],"day":"01"},{"publist_id":"2943","oa_version":"Published Version","date_created":"2018-12-11T12:03:22Z","publisher":"Society for Neuroscience","title":"Fast network oscillations in the hippocampal CA1 region of the behaving rat","publication":"Journal of Neuroscience","extern":"1","abstract":[{"lang":"eng","text":"This study examined intermittent, high-frequency (100-200 Hz) oscillatory patterns in the CA1 region of the hippocampus in the absence of theta activity, i.e., during and in between sharp wave (SPW) bursts. Pyramidal and interneuronal activity was phase-locked not only to large amplitude (>7 SD from baseline) oscillatory events, which are present mainly during SPWs, but to smaller amplitude (<4 SD) patterns, as well. Large-amplitude events were in the 140-200 Hz, "ripple" frequency range. Lower-amplitude events, however, contained slower, 100-130 Hz ("slow") oscillatory patterns. Fast ripple waves reversed just below the CA1 pyramidal layer, whereas slow oscillatory potentials reversed in the stratum radiatum and/or in the stratum oriens. Parallel CA1-CA3 recordings revealed correlated CA3 field and unit activity to the slow CA1 waves but not to fast ripple waves. These findings suggest that fast ripples emerge in the CA1 region, whereas slow (100-130 Hz) oscillatory patterns are generated in the CA3 region and transferred to the CA1 field."}],"year":"1999","_id":"3444","type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","volume":19,"publication_identifier":{"issn":["0270-6474"]},"citation":{"apa":"Csicsvari, J. L., Hirase, H., Czurkó, A., Mamiya, A., & Buzsáki, G. (1999). Fast network oscillations in the hippocampal CA1 region of the behaving rat. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.19-16-j0001.1999","chicago":"Csicsvari, Jozsef L, Hajima Hirase, András Czurkó, Akira Mamiya, and György Buzsáki. “Fast Network Oscillations in the Hippocampal CA1 Region of the Behaving Rat.” Journal of Neuroscience. Society for Neuroscience, 1999. https://doi.org/10.1523/JNEUROSCI.19-16-j0001.1999.","ieee":"J. L. Csicsvari, H. Hirase, A. Czurkó, A. Mamiya, and G. Buzsáki, “Fast network oscillations in the hippocampal CA1 region of the behaving rat,” Journal of Neuroscience, vol. 19, no. 16. Society for Neuroscience, 1999.","short":"J.L. Csicsvari, H. Hirase, A. Czurkó, A. Mamiya, G. Buzsáki, Journal of Neuroscience 19 (1999).","mla":"Csicsvari, Jozsef L., et al. “Fast Network Oscillations in the Hippocampal CA1 Region of the Behaving Rat.” Journal of Neuroscience, vol. 19, no. 16, Society for Neuroscience, 1999, doi:10.1523/JNEUROSCI.19-16-j0001.1999.","ista":"Csicsvari JL, Hirase H, Czurkó A, Mamiya A, Buzsáki G. 1999. Fast network oscillations in the hippocampal CA1 region of the behaving rat. Journal of Neuroscience. 19(16).","ama":"Csicsvari JL, Hirase H, Czurkó A, Mamiya A, Buzsáki G. Fast network oscillations in the hippocampal CA1 region of the behaving rat. Journal of Neuroscience. 1999;19(16). doi:10.1523/JNEUROSCI.19-16-j0001.1999"},"article_type":"original","external_id":{"pmid":["10436076"]},"issue":"16","status":"public","oa":1,"quality_controlled":"1","scopus_import":"1","date_updated":"2022-09-07T13:41:18Z","doi":"10.1523/JNEUROSCI.19-16-j0001.1999","article_processing_charge":"No","author":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"},{"full_name":"Hirase, Hajima","first_name":"Hajima","last_name":"Hirase"},{"full_name":"Czurkó, András","last_name":"Czurkó","first_name":"András"},{"last_name":"Mamiya","first_name":"Akira","full_name":"Mamiya, Akira"},{"last_name":"Buzsáki","first_name":"György","full_name":"Buzsáki, György"}],"date_published":"1999-08-15T00:00:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782850/"}],"intvolume":" 19","language":[{"iso":"eng"}],"month":"08","day":"15","pmid":1},{"oa_version":"Published Version","date_created":"2018-12-11T12:03:22Z","publist_id":"2942","title":"Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat","publication":"Journal of Neuroscience","publisher":"Society for Neuroscience","abstract":[{"lang":"eng","text":"The medial septal region and the hippocampus are connected reciprocally via GABAergic neurons, but the physiological role of this loop is still not well understood. In an attempt to reveal the physiological effects of the hippocamposeptal GABAergic projection, we cross-correlated hippocampal sharp wave (SPW) ripples or theta activity and extracellular units recorded in the medial septum and diagonal band of Broca (MSDB) in freely moving rats. The majority of single MSDB cells (60%) were significantly suppressed during SPWs. Most cells inhibited during SPW (80%) fired rhythmically and phase-locked to the negative peak of the CA1 pyramidal layer theta waves. Because both SPW and the negative peak of local theta waves correspond to the maximum discharge probability of CA1 pyramidal cells and interneuron classes, the findings indicate that the activity of medial septal neurons can be negatively (during SPW) or positively (during theta waves) correlated with the activity of hippocampal interneurons. We hypothesize that the functional coupling between medial septal neurons and hippocampal interneurons varies in a state-dependent manner."}],"extern":"1","_id":"3445","year":"1999","page":"6191 - 6199","volume":19,"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","citation":{"short":"G. Dragoi, D. Carpi, M. Recce, J.L. Csicsvari, G. Buzsáki, Journal of Neuroscience 19 (1999) 6191–6199.","ista":"Dragoi G, Carpi D, Recce M, Csicsvari JL, Buzsáki G. 1999. Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat. Journal of Neuroscience. 19(14), 6191–6199.","mla":"Dragoi, George, et al. “Interactions between Hippocampus and Medial Septum during Sharp Waves and Theta Oscillation in the Behaving Rat.” Journal of Neuroscience, vol. 19, no. 14, Society for Neuroscience, 1999, pp. 6191–99, doi:10.1523/JNEUROSCI.19-14-06191.1999.","ama":"Dragoi G, Carpi D, Recce M, Csicsvari JL, Buzsáki G. Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat. Journal of Neuroscience. 1999;19(14):6191-6199. doi:10.1523/JNEUROSCI.19-14-06191.1999","apa":"Dragoi, G., Carpi, D., Recce, M., Csicsvari, J. L., & Buzsáki, G. (1999). Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.19-14-06191.1999","chicago":"Dragoi, George, Daniel Carpi, Michael Recce, Jozsef L Csicsvari, and György Buzsáki. “Interactions between Hippocampus and Medial Septum during Sharp Waves and Theta Oscillation in the Behaving Rat.” Journal of Neuroscience. Society for Neuroscience, 1999. https://doi.org/10.1523/JNEUROSCI.19-14-06191.1999.","ieee":"G. Dragoi, D. Carpi, M. Recce, J. L. Csicsvari, and G. Buzsáki, “Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat,” Journal of Neuroscience, vol. 19, no. 14. Society for Neuroscience, pp. 6191–6199, 1999."},"publication_identifier":{"issn":["0270-6474"]},"oa":1,"acknowledgement":"This work was supported by National Institutes of Health Grants NS34994 and MH54671. We thank Z. Borhegyi, H. Hirase, C. King, and Z. Nadásdy for help and support and T. F. Freund for his comments on this manuscript.","status":"public","article_type":"original","external_id":{"pmid":["10407055"]},"issue":"14","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Dragoi, George","first_name":"George","last_name":"Dragoi"},{"full_name":"Carpi, Daniel","last_name":"Carpi","first_name":"Daniel"},{"last_name":"Recce","first_name":"Michael","full_name":"Recce, Michael"},{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Buzsáki, György","first_name":"György","last_name":"Buzsáki"}],"date_published":"1999-07-15T00:00:00Z","doi":"10.1523/JNEUROSCI.19-14-06191.1999","date_updated":"2022-09-07T13:37:41Z","article_processing_charge":"No","intvolume":" 19","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6783073/","open_access":"1"}],"publication_status":"published","language":[{"iso":"eng"}],"month":"07","pmid":1,"day":"15"},{"extern":"1","abstract":[{"lang":"eng","text":"Information in neuronal networks may be represented by the spatiotemporal patterns of spikes. Here we examined the temporal coordination of pyramidal cell spikes in the rat hippocampus during slow-wave sleep. In addition, rats were trained to run in a defined position in space (running wheel) to activate a selected group of pyramidal cells. A template-matching method and a joint probability map method were used for sequence search. Repeating spike sequences in excess of chance occurrence were examined by comparing the number of repeating sequences in the original spike trains and in surrogate trains after Monte Carlo shuffling of the spikes. Four different shuffling procedures were used to control for the population dynamics of hippocampal neurons. Repeating spike sequences in the recorded cell assemblies were present in both the awake and sleeping animal in excess of what might be predicted by random variations. Spike sequences observed during wheel running were “replayed” at a faster timescale during single sharp-wave bursts of slow-wave sleep. We hypothesize that the endogenously expressed spike sequences during sleep reflect reactivation of the circuitry modified by previous experience. Reactivation of acquired sequences may serve to consolidate information."}],"publist_id":"2866","oa_version":"Published Version","date_created":"2018-12-11T12:03:45Z","publisher":"Society for Neuroscience","title":"Replay and time compression of recurring spike sequences in the hippocampus","publication":"Journal of Neuroscience","publication_identifier":{"issn":["0270-6474"]},"citation":{"ieee":"Z. Nádasdy, H. Hirase, A. Czurkó, J. L. Csicsvari, and G. Buzsáki, “Replay and time compression of recurring spike sequences in the hippocampus,” Journal of Neuroscience, vol. 19, no. 21. Society for Neuroscience, pp. 9497–9507, 1999.","chicago":"Nádasdy, Zoltán, Hajima Hirase, András Czurkó, Jozsef L Csicsvari, and György Buzsáki. “Replay and Time Compression of Recurring Spike Sequences in the Hippocampus.” Journal of Neuroscience. Society for Neuroscience, 1999. https://doi.org/10.1523/JNEUROSCI.19-21-09497.1999.","apa":"Nádasdy, Z., Hirase, H., Czurkó, A., Csicsvari, J. L., & Buzsáki, G. (1999). Replay and time compression of recurring spike sequences in the hippocampus. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.19-21-09497.1999","ama":"Nádasdy Z, Hirase H, Czurkó A, Csicsvari JL, Buzsáki G. Replay and time compression of recurring spike sequences in the hippocampus. Journal of Neuroscience. 1999;19(21):9497-9507. doi:10.1523/JNEUROSCI.19-21-09497.1999","ista":"Nádasdy Z, Hirase H, Czurkó A, Csicsvari JL, Buzsáki G. 1999. Replay and time compression of recurring spike sequences in the hippocampus. Journal of Neuroscience. 19(21), 9497–9507.","short":"Z. Nádasdy, H. Hirase, A. Czurkó, J.L. Csicsvari, G. Buzsáki, Journal of Neuroscience 19 (1999) 9497–9507.","mla":"Nádasdy, Zoltán, et al. “Replay and Time Compression of Recurring Spike Sequences in the Hippocampus.” Journal of Neuroscience, vol. 19, no. 21, Society for Neuroscience, 1999, pp. 9497–507, doi:10.1523/JNEUROSCI.19-21-09497.1999."},"external_id":{"pmid":["10531452"]},"article_type":"original","issue":"21","acknowledgement":"This work was supported by National Institutes of Health Grants NS34994 and MH54671 and by the Human Science Frontier Program. We thank Moshe Abeles, Michale Fee, Stuart Geman, Stephen Hanson, Darrell Henze, Günther Palm, Michael Recce, and Matthew Wilson for their suggestions with data analysis and comments on this manuscript.","status":"public","oa":1,"year":"1999","_id":"3518","type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"9497 - 9507","volume":19,"quality_controlled":"1","scopus_import":"1","date_updated":"2022-09-07T12:48:08Z","doi":"10.1523/JNEUROSCI.19-21-09497.1999","article_processing_charge":"No","author":[{"first_name":"Zoltán","last_name":"Nádasdy","full_name":"Nádasdy, Zoltán"},{"full_name":"Hirase, Hajima","last_name":"Hirase","first_name":"Hajima"},{"full_name":"Czurkó, András","first_name":"András","last_name":"Czurkó"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"},{"last_name":"Buzsáki","first_name":"György","full_name":"Buzsáki, György"}],"date_published":"1999-11-01T00:00:00Z","language":[{"iso":"eng"}],"month":"11","day":"01","pmid":1,"publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782894/","open_access":"1"}],"intvolume":" 19"},{"intvolume":" 19","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782375/"}],"publication_status":"published","pmid":1,"day":"01","month":"01","language":[{"iso":"eng"}],"author":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"},{"last_name":"Hirase","first_name":"Hajima","full_name":"Hirase, Hajima"},{"full_name":"Czurkó, András","last_name":"Czurkó","first_name":"András"},{"last_name":"Mamiya","first_name":"Akira","full_name":"Mamiya, Akira"},{"full_name":"Buzsáki, György","last_name":"Buzsáki","first_name":"György"}],"date_published":"1999-01-01T00:00:00Z","article_processing_charge":"No","date_updated":"2022-09-07T10:00:45Z","doi":"10.1523/JNEUROSCI.19-01-00274.1999","scopus_import":"1","quality_controlled":"1","volume":19,"page":"274 - 287","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","_id":"3524","year":"1999","oa":1,"acknowledgement":"This work was supported by National Institutes of Health Grants NS34994, MH54671, and 1P41RR09754 and by the Human Frontier Science Program. We thank Darrell A. Henze and M. Recce for their comments on this manuscript and Jamie Hetke and Ken Wise for supplying us with silicon probes.","status":"public","issue":"1","external_id":{"pmid":["9870957"]},"article_type":"original","citation":{"ama":"Csicsvari JL, Hirase H, Czurkó A, Mamiya A, Buzsáki G. Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving rat. Journal of Neuroscience. 1999;19(1):274-287. doi:10.1523/JNEUROSCI.19-01-00274.1999","short":"J.L. Csicsvari, H. Hirase, A. Czurkó, A. Mamiya, G. Buzsáki, Journal of Neuroscience 19 (1999) 274–287.","ista":"Csicsvari JL, Hirase H, Czurkó A, Mamiya A, Buzsáki G. 1999. Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving rat. Journal of Neuroscience. 19(1), 274–287.","mla":"Csicsvari, Jozsef L., et al. “Oscillatory Coupling of Hippocampal Pyramidal Cells and Interneurons in the Behaving Rat.” Journal of Neuroscience, vol. 19, no. 1, Society for Neuroscience, 1999, pp. 274–87, doi:10.1523/JNEUROSCI.19-01-00274.1999.","ieee":"J. L. Csicsvari, H. Hirase, A. Czurkó, A. Mamiya, and G. Buzsáki, “Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving rat,” Journal of Neuroscience, vol. 19, no. 1. Society for Neuroscience, pp. 274–287, 1999.","chicago":"Csicsvari, Jozsef L, Hajima Hirase, András Czurkó, Akira Mamiya, and György Buzsáki. “Oscillatory Coupling of Hippocampal Pyramidal Cells and Interneurons in the Behaving Rat.” Journal of Neuroscience. Society for Neuroscience, 1999. https://doi.org/10.1523/JNEUROSCI.19-01-00274.1999.","apa":"Csicsvari, J. L., Hirase, H., Czurkó, A., Mamiya, A., & Buzsáki, G. (1999). Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving rat. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.19-01-00274.1999"},"publication_identifier":{"issn":["0270-6474"]},"publication":"Journal of Neuroscience","title":"Oscillatory coupling of hippocampal pyramidal cells and interneurons in the behaving rat","publisher":"Society for Neuroscience","date_created":"2018-12-11T12:03:47Z","oa_version":"Published Version","publist_id":"2860","abstract":[{"lang":"eng","text":"We examined whether excitation and inhibition are balanced in hippocampal cortical networks. Extracellular field and single-unit activity were recorded by multiple tetrodes and multisite silicon probes to reveal the timing of the activity of hippocampal CAI pyramidal cells and classes of interneurons during theta waves and sharp wave burst (SPW)-associated field ripples. The somatic and dendritic inhibition of pyramidal cells was deduced from the activity of interneurons in the pyramidal layer [int(p)] and in the alveus and st. oriens [int(a/o)], respectively. int(p) and int(a/o) discharged an average of 60 and 20 degrees before the population discharge of pyramidal cells during the theta cycle, respectively. SPW ripples were associated with a 2.5-fold net increase of excitation. The discharge frequency of int(a/o) increased, decreased (”anti-SPW” cells), or did not change (”SPW-independent” cells) during SPW suggesting that not all interneurons are innervated by pyramidal cells. Int(p) either fired together with (unimodal cells) or both before and after (bimodal cells) the pyramidal cell burst. During fast-ripple oscillation, the activity of interneurons in both the int(p) and int(a/o) groups lagged the maximum discharge probability of pyramidal neurons by 1-2 msec. Network state changes, as reflected by field activity, covaried with changes in the spike train dynamics of single cells and their interactions. Summed activity of parallel-recorded interneurons, but not of pyramidal cells, reliably predicted theta cycles, whereas the reverse was true for the ripple cycles of SPWs. We suggest that network-driven excitability changes provide temporal windows of opportunity for single pyramidal cells to suppress, enable, or facilitate selective synaptic inputs."}],"extern":"1"},{"main_file_link":[{"url":"https://www.emis.de/journals/PIMB/080/3.html","open_access":"1"}],"intvolume":" 66","publication_status":"published","day":"01","month":"01","language":[{"iso":"eng"}],"date_published":"1999-01-01T00:00:00Z","author":[{"last_name":"Dey","first_name":"Tamal","full_name":"Dey, Tamal"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Guha, Sumanta","first_name":"Sumanta","last_name":"Guha"},{"last_name":"Nekhayev","first_name":"Dmitry","full_name":"Nekhayev, Dmitry"}],"article_processing_charge":"No","date_updated":"2023-03-22T13:20:32Z","quality_controlled":"1","volume":66,"page":"23 - 45","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","_id":"3582","year":"1999","oa":1,"acknowledgement":"The second author thanks Wolfgang Haken and Min Yan for interesting discussions and Günter Ziegler for suggesting the knot construction in the triangulation of the 3-sphere mentioned in Section 7.","status":"public","article_type":"original","citation":{"short":"T. Dey, H. Edelsbrunner, S. Guha, D. Nekhayev, Publications de l’Institut Mathématique 66 (1999) 23–45.","ista":"Dey T, Edelsbrunner H, Guha S, Nekhayev D. 1999. Topology preserving edge contraction. Publications de l’Institut Mathématique. 66, 23–45.","mla":"Dey, Tamal, et al. “Topology Preserving Edge Contraction.” Publications de l’Institut Mathématique, vol. 66, Mathematical Institute, Serbian Academy of Sciences and Arts, 1999, pp. 23–45.","ama":"Dey T, Edelsbrunner H, Guha S, Nekhayev D. Topology preserving edge contraction. Publications de l’Institut Mathématique. 1999;66:23-45.","apa":"Dey, T., Edelsbrunner, H., Guha, S., & Nekhayev, D. (1999). Topology preserving edge contraction. Publications de l’Institut Mathématique. Mathematical Institute, Serbian Academy of Sciences and Arts.","ieee":"T. Dey, H. Edelsbrunner, S. Guha, and D. Nekhayev, “Topology preserving edge contraction,” Publications de l’Institut Mathématique, vol. 66. Mathematical Institute, Serbian Academy of Sciences and Arts, pp. 23–45, 1999.","chicago":"Dey, Tamal, Herbert Edelsbrunner, Sumanta Guha, and Dmitry Nekhayev. “Topology Preserving Edge Contraction.” Publications de l’Institut Mathématique. Mathematical Institute, Serbian Academy of Sciences and Arts, 1999."},"publication_identifier":{"issn":["0350-1302"]},"publication":"Publications de l'Institut Mathématique","title":"Topology preserving edge contraction","publisher":"Mathematical Institute, Serbian Academy of Sciences and Arts","date_created":"2018-12-11T12:04:05Z","oa_version":"None","publist_id":"2803","abstract":[{"lang":"eng","text":"We study edge contractions in simplicial complexes and local conditions under which they preserve the topological type. The conditions are based on a generalized notion of boundary, which lends itself to defining a nested hierarchy of triangulable spaces measuring the distance to being a manifold."}],"extern":"1"},{"scopus_import":"1","quality_controlled":"1","date_published":"1998-02-04T00:00:00Z","author":[{"first_name":"Paul","last_name":"Burrows","full_name":"Burrows, Paul"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"},{"first_name":"Zóra","last_name":"Sváb","full_name":"Sváb, Zóra"},{"first_name":"Pàl","last_name":"Maliga","full_name":"Maliga, Pàl"},{"first_name":"Peter","last_name":"Nixon","full_name":"Nixon, Peter"}],"doi":"10.1093/emboj/17.4.868","date_updated":"2022-09-01T13:17:49Z","article_processing_charge":"No","language":[{"iso":"eng"}],"month":"02","pmid":1,"day":"04","intvolume":" 17","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1170436/"}],"publication_status":"published","abstract":[{"text":"The plastid genomes of several plants contain homologues, termed ndh genes, of genes encoding subunits of the NADH:ubiquinone oxidoreductase or complex I of mitochondria and eubacteria. The functional significance of the Ndh proteins in higher plants is uncertain. We show here that tobacco chloroplasts contain a protein complex of 550 kDa consisting of at least three of the ndh gene products: NdhI, NdhJ and NdhK. We have constructed mutant tobacco plants with disrupted ndhC, ndhK and ndhJ plastid genes, indicating that the Ndh complex is dispensible for plant growth under optimal growth conditions. Chlorophyll fluorescence analysis shows that in vivo the Ndh complex catalyses the post-illumination reduction of the plastoquinone pool and in the light optimizes the induction of photosynthesis under conditions of water stress. We conclude that the Ndh complex catalyses the reduction of the plastoquinone pool using stromal reductant and so acts as a respiratory complex. Overall, our data are compatible with the participation of the Ndh complex in cyclic electron flow around the photosystem I complex in the light and possibly in a chloroplast respiratory chain in the dark.","lang":"eng"}],"extern":"1","oa_version":"None","date_created":"2018-12-11T11:54:54Z","publist_id":"5129","title":"Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes","publication":"EMBO Journal","publisher":"Wiley-Blackwell","citation":{"apa":"Burrows, P., Sazanov, L. A., Sváb, Z., Maliga, P., & Nixon, P. (1998). Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1093/emboj/17.4.868","chicago":"Burrows, Paul, Leonid A Sazanov, Zóra Sváb, Pàl Maliga, and Peter Nixon. “Identification of a Functional Respiratory Complex in Chloroplasts through Analysis of Tobacco Mutants Containing Disrupted Plastid Ndh Genes.” EMBO Journal. Wiley-Blackwell, 1998. https://doi.org/10.1093/emboj/17.4.868.","ieee":"P. Burrows, L. A. Sazanov, Z. Sváb, P. Maliga, and P. Nixon, “Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes,” EMBO Journal, vol. 17, no. 4. Wiley-Blackwell, pp. 868–876, 1998.","mla":"Burrows, Paul, et al. “Identification of a Functional Respiratory Complex in Chloroplasts through Analysis of Tobacco Mutants Containing Disrupted Plastid Ndh Genes.” EMBO Journal, vol. 17, no. 4, Wiley-Blackwell, 1998, pp. 868–76, doi:10.1093/emboj/17.4.868.","short":"P. Burrows, L.A. Sazanov, Z. Sváb, P. Maliga, P. Nixon, EMBO Journal 17 (1998) 868–876.","ista":"Burrows P, Sazanov LA, Sváb Z, Maliga P, Nixon P. 1998. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO Journal. 17(4), 868–876.","ama":"Burrows P, Sazanov LA, Sváb Z, Maliga P, Nixon P. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO Journal. 1998;17(4):868-876. doi:10.1093/emboj/17.4.868"},"publication_identifier":{"issn":["0261-4189"]},"oa":1,"acknowledgement":"We thank Professor Süss (Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany) for the gift of the anti-FNR antiserum, Professor Masahiro Sugiura (Nagoya University, Japan) for the gift of plasmid pTB19 and Professor Peter Horton (University of Sheffield) for the loan of his ED-800T unit. P.B. is a recipient of a BBSRC studentship and the work was supported by grants from the BBSRC, The Royal Society (to P.J.N.) and The National Science Foundation (to P.M.).","status":"public","external_id":{"pmid":["9463365"]},"article_type":"original","issue":"4","_id":"1955","year":"1998","page":"868 - 876","volume":17,"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17"},{"extern":"1","abstract":[{"text":"\r\nThe plastid genomes of several plants contain ndh genes-homologues of genes encoding subunits of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I, involved in respiration in mitochondria and eubacteria. From sequence similarities with these genes, the ndh gene products have been suggested to form a large protein complex (Ndh complex); however, the structure and function of this complex remains to be established. Herein we report the isolation of the Ndh complex from the chloroplasts of the higher plant Pisum sativum. The purification procedure involved selective solubilization of the thylakoid membrane with dodecyl maltoside, followed by two anion-exchange chromatography steps and one size-exclusion chromatography step. The isolated Ndh complex has an apparent total molecular mass of approximately 550 kDa and according to SDS/PAGE consists of at least 16 subunits including NdhA, NdhI, NdhJ, NdhK, and NdhH, which were identified by N-terminal sequencing and immunoblotting. The Ndh complex showed an NADH- and deamino-NADH-specific dehydrogenase activity, characteristic of complex I, when either ferricyanide or the quinones menadione and duroquinone were used as electron acceptors. This study describes the isolation of the chloroplast analogue of the respiratory complex I and provides direct evidence for the function of the plastid Ndh complex as an NADH:plastoquinone oxidoreductase. Our results are compatible with a dual role for the Ndh complex in the chloro-respiratory and cyclic photophosphorylation pathways.","lang":"eng"}],"publisher":"National Academy of Sciences","publication":"PNAS","title":"The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes","publist_id":"5130","date_created":"2018-12-11T11:54:54Z","oa_version":"None","issue":"3","external_id":{"pmid":["9448329 "]},"article_type":"original","acknowledgement":"We gratefully acknowledge Dr. A.Carne (Institute of Cancer Research, London, U.K.) for help with N-terminal sequencing. We thank Prof. C. J. Leaver (University of Oxford, U.K.), Prof. K.-H. Süss (Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany), and Prof. L. J. Rogers (University of Aberystwyth, U.K.) for gifts of antiserum against maize mitochondrial cytochrome oxidase subunit 1 and cytochrome bc1 complex, spinach FNR, and spinach ferredoxin, respectively. This work was supported by grants from The Royal Society and the Biotechnology and Biological Sciences Research Council.","status":"public","oa":1,"publication_identifier":{"issn":["0027-8424"]},"citation":{"ama":"Sazanov LA, Burrows P, Nixon P. The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes. PNAS. 1998;95(3):1319-1324. doi:10.1073/pnas.95.3.1319","mla":"Sazanov, Leonid A., et al. “The Plastid Ndh Genes Code for an NADH-Specific Dehydrogenase: Isolation of a Complex I Analogue from Pea Thylakoid Membranes.” PNAS, vol. 95, no. 3, National Academy of Sciences, 1998, pp. 1319–24, doi:10.1073/pnas.95.3.1319.","ista":"Sazanov LA, Burrows P, Nixon P. 1998. The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes. PNAS. 95(3), 1319–1324.","short":"L.A. Sazanov, P. Burrows, P. Nixon, PNAS 95 (1998) 1319–1324.","chicago":"Sazanov, Leonid A, Paul Burrows, and Peter Nixon. “The Plastid Ndh Genes Code for an NADH-Specific Dehydrogenase: Isolation of a Complex I Analogue from Pea Thylakoid Membranes.” PNAS. National Academy of Sciences, 1998. https://doi.org/10.1073/pnas.95.3.1319.","ieee":"L. A. Sazanov, P. Burrows, and P. Nixon, “The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes,” PNAS, vol. 95, no. 3. National Academy of Sciences, pp. 1319–1324, 1998.","apa":"Sazanov, L. A., Burrows, P., & Nixon, P. (1998). The plastid ndh genes code for an NADH-specific dehydrogenase: Isolation of a complex I analogue from pea thylakoid membranes. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.95.3.1319"},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","volume":95,"page":"1319 - 1324","year":"1998","_id":"1956","article_processing_charge":"No","doi":"10.1073/pnas.95.3.1319","date_updated":"2022-09-01T13:47:05Z","date_published":"1998-02-03T00:00:00Z","author":[{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"},{"first_name":"Paul","last_name":"Burrows","full_name":"Burrows, Paul"},{"last_name":"Nixon","first_name":"Peter","full_name":"Nixon, Peter"}],"quality_controlled":"1","scopus_import":"1","day":"03","pmid":1,"month":"02","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 95","main_file_link":[{"url":"https://europepmc.org/article/pmc/18756","open_access":"1"}]},{"citation":{"ieee":"T. Hausel, “Compactification of moduli of Higgs bundles,” Journal fur die Reine und Angewandte Mathematik, vol. 1998, no. 503. Walter de Gruyter, pp. 169–192, 1998.","chicago":"Hausel, Tamás. “Compactification of Moduli of Higgs Bundles.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 1998. https://doi.org/10.1515/crll.1998.096.","apa":"Hausel, T. (1998). Compactification of moduli of Higgs bundles. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crll.1998.096","ama":"Hausel T. Compactification of moduli of Higgs bundles. Journal fur die Reine und Angewandte Mathematik. 1998;1998(503):169-192. doi:10.1515/crll.1998.096","mla":"Hausel, Tamás. “Compactification of Moduli of Higgs Bundles.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 1998, no. 503, Walter de Gruyter, 1998, pp. 169–92, doi:10.1515/crll.1998.096.","ista":"Hausel T. 1998. Compactification of moduli of Higgs bundles. Journal fur die Reine und Angewandte Mathematik. 1998(503), 169–192.","short":"T. Hausel, Journal Fur Die Reine Und Angewandte Mathematik 1998 (1998) 169–192."},"publication_identifier":{"issn":["1435-5345"]},"status":"public","oa":1,"article_type":"original","external_id":{"arxiv":["math/9804083"]},"issue":"503","_id":"1449","year":"1998","page":"169 - 192","volume":1998,"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","abstract":[{"lang":"eng","text":"In this paper we consider a canonical compactification of M, the moduli space of stable Higgs bundles with fixed determinant of odd degree over a Riemann surface Σ, producing a projective variety M̄ = M ∪ Z. We give a detailed study of the spaces M̄, Z and M. In doing so we reprove some assertions of Laumon and Thaddeus on the nilpotent cone."}],"extern":"1","arxiv":1,"oa_version":"Preprint","date_created":"2018-12-11T11:52:05Z","publist_id":"5746","title":"Compactification of moduli of Higgs bundles","publication":"Journal fur die Reine und Angewandte Mathematik","publisher":"Walter de Gruyter","language":[{"iso":"eng"}],"month":"10","day":"01","intvolume":" 1998","main_file_link":[{"url":"http://arxiv.org/abs/math/9804083","open_access":"1"}],"publication_status":"published","scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Tamas","last_name":"Hausel","full_name":"Hausel, Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"date_published":"1998-10-01T00:00:00Z","doi":"10.1515/crll.1998.096","date_updated":"2022-09-01T13:51:07Z","article_processing_charge":"No"},{"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"1011 - 1040","volume":2,"year":"1998","_id":"1450","external_id":{"arxiv":["math/9805071"]},"article_type":"original","issue":"5","acknowledgement":"First of all I would like to thank my supervisor Nigel Hitchin for suggesting Problem 1, and for his help and \r\n encouragement. I am grateful to Michael Thaddeus for his inspiring paper [Thai], enlightening communications and his constant interest in my work. I am also indebted to Manfred Lehn for the idea of the proof of Theorem 6.2. I have found\r\nconversations with Michael Atiyah, Frances Kirwan and Graeme Segal very stimulating. I thank the Mathematical Institute and St. Catherine's College, Oxford for their hospitality during the preparation of this work. Finally I thank Trinity College, Cambridge for financial support.","oa":1,"status":"public","publication_identifier":{"issn":["1095-0761"]},"citation":{"apa":"Hausel, T. (1998). Vanishing of intersection numbers on the moduli space of Higgs bundles. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.1998.v2.n5.a3","chicago":"Hausel, Tamás. “Vanishing of Intersection Numbers on the Moduli Space of Higgs Bundles.” Advances in Theoretical and Mathematical Physics. International Press, 1998. https://doi.org/10.4310/ATMP.1998.v2.n5.a3.","ieee":"T. Hausel, “Vanishing of intersection numbers on the moduli space of Higgs bundles,” Advances in Theoretical and Mathematical Physics, vol. 2, no. 5. International Press, pp. 1011–1040, 1998.","short":"T. Hausel, Advances in Theoretical and Mathematical Physics 2 (1998) 1011–1040.","mla":"Hausel, Tamás. “Vanishing of Intersection Numbers on the Moduli Space of Higgs Bundles.” Advances in Theoretical and Mathematical Physics, vol. 2, no. 5, International Press, 1998, pp. 1011–40, doi:10.4310/ATMP.1998.v2.n5.a3.","ista":"Hausel T. 1998. Vanishing of intersection numbers on the moduli space of Higgs bundles. Advances in Theoretical and Mathematical Physics. 2(5), 1011–1040.","ama":"Hausel T. Vanishing of intersection numbers on the moduli space of Higgs bundles. Advances in Theoretical and Mathematical Physics. 1998;2(5):1011-1040. doi:10.4310/ATMP.1998.v2.n5.a3"},"publisher":"International Press","title":"Vanishing of intersection numbers on the moduli space of Higgs bundles","publication":"Advances in Theoretical and Mathematical Physics","publist_id":"5747","oa_version":"Preprint","date_created":"2018-12-11T11:52:06Z","arxiv":1,"extern":"1","abstract":[{"lang":"eng","text":"In this paper we consider the topological side of a problem which is the analogue of Sen's S-duality testing conjecture for Hitchin's moduli space M of rank 2 stable Higgs bundles of fixed determinant of odd degree over a Riemann surface ∑. We prove that all intersection numbers in the compactly supported cohomology of M vanish, i.e. "there are no topological L2 harmonic forms on M". This result generalizes the well known vanishing of the Euler characteristic of the moduli space of rank 2 stable bundles N of fixed determinant of odd degree over ∑. Our proof shows that the vanishing of all intersection numbers of H* cpt(M) is given by relations analogous to the Mumford relations in the cohomology ring of N."}],"publication_status":"published","intvolume":" 2","main_file_link":[{"url":"http://arxiv.org/abs/math/9805071","open_access":"1"}],"day":"01","language":[{"iso":"eng"}],"month":"09","doi":"10.4310/ATMP.1998.v2.n5.a3","date_updated":"2022-09-01T14:09:49Z","article_processing_charge":"No","author":[{"first_name":"Tamas","last_name":"Hausel","full_name":"Hausel, Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"date_published":"1998-09-01T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"doi":"10.1523/JNEUROSCI.18-20-08111.1998","date_updated":"2022-08-29T14:20:39Z","article_processing_charge":"No","author":[{"first_name":"Marco","last_name":"Martina","full_name":"Martina, Marco"},{"last_name":"Schultz","first_name":"Jobst","full_name":"Schultz, Jobst"},{"full_name":"Ehmke, Heimo","last_name":"Ehmke","first_name":"Heimo"},{"last_name":"Monyer","first_name":"Hannah","full_name":"Monyer, Hannah"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_published":"1998-10-15T00:00:00Z","quality_controlled":"1","scopus_import":"1","day":"15","pmid":1,"language":[{"iso":"eng"}],"month":"10","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792860/","open_access":"1"}],"intvolume":" 18","extern":"1","abstract":[{"lang":"eng","text":"We have examined gating and pharmacological characteristics of somatic K+ channels in fast-spiking interneurons and regularly spiking principal neurons of hippocampal slices. In nucleated patches isolated from basket cells of the dentate gyrus, a fast delayed rectifier K+ current component that was highly sensitive to tetraethylammonium (TEA) and 4-aminopyridine (4- AP) (half-maximal inhibitory concentrations <0.1 mM) predominated, contributing an average of 58% to the total K+ current in these cells. By contrast, in pyramidal neurons of the CA1 region a rapidly inactivating A- type K+ current component that was TEA-resistant prevailed, contributing 61% to the total K+ current. Both types of neurons also showed small amounts of the K+ current component mainly found in the other type of neuron and, in addition, a slow delayed rectifier K+ current component with intermediate properties (sow inactivation, intermediate sensitivity to TEA). Single-cell RT-PCR analysis of mRNA revealed that Kv3 (Kv3.1, Kv3.2) subunit transcripts were expressed in almost all (89%) of the interneurons but only in 17% of the pyramidal neurons. In contrast, Kv4 (Kv4.2, Kv4.3) subunit mRNAs were present in 87% of pyramidal neurons but only in 55% of interneurons. Selective block of fast delayed rectifier K+ channels, presumably assembled from Kv3 subunits, by 4-AP reduced substantially the action potential frequency in interneurons. These results indicate that the differential expression of Kv3 and Kv4 subunits shapes the action potential phenotypes of principal neurons and interneurons in the cortex."}],"publisher":"Society for Neuroscience","title":"Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus","publication":"Journal of Neuroscience","publist_id":"2899","oa_version":"None","date_created":"2018-12-11T12:03:35Z","article_type":"original","external_id":{"pmid":["9763458"]},"issue":"20","acknowledgement":"Supported by German Israeli Foundation Grant I 0352–073.01/94 to P.J. and Deutsche Forschungsgemeinschaft Grant Mo 432/3–1 to H.M. We thank Drs. L. Y. Jan, D. McKinnon, O. Pongs, L. Salkoff, S. H. Snyder, and J. S. Trimmer for providing plasmids, Dr. D. J. Surmeier for sharing unpublished data, and Drs. J. Bischofberger and J. R. P. Geiger for critically reading this manuscript. M.M. and J.H.S. contributed equally to this work.","status":"public","oa":1,"publication_identifier":{"issn":["0270-6474"]},"citation":{"apa":"Martina, M., Schultz, J., Ehmke, H., Monyer, H., & Jonas, P. M. (1998). Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.18-20-08111.1998","chicago":"Martina, Marco, Jobst Schultz, Heimo Ehmke, Hannah Monyer, and Peter M Jonas. “Functional and Molecular Differences between Voltage-Gated K+ Channels of Fast-Spiking Interneurons and Pyramidal Neurons of Rat Hippocampus.” Journal of Neuroscience. Society for Neuroscience, 1998. https://doi.org/10.1523/JNEUROSCI.18-20-08111.1998.","ieee":"M. Martina, J. Schultz, H. Ehmke, H. Monyer, and P. M. Jonas, “Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus,” Journal of Neuroscience, vol. 18, no. 20. Society for Neuroscience, pp. 8111–8125, 1998.","mla":"Martina, Marco, et al. “Functional and Molecular Differences between Voltage-Gated K+ Channels of Fast-Spiking Interneurons and Pyramidal Neurons of Rat Hippocampus.” Journal of Neuroscience, vol. 18, no. 20, Society for Neuroscience, 1998, pp. 8111–25, doi:10.1523/JNEUROSCI.18-20-08111.1998.","short":"M. Martina, J. Schultz, H. Ehmke, H. Monyer, P.M. Jonas, Journal of Neuroscience 18 (1998) 8111–8125.","ista":"Martina M, Schultz J, Ehmke H, Monyer H, Jonas PM. 1998. Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus. Journal of Neuroscience. 18(20), 8111–8125.","ama":"Martina M, Schultz J, Ehmke H, Monyer H, Jonas PM. Functional and molecular differences between voltage-gated K+ channels of fast-spiking interneurons and pyramidal neurons of rat hippocampus. Journal of Neuroscience. 1998;18(20):8111-8125. doi:10.1523/JNEUROSCI.18-20-08111.1998"},"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"8111 - 8125","volume":18,"year":"1998","_id":"3488"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ipn":"US5850229A","type":"patent","ipc":"G06T13/20 ; G06T2210/44","year":"1998","publication_date":"1998-12-15","_id":"3506","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US5850229A"}],"day":"15","oa":1,"status":"public","month":"12","citation":{"apa":"Edelsbrunner, H., & Fu, P. (1998). Apparatus and method for geometric morphing.","ieee":"H. Edelsbrunner and P. Fu, “Apparatus and method for geometric morphing.” 1998.","chicago":"Edelsbrunner, Herbert, and Ping Fu. “Apparatus and Method for Geometric Morphing,” 1998.","mla":"Edelsbrunner, Herbert, and Ping Fu. Apparatus and Method for Geometric Morphing. 1998.","short":"H. Edelsbrunner, P. Fu, (1998).","ista":"Edelsbrunner H, Fu P. 1998. Apparatus and method for geometric morphing.","ama":"Edelsbrunner H, Fu P. Apparatus and method for geometric morphing. 1998."},"title":"Apparatus and method for geometric morphing","applicant":["Raindrop Geomagic, Inc."],"publist_id":"2881","date_created":"2018-12-11T12:03:41Z","oa_version":"Published Version","article_processing_charge":"No","date_updated":"2022-01-05T15:16:35Z","date_published":"1998-12-15T00:00:00Z","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Fu","first_name":"Ping","full_name":"Fu, Ping"}],"extern":"1","abstract":[{"text":"A method of geometric morphing between a first object having a first shape and a second object having a second shape. The method includes the steps of generating a first Delaunay complex corresponding to the first shape and a second Delaunay complex corresponding to the second shape and generating a plurality of intermediary Delaunay complexes defined by a continuous family of mixed shapes corresponding to a mixing of the first shape and the second shape. The method further includes the steps of constructing a first skin corresponding to the first Delaunay complex and a second skin corresponding to the second Delaunay complex and constructing a plurality of intermediary skins corresponding to the plurality of intermediary Delaunay complexes. The first skin, second skin and plurality of intermediary skins may be visually displayed on an output device.","lang":"eng"}]},{"abstract":[{"text":"Determining the way in which deleterious mutations interact in their effects on fitness is crucial to numerous areas in population genetics and evolutionary biology. For example, if each additional mutation leads to a greater decrease in log fitness than the last (synergistic epistasis), then the evolution of sex and recombination may be favored to facilitate the elimination of deleterious mutations. However, there is a severe shortage of relevant data. Three relatively simple experimental methods to test for epistasis between deleterious mutations in haploid species have recently been proposed. These methods involve crossing individuals and examining the mean and/or skew in log fitness of the offspring and parents. The main aim of this paper is to formalize these methods, and determine the most effective way in which tests for epistasis could be carried out. We show that only one of these methods is likely to give useful results: crossing individuals that have very different numbers of deleterious mutations, and comparing the mean log fitness of the parents with that of their offspring. We also reconsider experimental data collected on Chlamydomonas moewussi using two of the three methods. Finally, we suggest how the test could be applied to diploid species.","lang":"eng"}],"extern":"1","publication":"Genetics","title":"Testing for epistasis between deleterious mutations","publisher":"Genetics Society of America","date_created":"2018-12-11T12:04:19Z","oa_version":"None","publist_id":"2755","acknowledgement":"We thank BRIAN CHARLESWORTH, ANDREW CLARK, LAURENCE HURST, PETER KEIGHTLEY, ALEXEY KONDRASHOV, CURT LIVELY, MARGARET MACKINNON, KATRINA LYTHGOE, SALLY OTTO, ANDREW READ and ARJAN DE VISSER for useful discussion and comments on the manuscript. This work was supported by the Biotechnology and Biological Sciences Research Council.","oa":1,"status":"public","issue":"1","external_id":{"pmid":["9584115"]},"article_type":"original","citation":{"short":"S. West, A. Peters, N.H. Barton, Genetics 149 (1998) 435–444.","mla":"West, Stuart, et al. “Testing for Epistasis between Deleterious Mutations.” Genetics, vol. 149, no. 1, Genetics Society of America, 1998, pp. 435–44, doi:10.1093/genetics/149.1.435.","ista":"West S, Peters A, Barton NH. 1998. Testing for epistasis between deleterious mutations. Genetics. 149(1), 435–444.","ama":"West S, Peters A, Barton NH. Testing for epistasis between deleterious mutations. Genetics. 1998;149(1):435-444. doi:10.1093/genetics/149.1.435","apa":"West, S., Peters, A., & Barton, N. H. (1998). Testing for epistasis between deleterious mutations. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/149.1.435","ieee":"S. West, A. Peters, and N. H. Barton, “Testing for epistasis between deleterious mutations,” Genetics, vol. 149, no. 1. Genetics Society of America, pp. 435–444, 1998.","chicago":"West, Stuart, Andrew Peters, and Nicholas H Barton. “Testing for Epistasis between Deleterious Mutations.” Genetics. Genetics Society of America, 1998. https://doi.org/10.1093/genetics/149.1.435."},"publication_identifier":{"issn":["0016-6731"]},"volume":149,"page":"435 - 444","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","_id":"3628","year":"1998","author":[{"first_name":"Stuart","last_name":"West","full_name":"West, Stuart"},{"full_name":"Peters, Andrew","last_name":"Peters","first_name":"Andrew"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"date_published":"1998-05-01T00:00:00Z","article_processing_charge":"No","date_updated":"2022-08-29T08:53:09Z","doi":"10.1093/genetics/149.1.435","scopus_import":"1","quality_controlled":"1","pmid":1,"day":"01","month":"05","language":[{"iso":"eng"}],"intvolume":" 149","main_file_link":[{"url":"https://academic.oup.com/genetics/article/149/1/435/6034229","open_access":"1"}],"publication_status":"published"},{"publist_id":"2114","date_created":"2018-12-11T12:06:26Z","oa_version":"Published Version","publisher":"Elsevier","publication":"Discrete Applied Mathematics","title":"On the definition and the construction of pockets in macromolecules","extern":"1","abstract":[{"text":"The shape of a protein is important for its functions, This includes the location and size of identifiable regions in its complement space. We formally define pockets as regions in the complement with limited accessibility from the outside. Pockets can be efficiently constructed by an algorithm based on alpha complexes. The algorithm is implemented and applied to proteins with known three-dimensional conformations. 1998 Published by Elsevier Science B.V. All rights reserved.","lang":"eng"}],"year":"1998","_id":"4013","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","volume":88,"page":"83 - 102","publication_identifier":{"issn":["0166-218X"]},"citation":{"ieee":"H. Edelsbrunner, M. Facello, and J. Liang, “On the definition and the construction of pockets in macromolecules,” Discrete Applied Mathematics, vol. 88, no. 1–3. Elsevier, pp. 83–102, 1998.","chicago":"Edelsbrunner, Herbert, Michael Facello, and Jie Liang. “On the Definition and the Construction of Pockets in Macromolecules.” Discrete Applied Mathematics. Elsevier, 1998. https://doi.org/10.1016/S0166-218X(98)00067-5.","apa":"Edelsbrunner, H., Facello, M., & Liang, J. (1998). On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/S0166-218X(98)00067-5","ama":"Edelsbrunner H, Facello M, Liang J. On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics. 1998;88(1-3):83-102. doi:10.1016/S0166-218X(98)00067-5","short":"H. Edelsbrunner, M. Facello, J. Liang, Discrete Applied Mathematics 88 (1998) 83–102.","ista":"Edelsbrunner H, Facello M, Liang J. 1998. On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics. 88(1–3), 83–102.","mla":"Edelsbrunner, Herbert, et al. “On the Definition and the Construction of Pockets in Macromolecules.” Discrete Applied Mathematics, vol. 88, no. 1–3, Elsevier, 1998, pp. 83–102, doi:10.1016/S0166-218X(98)00067-5."},"issue":"1-3","external_id":{"pmid":["9390238"]},"article_type":"original","acknowledgement":"The authors thank Ping Fu and Ernst Miicke for their contributions to the alpha shapes software in which the pockets software is embedded. ","status":"public","oa":1,"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2022-08-25T15:06:30Z","doi":"10.1016/S0166-218X(98)00067-5","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Facello, Michael","first_name":"Michael","last_name":"Facello"},{"full_name":"Liang, Jie","first_name":"Jie","last_name":"Liang"}],"date_published":"1998-11-09T00:00:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0166218X98000675?via%3Dihub"}],"intvolume":" 88","month":"11","language":[{"iso":"eng"}],"day":"09","pmid":1},{"page":"1884 - 1897","volume":7,"type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"4017","year":"1998","status":"public","oa":1,"article_type":"original","external_id":{"pmid":["9761470 "]},"issue":"9","citation":{"chicago":"Liang, Jie, Herbert Edelsbrunner, and Clare Woodward. “Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design.” Protein Science. Wiley-Blackwell, 1998. https://doi.org/10.1002/pro.5560070905.","ieee":"J. Liang, H. Edelsbrunner, and C. Woodward, “Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design,” Protein Science, vol. 7, no. 9. Wiley-Blackwell, pp. 1884–1897, 1998.","apa":"Liang, J., Edelsbrunner, H., & Woodward, C. (1998). Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science. Wiley-Blackwell. https://doi.org/10.1002/pro.5560070905","ama":"Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science. 1998;7(9):1884-1897. doi:10.1002/pro.5560070905","ista":"Liang J, Edelsbrunner H, Woodward C. 1998. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science. 7(9), 1884–1897.","mla":"Liang, Jie, et al. “Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design.” Protein Science, vol. 7, no. 9, Wiley-Blackwell, 1998, pp. 1884–97, doi:10.1002/pro.5560070905.","short":"J. Liang, H. Edelsbrunner, C. Woodward, Protein Science 7 (1998) 1884–1897."},"publication_identifier":{"issn":["0961-8368"]},"title":"Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design","publication":"Protein Science","publisher":"Wiley-Blackwell","oa_version":"Published Version","date_created":"2018-12-11T12:06:27Z","publist_id":"2111","abstract":[{"text":"Identification and size characterization of surface pockets and occluded cavities are initial steps in protein structure-based ligand design. A new program, CAST, for automatically locating and measuring protein pockets and cavities, is based on precise computational geometry methods, including alpha shape and discrete flow theory. CAST identifies and measures pockets and pocket mouth openings, as well as cavities. The program specifies the atoms lining pockets, pocket openings. and buried cavities; the volume and area of pockets and cavities; and the area and circumference of mouth openings. CAST analysis of over 100 proteins has been carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures, several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor complexes, and a number of small and large protein inhibitors, Medium-sized globular proteins typically have 10-20 pockets/cavities. Most often, binding sites are pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand binding pockets vary widely in size, most within the range 10(2)-10(3) Angstrom(3). Statistical analysis reveals that the number of pockets and cavities is correlated with protein size, but there is no correlation between the size of the protein and the size of binding sites. Most frequently, the largest pocket/cavity is thp active site, but there are a number of instructive exceptions. Ligand volume and binding site volume are somewhat correlated when binding site volume is less than or equal to 700 Angstrom(3), but the ligand seldom occupies the entire site. Auxiliary pockets near the active site have been suggested as additional binding surface for designed ligands (Mattos C ct al., 1993, Nat Struct Biol 1:55-58). Analysis of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets, suitable for recruitment in ligand design strategies. Analysis of the FK506 binding protein, and of compounds developed in SAR by NMR (Shuker SE et al.. 1996, Science 274:1531-1534), indicates that CAST pocket computation may provide a priori identification of target proteins for Linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor complexes shows that the flexible active site pocket can vary over a range of 853-1,566 Angstrom(3), and that there are two pockets near or adjoining the active site that may be recruited for ligand design.","lang":"eng"}],"extern":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144175/"}],"intvolume":" 7","publication_status":"published","pmid":1,"day":"01","language":[{"iso":"eng"}],"month":"09","author":[{"full_name":"Liang, Jie","last_name":"Liang","first_name":"Jie"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Woodward, Clare","first_name":"Clare","last_name":"Woodward"}],"date_published":"1998-09-01T00:00:00Z","doi":"10.1002/pro.5560070905","date_updated":"2022-08-25T12:49:41Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1"},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.sciencedirect.com/science/article/pii/S0022000098915811"}],"intvolume":" 57","day":"01","language":[{"iso":"eng"}],"month":"01","date_updated":"2022-08-23T14:29:15Z","doi":"10.1006/jcss.1998.1581","article_processing_charge":"No","date_published":"1998-01-01T00:00:00Z","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Kopke, Peter","last_name":"Kopke","first_name":"Peter"},{"full_name":"Puri, Anuj","first_name":"Anuj","last_name":"Puri"},{"last_name":"Varaiya","first_name":"P.","full_name":"Varaiya, P."}],"quality_controlled":"1","type":"journal_article","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","page":"94 - 124","volume":57,"year":"1998","_id":"4492","article_type":"original","issue":"1","status":"public","oa":1,"acknowledgement":"This research was supported in part by the Office of Naval Research Young Investigator Award N00014-95-1-0520, by the National Science Foundation CAREER award CCR-9501708, by the National Science Foundation Grant CCR-9504469, by the Air Force Office of Scientific Research Contract F49620-93-1-0056, by the Army Research Office MURI Grant DAAH-04-96-1-0341, by the Army Research Office Contract DAAH-04-94-G-0026, by the Defense Advanced Research Projects Agency Grant NAG2-892, and by the California PATH program.","publication_identifier":{"isbn":["0022-0000"]},"citation":{"ama":"Henzinger TA, Kopke P, Puri A, Varaiya P. What’s decidable about hybrid automata? Journal of Computer and System Sciences. 1998;57(1):94-124. doi:10.1006/jcss.1998.1581","ista":"Henzinger TA, Kopke P, Puri A, Varaiya P. 1998. What’s decidable about hybrid automata? Journal of Computer and System Sciences. 57(1), 94–124.","mla":"Henzinger, Thomas A., et al. “What’s Decidable about Hybrid Automata?” Journal of Computer and System Sciences, vol. 57, no. 1, Elsevier, 1998, pp. 94–124, doi:10.1006/jcss.1998.1581.","short":"T.A. Henzinger, P. Kopke, A. Puri, P. Varaiya, Journal of Computer and System Sciences 57 (1998) 94–124.","chicago":"Henzinger, Thomas A, Peter Kopke, Anuj Puri, and P. Varaiya. “What’s Decidable about Hybrid Automata?” Journal of Computer and System Sciences. Elsevier, 1998. https://doi.org/10.1006/jcss.1998.1581.","ieee":"T. A. Henzinger, P. Kopke, A. Puri, and P. Varaiya, “What’s decidable about hybrid automata?,” Journal of Computer and System Sciences, vol. 57, no. 1. Elsevier, pp. 94–124, 1998.","apa":"Henzinger, T. A., Kopke, P., Puri, A., & Varaiya, P. (1998). What’s decidable about hybrid automata? Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1006/jcss.1998.1581"},"publisher":"Elsevier","title":"What's decidable about hybrid automata?","publication":"Journal of Computer and System Sciences","publist_id":"237","oa_version":"Published Version","date_created":"2018-12-11T12:09:08Z","extern":"1","abstract":[{"text":"Hybrid automata model systems with both digital and analog components, such as embedded control programs. Many verification tasks for such programs can be expressed as reachability problems for hybrid automata. By improving on previous decidability and undecidability results, we identify a boundary between decidability and undecidability for the reachability problem of hybrid automata. On the positive side, we give an (optimal) PSPACE reachability algorithm for the case of initialized rectangular automata, where all analog variables follow independent trajectories within piecewise-linear envelopes and are reinitialized whenever the envelope changes. Our algorithm is based on the construction of a timed automaton that contains all reachability information about a given initialized rectangular automaton. The translation has practical significance for verification, because it guarantees the termination of symbolic procedures for the reachability analysis of initialized rectangular automata. The translation also preserves theω-languages of initialized rectangular automata with bounded nondeterminism. On the negative side, we show that several slight generalizations of initialized rectangular automata lead to an undecidable reachability problem. In particular, we prove that the reachability problem is undecidable for timed automata augmented with a single stopwatch.","lang":"eng"}]},{"issue":"19","external_id":{"pmid":["9295396"]},"article_type":"original","oa":1,"status":"public","acknowledgement":"This work was supported by research grants from the Inamori Foundation and the Ministry of Education, Science, Sports and Culture of Japan. We thank Peter Somogyi for helpful discussion, David Roberts for technical assistance, and Akira Uesugi for photographic assistance. We are grateful to Atsu Aiba, David Hampson, John Roder, and Herman van der Putten for providing us with mGluR1-, mGluR4-, mGluR5-, and mGluR7-deficient mice, respectively, and to Corrado Corti and Francesco Ferraguti for sharing rat mGluR8 cDNA and unpublished results.","publication_identifier":{"issn":["0270-6474"]},"citation":{"mla":"Shigemoto, Ryuichi, et al. “Differential Presynaptic Localization of Metabotropic Glutamate Receptor Subtypes in the Rat Hippocampus.” Journal of Neuroscience, vol. 17, no. 19, Society for Neuroscience, 1997, pp. 7503–22, doi:10.1523/JNEUROSCI.17-19-07503.1997.","short":"R. Shigemoto, A. Kinoshita, E. Wada, S. Nomura, H. Ohishi, M. Takada, P. Flor, A. Neki, T. Abe, S. Nakanishi, N. Mizuno, Journal of Neuroscience 17 (1997) 7503–7522.","ista":"Shigemoto R, Kinoshita A, Wada E, Nomura S, Ohishi H, Takada M, Flor P, Neki A, Abe T, Nakanishi S, Mizuno N. 1997. Differential presynaptic localization of metabotropic glutamate receptor subtypes in the rat hippocampus. Journal of Neuroscience. 17(19), 7503–7522.","ama":"Shigemoto R, Kinoshita A, Wada E, et al. Differential presynaptic localization of metabotropic glutamate receptor subtypes in the rat hippocampus. Journal of Neuroscience. 1997;17(19):7503-7522. doi:10.1523/JNEUROSCI.17-19-07503.1997","apa":"Shigemoto, R., Kinoshita, A., Wada, E., Nomura, S., Ohishi, H., Takada, M., … Mizuno, N. (1997). Differential presynaptic localization of metabotropic glutamate receptor subtypes in the rat hippocampus. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.17-19-07503.1997","ieee":"R. Shigemoto et al., “Differential presynaptic localization of metabotropic glutamate receptor subtypes in the rat hippocampus,” Journal of Neuroscience, vol. 17, no. 19. Society for Neuroscience, pp. 7503–7522, 1997.","chicago":"Shigemoto, Ryuichi, Ayae Kinoshita, Eiki Wada, Sakashi Nomura, Hitoshi Ohishi, Masahiko Takada, Peter Flor, et al. “Differential Presynaptic Localization of Metabotropic Glutamate Receptor Subtypes in the Rat Hippocampus.” Journal of Neuroscience. Society for Neuroscience, 1997. https://doi.org/10.1523/JNEUROSCI.17-19-07503.1997."},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","type":"journal_article","volume":17,"page":"7503 - 7522","year":"1997","_id":"2582","extern":"1","abstract":[{"text":"Neurotransmission in the hippocampus is modulated variously through presynaptic metabotropic glutamate receptors (mGluRs). To establish the precise localization of presynaptic mGluRs in the rat hippocampus, we used subtype-specific antibodies for eight mGluRs (mGluR1-mGluR8) for immunohistochemistry combined with lesioning of the three major hippocampal pathways: the perforant path, mossy fiber, and Schaffer collateral. Immunoreactivity for group II (mGluR2) and group III (mGluR4a, mGluR7a, mGluR7b, and mGluR8) mGluRs was predominantly localized to presynaptic elements, whereas that for group I mGluRs (mGluR1 and mGluR5) was localized to postsynaptic elements. The medial perforant path was strongly immunoreactive for mGluR2 and mGluR7a throughout the hippocampus, and the lateral perforant path was prominently immunoreactive for mGluR8 in the dentate gyrus and CA3 area. The messy fiber was labeled for mGluR2, mGluR7a, and mGluR7b, whereas the Schaffer collateral was labeled only for mGluR7a. Electron microscopy further revealed the spatial segregation of group II and group III mGluRs within presynaptic elements. Immunolabeling for the group III receptors was predominantly observed in presynaptic active zones of asymmetrical and symmetrical synapses, whereas that for the group II receptor (mGluR2) was found in preterminal rather than terminal portions of axons. Target cell-specific segregation of receptors, first reported for mGluR7a (Shigemoto et al., 1996), was also apparent for the other group III mGluRs, suggesting that transmitter release is differentially regulated by 2-amino- 4-phosphonobutyrate-sensitive mGluRs in individual synapses on single axons according to the identity of postsynaptic neurons.","lang":"eng"}],"publisher":"Society for Neuroscience","publication":"Journal of Neuroscience","title":"Differential presynaptic localization of metabotropic glutamate receptor subtypes in the rat hippocampus","publist_id":"4317","date_created":"2018-12-11T11:58:30Z","oa_version":"Published Version","day":"01","pmid":1,"month":"10","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 17","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6573434/","open_access":"1"}],"article_processing_charge":"No","doi":"10.1523/JNEUROSCI.17-19-07503.1997","date_updated":"2022-08-22T11:32:01Z","author":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Kinoshita, Ayae","last_name":"Kinoshita","first_name":"Ayae"},{"full_name":"Wada, Eiki","last_name":"Wada","first_name":"Eiki"},{"first_name":"Sakashi","last_name":"Nomura","full_name":"Nomura, Sakashi"},{"first_name":"Hitoshi","last_name":"Ohishi","full_name":"Ohishi, Hitoshi"},{"last_name":"Takada","first_name":"Masahiko","full_name":"Takada, Masahiko"},{"full_name":"Flor, Peter","first_name":"Peter","last_name":"Flor"},{"last_name":"Neki","first_name":"Akio","full_name":"Neki, Akio"},{"last_name":"Abe","first_name":"Takaaki","full_name":"Abe, Takaaki"},{"last_name":"Nakanishi","first_name":"Shigetada","full_name":"Nakanishi, Shigetada"},{"full_name":"Mizuno, Noboru","first_name":"Noboru","last_name":"Mizuno"}],"date_published":"1997-10-01T00:00:00Z","quality_controlled":"1","scopus_import":"1"},{"month":"08","language":[{"iso":"eng"}],"day":"01","publication_status":"published","intvolume":" 55","main_file_link":[{"url":"https://doi.org/10.1006/jcss.1997.1493","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1006/jcss.1997.1493","date_updated":"2022-09-12T10:46:21Z","date_published":"1997-08-01T00:00:00Z","author":[{"first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Klein, Philip","last_name":"Klein","first_name":"Philip"},{"first_name":"Satish","last_name":"Rao","full_name":"Rao, Satish"},{"first_name":"Sairam","last_name":"Subramanian","full_name":"Subramanian, Sairam"}],"publication_identifier":{"issn":["0022-0000"]},"citation":{"ama":"Henzinger MH, Klein P, Rao S, Subramanian S. Faster shortest-path algorithms for planar graphs. Journal of Computer and System Sciences. 1997;55(1):3-23. doi:10.1006/jcss.1997.1493","short":"M.H. Henzinger, P. Klein, S. Rao, S. Subramanian, Journal of Computer and System Sciences 55 (1997) 3–23.","ista":"Henzinger MH, Klein P, Rao S, Subramanian S. 1997. Faster shortest-path algorithms for planar graphs. Journal of Computer and System Sciences. 55(1), 3–23.","mla":"Henzinger, Monika H., et al. “Faster Shortest-Path Algorithms for Planar Graphs.” Journal of Computer and System Sciences, vol. 55, no. 1, Elsevier, 1997, pp. 3–23, doi:10.1006/jcss.1997.1493.","chicago":"Henzinger, Monika H, Philip Klein, Satish Rao, and Sairam Subramanian. “Faster Shortest-Path Algorithms for Planar Graphs.” Journal of Computer and System Sciences. Elsevier, 1997. https://doi.org/10.1006/jcss.1997.1493.","ieee":"M. H. Henzinger, P. Klein, S. Rao, and S. Subramanian, “Faster shortest-path algorithms for planar graphs,” Journal of Computer and System Sciences, vol. 55, no. 1. Elsevier, pp. 3–23, 1997.","apa":"Henzinger, M. H., Klein, P., Rao, S., & Subramanian, S. (1997). Faster shortest-path algorithms for planar graphs. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1006/jcss.1997.1493"},"issue":"1","article_type":"original","oa":1,"status":"public","year":"1997","_id":"11767","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":55,"page":"3-23","extern":"1","abstract":[{"text":"We give a linear-time algorithm for single-source shortest paths in planar graphs with nonnegative edge-lengths. Our algorithm also yields a linear-time algorithm for maximum flow in a planar graph with the source and sink on the same face. For the case where negative edge-lengths are allowed, we give an algorithm requiringO(n4/3 log(nL)) time, whereLis the absolute value of the most negative length. This algorithm can be used to obtain similar bounds for computing a feasible flow in a planar network, for finding a perfect matching in a planar bipartite graph, and for finding a maximum flow in a planar graph when the source and sink are not on the same face. We also give parallel and dynamic versions of these algorithms.","lang":"eng"}],"date_created":"2022-08-08T12:28:45Z","oa_version":"Published Version","publisher":"Elsevier","publication":"Journal of Computer and System Sciences","title":"Faster shortest-path algorithms for planar graphs"}]