[{"status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104"}],"citation":{"short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294.","ieee":"N. H. Barton, “Mutation and the evolution of recombination,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2009.0320","ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294.","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.","ama":"Barton NH. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294. doi:10.1098/rstb.2009.0320"},"intvolume":" 365","abstract":[{"text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3777","title":"Mutation and the evolution of recombination","pmid":1,"acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","issue":"1544","scopus_import":1,"volume":365,"type":"journal_article","date_published":"2010-04-27T00:00:00Z","external_id":{"pmid":["20308104"]},"oa_version":"Submitted Version","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","doi":"10.1098/rstb.2009.0320","date_updated":"2021-01-12T07:52:07Z","publisher":"Royal Society","month":"04","quality_controlled":"1","oa":1,"author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"page":"1281 - 1294","date_created":"2018-12-11T12:05:07Z","publist_id":"2451","publication_status":"published","day":"27","language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"NiBa"}]},{"date_created":"2018-12-11T12:05:07Z","publication_status":"published","publist_id":"2448","day":"20","pubrep_id":"366","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Lucy","full_name":"Copsey, Lucy","last_name":"Copsey"},{"first_name":"Pierre","full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"ddc":["576"],"year":"2010","related_material":{"record":[{"status":"public","relation":"research_data","id":"9764"}]},"oa_version":"Published Version","volume":8,"date_published":"2010-07-20T00:00:00Z","type":"journal_article","month":"07","article_number":"e1000429","file":[{"access_level":"open_access","file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","date_updated":"2020-07-14T12:46:15Z","file_size":1089530,"content_type":"application/pdf","file_id":"5060","date_created":"2018-12-12T10:14:11Z","creator":"system","relation":"main_file"}],"oa":1,"quality_controlled":"1","publication":"PLoS Biology","date_updated":"2023-02-23T14:07:34Z","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1000429","issue":"7","file_date_updated":"2020-07-14T12:46:15Z","scopus_import":1,"has_accepted_license":"1","intvolume":" 8","citation":{"chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 2010;8(7). doi:10.1371/journal.pbio.1000429","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” PLoS Biology, vol. 8, no. 7. Public Library of Science, 2010.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429."},"status":"public","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3779","title":"Cryptic variation between species and the basis of hybrid performance"},{"date_updated":"2021-01-12T07:52:10Z","publisher":"Springer","title":"Topology noise removal for curve and surface evolution","doi":"10.1007/978-3-642-18421-5_4","publication":" Conference proceedings MCV 2010","_id":"3782","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically.","lang":"eng"}],"quality_controlled":"1","acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","month":"12","status":"public","type":"conference","date_published":"2010-12-31T00:00:00Z","volume":6533,"intvolume":" 6533","citation":{"ista":"Chen C, Freedman D. 2010. Topology noise removal for curve and surface evolution. Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.","apa":"Chen, C., & Freedman, D. (2010). Topology noise removal for curve and surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp. 31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4","short":"C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42.","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve and surface evolution,” in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp. 31–42.","ama":"Chen C, Freedman D. Topology noise removal for curve and surface evolution. In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4","mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010, pp. 31–42, doi:10.1007/978-3-642-18421-5_4.","chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve and Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer, 2010. https://doi.org/10.1007/978-3-642-18421-5_4."},"oa_version":"None","language":[{"iso":"eng"}],"year":"2010","scopus_import":1,"department":[{"_id":"HeEd"}],"conference":{"start_date":"2010-09-20","name":"MCV: Medical Computer Vision","location":"Beijing, China","end_date":"2010-09-20"},"page":"31 - 42","alternative_title":["LNCS"],"author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"},{"last_name":"Freedman","first_name":"Daniel","full_name":"Freedman, Daniel"}],"day":"31","publist_id":"2445","publication_status":"published","date_created":"2018-12-11T12:05:08Z"},{"oa_version":"None","citation":{"ista":"Palero F, González Candelas F, Pascual M. 2010. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 102(2), 247–249.","apa":"Palero, F., González Candelas, F., & Pascual, M. (2010). Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/esq111","ieee":"F. Palero, F. González Candelas, and M. Pascual, “Microsatelight – Pipeline to expedite microsatellite analysis,” Journal of Heredity, vol. 102, no. 2. Oxford University Press, pp. 247–249, 2010.","short":"F. Palero, F. González Candelas, M. Pascual, Journal of Heredity 102 (2010) 247–249.","ama":"Palero F, González Candelas F, Pascual M. Microsatelight – Pipeline to expedite microsatellite analysis. Journal of Heredity. 2010;102(2):247-249. doi:10.1093/jhered/esq111","mla":"Palero, Ferran, et al. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity, vol. 102, no. 2, Oxford University Press, 2010, pp. 247–49, doi:10.1093/jhered/esq111.","chicago":"Palero, Ferran, Fernando González Candelas, and Marta Pascual. “Microsatelight – Pipeline to Expedite Microsatellite Analysis.” Journal of Heredity. Oxford University Press, 2010. https://doi.org/10.1093/jhered/esq111."},"intvolume":" 102","date_published":"2010-12-02T00:00:00Z","type":"journal_article","volume":102,"status":"public","month":"12","quality_controlled":"1","acknowledgement":"Ministerio de Educación y Ciencia (CGL2006-13423, CTM2007-66635). M.P. and FP are part of the research group 2009SGR-636 of the Generalitat de Catalunya. F.P. acknowledges an EU-Synthesys grant (GB-TAF-4474).\r\n\r\nThanks to José Gabriel Segarra-Moragues (Centro de Investigaciones sobre Desertificación) for sending us pictures with several types of stuttering and Pedro Simões and Gemma Calàbria (Universitat de Barcelona) for testing this software. Finally, thanks are due to 2 anonymous referees for their valuable comments. These comments certainly helped to improve the manuscript.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/."}],"publisher":"Oxford University Press","date_updated":"2021-01-12T07:52:10Z","doi":"10.1093/jhered/esq111","title":"Microsatelight – Pipeline to expedite microsatellite analysis","publication":"Journal of Heredity","_id":"3783","date_created":"2018-12-11T12:05:09Z","day":"02","publist_id":"2444","publication_status":"published","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran","full_name":"Palero, Ferran","last_name":"Palero","orcid":"0000-0002-0343-8329"},{"first_name":"Fernando","full_name":"González Candelas, Fernando","last_name":"González Candelas"},{"first_name":"Marta","full_name":"Pascual, Marta","last_name":"Pascual"}],"issue":"2","page":"247 - 249","department":[{"_id":"NiBa"}],"scopus_import":1,"language":[{"iso":"eng"}],"year":"2010"},{"status":"public","volume":30,"date_published":"2010-10-01T00:00:00Z","type":"journal_article","intvolume":" 30","citation":{"mla":"Palero, Ferran, et al. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology, vol. 30, no. 4, Oxford University Press, 2010, pp. 658–63, doi:10.1651/09-3192.1.","ama":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 2010;30(4):658-663. doi:10.1651/09-3192.1","chicago":"Palero, Ferran, Pere Abello, E. Macpherson, C. Matthee, and Marta Pascual. “Genetic Diversity Levels in Fishery-Exploited Spiny Lobsters of the Genus Palinurus (Decapoda: Achelata).” Journal of Crustacean Biology. Oxford University Press, 2010. https://doi.org/10.1651/09-3192.1.","apa":"Palero, F., Abello, P., Macpherson, E., Matthee, C., & Pascual, M. (2010). Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. Oxford University Press. https://doi.org/10.1651/09-3192.1","ista":"Palero F, Abello P, Macpherson E, Matthee C, Pascual M. 2010. Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata). Journal of Crustacean Biology. 30(4), 658–663.","ieee":"F. Palero, P. Abello, E. Macpherson, C. Matthee, and M. Pascual, “Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata),” Journal of Crustacean Biology, vol. 30, no. 4. Oxford University Press, pp. 658–663, 2010.","short":"F. Palero, P. Abello, E. Macpherson, C. Matthee, M. Pascual, Journal of Crustacean Biology 30 (2010) 658–663."},"oa_version":"None","_id":"3785","publication":"Journal of Crustacean Biology","date_updated":"2023-10-16T09:51:05Z","title":"Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)","publisher":"Oxford University Press","doi":"10.1651/09-3192.1","abstract":[{"text":"Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","quality_controlled":"1","month":"10","page":"658 - 663","issue":"4","author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","first_name":"Ferran","full_name":"Palero, Ferran","last_name":"Palero","orcid":"0000-0002-0343-8329"},{"full_name":"Abello, Pere","first_name":"Pere","last_name":"Abello"},{"first_name":"E.","full_name":"Macpherson, E.","last_name":"Macpherson"},{"first_name":"C.","full_name":"Matthee, C.","last_name":"Matthee"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"}],"publist_id":"2442","publication_status":"published","day":"01","date_created":"2018-12-11T12:05:09Z","publication_identifier":{"eissn":["1937-240X"],"issn":["0278-0372"]},"year":"2010","language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"NiBa"}]},{"month":"03","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Four rare palinurid phyllosoma larvae, one mid-stage and three final stage, were found among the unclassified collections in the Crustacea Section, Natural History Museum, London. Detailed morphological analysis of the larvae indicated that they belong to several Palinustus species given the presence of incipient blunt-horns, length of antennula, length ratio of segments of antennular peduncle, distribution of pereiopod spines, and shape of uropods and telson. Moreover, the size of the final-stage larvae agrees with that expected given the size of the recently described puerulus stage of Palinustus mossambicus. This constitutes the first description of a complete phyllosoma assigned to Palinustus species. The phyllosoma described in the present study include the largest Palinuridae larva ever found."}],"title":"Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description","publisher":"Magnolia Press","doi":"10.11646/zootaxa.2403.1.4","date_updated":"2022-03-21T08:22:58Z","_id":"3786","publication":"Zootaxa","oa_version":"None","article_type":"original","citation":{"ista":"Palero F, Guerao G, Clark P, Abello P. 2010. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2403(1), 42–58.","apa":"Palero, F., Guerao, G., Clark, P., & Abello, P. (2010). Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. Magnolia Press. https://doi.org/10.11646/zootaxa.2403.1.4","ieee":"F. Palero, G. Guerao, P. Clark, and P. Abello, “Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description,” Zootaxa, vol. 2403, no. 1. Magnolia Press, pp. 42–58, 2010.","short":"F. Palero, G. Guerao, P. Clark, P. Abello, Zootaxa 2403 (2010) 42–58.","ama":"Palero F, Guerao G, Clark P, Abello P. Final-stage phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The first complete description. Zootaxa. 2010;2403(1):42-58. doi:10.11646/zootaxa.2403.1.4","mla":"Palero, Ferran, et al. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa, vol. 2403, no. 1, Magnolia Press, 2010, pp. 42–58, doi:10.11646/zootaxa.2403.1.4.","chicago":"Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Final-Stage Phyllosoma of Palinustus A. Milne-Edwards, 1880 (Crustacea: Decapoda: Achelata: Palinuridae)-The First Complete Description.” Zootaxa. Magnolia Press, 2010. https://doi.org/10.11646/zootaxa.2403.1.4."},"intvolume":" 2403","type":"journal_article","date_published":"2010-03-19T00:00:00Z","volume":2403,"status":"public","department":[{"_id":"NiBa"}],"scopus_import":"1","language":[{"iso":"eng"}],"year":"2010","date_created":"2018-12-11T12:05:10Z","day":"19","publist_id":"2441","publication_status":"published","author":[{"full_name":"Palero, Ferran","first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0343-8329","last_name":"Palero"},{"first_name":"Guillermo","full_name":"Guerao, Guillermo","last_name":"Guerao"},{"last_name":"Clark","first_name":"Paul","full_name":"Clark, Paul"},{"last_name":"Abello","first_name":"Pere","full_name":"Abello, Pere"}],"issue":"1","page":"42 - 58"},{"publication_status":"published","publist_id":"2440","day":"01","date_created":"2018-12-11T12:05:10Z","page":"465 - 470","author":[{"last_name":"Palero","orcid":"0000-0002-0343-8329","full_name":"Palero, Ferran","first_name":"Ferran","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hall","full_name":"Hall, Sally","first_name":"Sally"},{"full_name":"Clark, Paul","first_name":"Paul","last_name":"Clark"},{"last_name":"Johnston","first_name":"David","full_name":"Johnston, David"},{"last_name":"Mackenzie Dodds","full_name":"Mackenzie Dodds, Jackie","first_name":"Jackie"},{"full_name":"Thatje, Sven","first_name":"Sven","last_name":"Thatje"}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"year":"2010","oa_version":"Submitted Version","volume":74,"date_published":"2010-09-01T00:00:00Z","type":"journal_article","oa":1,"quality_controlled":"1","month":"09","publication":"Scientia Marina","doi":"10.3989/scimar.2010.74n3465","date_updated":"2021-01-12T07:52:11Z","publisher":"Consejo Superior de Investigaciones Científicas","issue":"3","scopus_import":1,"main_file_link":[{"url":"https://eprints.soton.ac.uk/68731/","open_access":"1"}],"intvolume":" 74","citation":{"chicago":"Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.","ama":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465","mla":"Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.","short":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje, Scientia Marina 74 (2010) 465–470.","ieee":"F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje, “DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp. 465–470, 2010.","ista":"Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010. DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. 74(3), 465–470.","apa":"Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., & Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas. https://doi.org/10.3989/scimar.2010.74n3465"},"status":"public","acknowledgement":"The authors would like to thank two anonymous reviewers for their remarks, which helped to improve the manuscript. This project was supported by the Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS Project http://www.synthesys. info/ which is financed by European Community Research Infrastructure Action under the FP6 “Structuring the European Research Area” Programme. Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical point drying, P.Crabb for helping with the UV-light photography setting and our colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology NHM \r\n\r\n","_id":"3787","title":"DNA extraction from formalin-fixed tissue: new light from the deep sea","abstract":[{"lang":"eng","text":"DNA samples were extracted from ethanol and formalin-fixed decapod crustacean tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors impede PCR success when dealing with formalin-fixed material. Instead, amplification success from formalin-fixed tissue appears to depend on the presence of unmodified DNA in the extracted sample. A staining method that facilitates the targeting of samples with a high content of unmodified DNA is provided."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"month":"09","publication":"The European Physical Journal E: Soft Matter and Biological Physics","_id":"3788","doi":"10.1140/epje/i2010-10642-y","publisher":"Springer","date_updated":"2021-01-12T07:52:12Z","title":"Finite-size corrections to scaling behavior in sorted cell aggregates","abstract":[{"text":"Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect.","lang":"eng"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Klopper, A., Krens, G., Grill, S., & Heisenberg, C.-P. J. (2010). Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. Springer. https://doi.org/10.1140/epje/i2010-10642-y","ista":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. 2010. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 33(2), 99–103.","ieee":"A. Klopper, G. Krens, S. Grill, and C.-P. J. Heisenberg, “Finite-size corrections to scaling behavior in sorted cell aggregates,” The European Physical Journal E: Soft Matter and Biological Physics, vol. 33, no. 2. Springer, pp. 99–103, 2010.","short":"A. Klopper, G. Krens, S. Grill, C.-P.J. Heisenberg, The European Physical Journal E: Soft Matter and Biological Physics 33 (2010) 99–103.","mla":"Klopper, Abigail, et al. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological Physics, vol. 33, no. 2, Springer, 2010, pp. 99–103, doi:10.1140/epje/i2010-10642-y.","ama":"Klopper A, Krens G, Grill S, Heisenberg C-PJ. Finite-size corrections to scaling behavior in sorted cell aggregates. The European Physical Journal E: Soft Matter and Biological Physics. 2010;33(2):99-103. doi:10.1140/epje/i2010-10642-y","chicago":"Klopper, Abigail, Gabriel Krens, Stephan Grill, and Carl-Philipp J Heisenberg. “Finite-Size Corrections to Scaling Behavior in Sorted Cell Aggregates.” The European Physical Journal E: Soft Matter and Biological Physics. Springer, 2010. https://doi.org/10.1140/epje/i2010-10642-y."},"intvolume":" 33","oa_version":"None","status":"public","volume":33,"date_published":"2010-09-18T00:00:00Z","type":"journal_article","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"year":"2010","scopus_import":1,"publication_status":"published","publist_id":"2439","day":"18","date_created":"2018-12-11T12:05:10Z","page":"99 - 103","author":[{"last_name":"Klopper","full_name":"Klopper, Abigail","first_name":"Abigail"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"last_name":"Grill","first_name":"Stephan","full_name":"Grill, Stephan"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"issue":"2"},{"day":"09","publication_status":"published","publist_id":"2438","date_created":"2018-12-11T12:05:11Z","page":"1966 - 1972","author":[{"full_name":"Quesada-Hernández, Elena","id":"EA35229E-E909-11E9-8DF8-C90C5D5AF86E","first_name":"Elena","last_name":"Quesada-Hernández"},{"full_name":"Caneparo, Luca","first_name":"Luca","last_name":"Caneparo"},{"first_name":"Sylvia","id":"1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F","full_name":"Schneider, Sylvia","last_name":"Schneider"},{"last_name":"Winkler","first_name":"Sylke","full_name":"Winkler, Sylke"},{"first_name":"Michael","full_name":"Liebling, Michael","last_name":"Liebling"},{"full_name":"Fraser, Scott","first_name":"Scott","last_name":"Fraser"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"issue":"21","department":[{"_id":"CaHe"}],"year":"2010","language":[{"iso":"eng"}],"scopus_import":1,"citation":{"mla":"Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology, vol. 20, no. 21, Cell Press, 2010, pp. 1966–72, doi:10.1016/j.cub.2010.10.009.","ama":"Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 2010;20(21):1966-1972. doi:10.1016/j.cub.2010.10.009","chicago":"Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler, Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.10.009.","apa":"Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S., & Heisenberg, C.-P. J. (2010). Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2010.10.009","ista":"Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972.","short":"E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling, S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972.","ieee":"E. Quesada-Hernández et al., “Stereotypical cell division orientation controls neural rod midline formation in zebrafish,” Current Biology, vol. 20, no. 21. Cell Press, pp. 1966–1972, 2010."},"intvolume":" 20","oa_version":"None","status":"public","type":"journal_article","date_published":"2010-11-09T00:00:00Z","volume":20,"quality_controlled":"1","acknowledgement":"This work was supported by grants from the Fundacion Caja Madrid to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society, and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke, Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript. We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice in multi-photon microscopy and D. White for assistance during the image-processing steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans for excellent fish care. ","month":"11","publisher":"Cell Press","doi":"10.1016/j.cub.2010.10.009","title":"Stereotypical cell division orientation controls neural rod midline formation in zebrafish","date_updated":"2021-01-12T07:52:12Z","_id":"3789","publication":"Current Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The development of multicellular organisms is dependent on the tight coordination between tissue growth and morphogenesis. The stereotypical orientation of cell divisions has been proposed to be a fundamental mechanism by which proliferating and growing tissues take shape. However, the actual contribution of stereotypical division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell divisions with stereotypical orientation have been implicated in both body-axis elongation and neural rod formation [1, 2], although there is little direct evidence for a critical function of SDO in either of these processes. Here we show that SDO is required for formation of the neural rod midline during neurulation but dispensable for elongation of the body axis during gastrulation. Our data indicate that SDO during both gastrulation and neurulation is dependent on the noncanonical Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation leads to severe defects in neural rod midline formation but not body-axis elongation. These findings suggest a novel function for Fz7-controlled cell division orientation in neural rod midline formation during neurulation. "}]},{"volume":8,"type":"journal_article","date_published":"2010-11-30T00:00:00Z","oa_version":"Published Version","publication":"PLoS Biology","date_updated":"2021-01-12T07:52:13Z","doi":"10.1371/journal.pbio.1000544","publisher":"Public Library of Science","month":"11","article_number":"e1000544","quality_controlled":"1","oa":1,"file":[{"checksum":"52d18c90ca6b02234cea5e8b399b7f46","access_level":"open_access","file_name":"IST-2015-365-v1+1_journal.pbio.1000544.pdf","file_size":799506,"date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:08:24Z","file_id":"4685","content_type":"application/pdf","relation":"main_file","creator":"system"}],"pubrep_id":"365","author":[{"last_name":"Diz Muñoz","first_name":"Alba","full_name":"Diz Muñoz, Alba"},{"last_name":"Krieg","full_name":"Krieg, Michael","first_name":"Michael"},{"last_name":"Bergert","first_name":"Martin","full_name":"Bergert, Martin"},{"last_name":"Ibarlucea Benitez","first_name":"Itziar","full_name":"Ibarlucea Benitez, Itziar"},{"first_name":"Daniel","full_name":"Müller, Daniel","last_name":"Müller"},{"first_name":"Ewa","full_name":"Paluch, Ewa","last_name":"Paluch"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"date_created":"2018-12-11T12:05:11Z","publication_status":"published","publist_id":"2437","day":"30","language":[{"iso":"eng"}],"year":"2010","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"CaHe"}],"status":"public","has_accepted_license":"1","intvolume":" 8","citation":{"chicago":"Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez, Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.","mla":"Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of Science, 2010, doi:10.1371/journal.pbio.1000544.","ama":"Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544","short":"A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch, C.-P.J. Heisenberg, PLoS Biology 8 (2010).","ieee":"A. Diz Muñoz et al., “Control of directed cell migration in vivo by membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library of Science, 2010.","apa":"Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch, E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000544","ista":"Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E, Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology. 8(11), e1000544."},"abstract":[{"lang":"eng","text":"Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3790","title":"Control of directed cell migration in vivo by membrane-to-cortex attachment","acknowledgement":"We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz, L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans, M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for help and advice at various stages of this project and to J. Helenius for help with programming. This work was supported by grants from the Boehringer Ingelheim Fonds to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n","issue":"11","scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z"},{"date_published":"2010-11-04T00:00:00Z","type":"conference","volume":6316,"oa_version":"Submitted Version","date_updated":"2021-01-12T07:52:14Z","publisher":"Springer","doi":"10.1007/978-3-642-15567-3_8","article_processing_charge":"No","quality_controlled":"1","oa":1,"file":[{"file_id":"7871","date_created":"2020-05-19T16:27:34Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","checksum":"3716e10e161f7c714fd17ec193a223c3","file_name":"2010_ECCV_Nowozin.pdf","access_level":"open_access","file_size":4087332,"date_updated":"2020-07-14T12:46:16Z"}],"month":"11","conference":{"location":"Heraklion, Crete, Greece","end_date":"2010-09-11","start_date":"2010-09-05","name":"ECCV: European Conference on Computer Vision"},"page":"98 - 111","alternative_title":["LNCS"],"author":[{"first_name":"Sebastian","full_name":"Nowozin, Sebastian","last_name":"Nowozin"},{"last_name":"Gehler","full_name":"Gehler, Peter","first_name":"Peter"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"day":"04","publication_status":"published","publist_id":"2431","date_created":"2018-12-11T12:05:12Z","year":"2010","ddc":["000"],"language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"status":"public","intvolume":" 6316","citation":{"ieee":"S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based approaches to object class image segmentation,” presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp. 98–111.","short":"S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.","apa":"Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111). Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8","ista":"Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based approaches to object class image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 6316, 98–111.","chicago":"Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111. Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.","mla":"Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111, doi:10.1007/978-3-642-15567-3_8.","ama":"Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8"},"has_accepted_license":"1","title":"On parameter learning in CRF-based approaches to object class image segmentation","_id":"3793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Recent progress in per-pixel object class labeling of natural images can be attributed to the use of multiple types of image features and sound statistical learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently used for their ability to represent interactions between random variables. Despite their popularity in computer vision, parameter learning for CRFs has remained difficult, popular approaches being cross-validation and piecewise training.\r\nIn this work, we propose a simple yet expressive tree-structured CRF based on a recent hierarchical image segmentation method. Our model combines and weights multiple image features within a hierarchical representation and allows simple and efficient globally-optimal learning of ≈ 105 parameters. The tractability of our model allows us to pose and answer some of the open questions regarding parameter learning applying to CRF-based approaches. The key findings for learning CRF models are, from the obvious to the surprising, i) multiple image features always help, ii) the limiting dimension with respect to current models is the amount of training data, iii) piecewise training is competitive, iv) current methods for max-margin training fail for models with many parameters.\r\n","lang":"eng"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z"},{"page":"566 - 579","alternative_title":["LNCS"],"conference":{"name":"ECCV: European Conference on Computer Vision","start_date":"2010-09-05","end_date":"2010-09-11","location":"Heraklion, Crete, Greece"},"author":[{"full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887"},{"last_name":"Krömer","full_name":"Krömer, Oliver","first_name":"Oliver"}],"publist_id":"2433","publication_status":"published","day":"10","date_created":"2018-12-11T12:05:12Z","language":[{"iso":"eng"}],"year":"2010","scopus_import":1,"department":[{"_id":"ChLa"}],"status":"public","volume":6312,"date_published":"2010-11-10T00:00:00Z","type":"conference","main_file_link":[{"url":"http://www.ics.forth.gr/eccv2010/intro.php"}],"intvolume":" 6312","citation":{"chicago":"Lampert, Christoph, and Oliver Krömer. “Weakly-Paired Maximum Covariance Analysis for Multimodal Dimensionality Reduction and Transfer Learning,” 6312:566–79. Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_41.","ama":"Lampert C, Krömer O. Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning. In: Vol 6312. Springer; 2010:566-579. doi:10.1007/978-3-642-15552-9_41","mla":"Lampert, Christoph, and Oliver Krömer. Weakly-Paired Maximum Covariance Analysis for Multimodal Dimensionality Reduction and Transfer Learning. Vol. 6312, Springer, 2010, pp. 566–79, doi:10.1007/978-3-642-15552-9_41.","short":"C. Lampert, O. Krömer, in:, Springer, 2010, pp. 566–579.","ieee":"C. Lampert and O. Krömer, “Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning,” presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6312, pp. 566–579.","ista":"Lampert C, Krömer O. 2010. Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning. ECCV: European Conference on Computer Vision, LNCS, vol. 6312, 566–579.","apa":"Lampert, C., & Krömer, O. (2010). Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning (Vol. 6312, pp. 566–579). Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete, Greece: Springer. https://doi.org/10.1007/978-3-642-15552-9_41"},"oa_version":"None","_id":"3794","date_updated":"2021-01-12T07:52:14Z","title":"Weakly-paired maximum covariance analysis for multimodal dimensionality reduction and transfer learning","doi":"10.1007/978-3-642-15552-9_41","publisher":"Springer","abstract":[{"lang":"eng","text":"We study the problem of multimodal dimensionality reduction assuming that data samples can be missing at training time, and not all data modalities may be present at application time. Maximum covariance analysis, as a generalization of PCA, has many desirable properties, but its application to practical problems is limited by its need for perfectly paired data. We overcome this limitation by a latent variable approach that allows working with weakly paired data and is still able to efficiently process large datasets using standard numerical routines. The resulting weakly paired maximum covariance analysis often finds better representations than alternative methods, as we show in two exemplary tasks: texture discrimination and transfer learning."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","month":"11"},{"scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","abstract":[{"text":"The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3795","title":"The stability of the apparent contour of an orientable 2-manifold","acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","status":"public","has_accepted_license":"1","citation":{"mla":"Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.","ama":"Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour of an orientable 2-manifold. In: Topological Data Analysis and Visualization: Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3","chicago":"Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010. https://doi.org/10.1007/978-3-642-15014-2_3.","apa":"Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the apparent contour of an orientable 2-manifold. In Topological Data Analysis and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer. https://doi.org/10.1007/978-3-642-15014-2_3","ista":"Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour of an orientable 2-manifold. In: Topological Data Analysis and Visualization: Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.","short":"H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.","ieee":"H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42."},"language":[{"iso":"eng"}],"year":"2010","ddc":["000"],"department":[{"_id":"HeEd"}],"pubrep_id":"538","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"first_name":"Dmitriy","full_name":"Morozov, Dmitriy","last_name":"Morozov"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit","full_name":"Patel, Amit","last_name":"Patel"}],"alternative_title":["Mathematics and Visualization"],"page":"27 - 42","date_created":"2018-12-11T12:05:13Z","publist_id":"2428","publication_status":"published","day":"22","publication":"Topological Data Analysis and Visualization: Theory, Algorithms and Applications","doi":"10.1007/978-3-642-15014-2_3","publisher":"Springer","date_updated":"2021-01-12T07:52:15Z","month":"12","oa":1,"file":[{"access_level":"open_access","file_name":"IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf","checksum":"f03a44c3d1c3e2d4fedb3b94404f3fd5","date_updated":"2020-07-14T12:46:16Z","file_size":210710,"content_type":"application/pdf","date_created":"2018-12-12T10:11:40Z","file_id":"4896","relation":"main_file","creator":"system"}],"quality_controlled":"1","type":"book_chapter","date_published":"2010-12-22T00:00:00Z","oa_version":"Submitted Version"},{"type":"journal_article","date_published":"2010-04-15T00:00:00Z","volume":66,"oa_version":"Published Version","external_id":{"pmid":["20399724"]},"publisher":"Elsevier","date_updated":"2021-01-12T07:52:31Z","doi":"10.1016/j.neuron.2010.04.003","publication":"Neuron","article_processing_charge":"No","oa":1,"quality_controlled":"1","month":"04","page":"8 - 10","author":[{"last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","full_name":"Guzmán, José"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"day":"15","publist_id":"2377","publication_status":"published","date_created":"2018-12-11T12:05:25Z","language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"PeJo"}],"status":"public","citation":{"mla":"Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” Neuron, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:10.1016/j.neuron.2010.04.003.","ama":"Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. 2010;66(1):8-10. doi:10.1016/j.neuron.2010.04.003","chicago":"Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.04.003.","apa":"Guzmán, J., & Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.04.003","ista":"Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. 66(1), 8–10.","short":"J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10.","ieee":"J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR subunits,” Neuron, vol. 66, no. 1. Elsevier, pp. 8–10, 2010."},"intvolume":" 66","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/20399724","open_access":"1"}],"title":"Beyond TARPs: The growing list of auxiliary AMPAR subunits","_id":"3832","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates desensitization and prolongs recovery from desensitization. CKAMP44 is highly expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR subunits control the time course of signaling at glutamatergic synapses."}],"pmid":1,"issue":"1","scopus_import":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"Wiley-Blackwell","doi":"10.1111/j.1460-9568.2010.07189.x","date_updated":"2021-01-12T07:52:31Z","title":"GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova)","publication":"The European Journal of Neuroscience","_id":"3833","month":"03","quality_controlled":"1","date_published":"2010-03-19T00:00:00Z","type":"journal_article","volume":31,"status":"public","oa_version":"None","intvolume":" 31","citation":{"mla":"Jonas, Peter M., and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali & Todorova).” The European Journal of Neuroscience, vol. 31, no. 7, Wiley-Blackwell, 2010, pp. 1194–95, doi:10.1111/j.1460-9568.2010.07189.x.","ama":"Jonas PM, Hefft S. GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. 2010;31(7):1194-1195. doi:10.1111/j.1460-9568.2010.07189.x","chicago":"Jonas, Peter M, and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali & Todorova).” The European Journal of Neuroscience. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1460-9568.2010.07189.x.","apa":"Jonas, P. M., & Hefft, S. (2010). GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/j.1460-9568.2010.07189.x","ista":"Jonas PM, Hefft S. 2010. GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova). The European Journal of Neuroscience. 31(7), 1194–1195.","short":"P.M. Jonas, S. Hefft, The European Journal of Neuroscience 31 (2010) 1194–1195.","ieee":"P. M. Jonas and S. Hefft, “GABA release at terminals of CCK-interneurons: synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali & Todorova),” The European Journal of Neuroscience, vol. 31, no. 7. Wiley-Blackwell, pp. 1194–1195, 2010."},"scopus_import":1,"language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"PeJo"}],"issue":"7","author":[{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hefft","full_name":"Hefft, Stefan","first_name":"Stefan"}],"page":"1194 - 1195","date_created":"2018-12-11T12:05:25Z","day":"19","publist_id":"2378","publication_status":"published"},{"issue":"42","scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","status":"public","citation":{"ama":"Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42","mla":"Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.","chicago":"Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology. BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.","ista":"Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master equation using sliding windows. BMC Systems Biology. 4(42), 1–19.","apa":"Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the chemical master equation using sliding windows. BMC Systems Biology. BioMed Central. https://doi.org/10.1186/1752-0509-4-42","ieee":"V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical master equation using sliding windows,” BMC Systems Biology, vol. 4, no. 42. BioMed Central, pp. 1–19, 2010.","short":"V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010) 1–19."},"intvolume":" 4","has_accepted_license":"1","title":"Solving the chemical master equation using sliding windows","_id":"3834","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary differential equations that describes the evolution of a network of chemical reactions as a stochastic process. Its solution yields the probability density vector of the system at each point in time. Solving the CME numerically is in many cases computationally expensive or even infeasible as the number of reachable states can be very large or infinite. We introduce the sliding window method, which computes an approximate solution of the CME by performing a sequence of local analysis steps. In each step, only a manageable subset of states is considered, representing a "window" into the state space. In subsequent steps, the window follows the direction in which the probability mass moves, until the time period of interest has elapsed. We construct the window based on a deterministic approximation of the future behavior of the system by estimating upper and lower bounds on the populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness of our approach, we apply it to several examples previously described in the literature. The experimental results show that the proposed method speeds up the analysis considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe sliding window method is a novel approach to address the performance problems of numerical algorithms for the solution of the chemical master equation. The method efficiently approximates the probability distributions at the time points of interest for a variety of chemically reacting systems, including systems for which no upper bound on the population sizes of the chemical species is known a priori.","lang":"eng"}],"acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","page":"1 - 19","author":[{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"},{"full_name":"Goel, Rushil","first_name":"Rushil","last_name":"Goel"},{"full_name":"Mateescu, Maria","first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"pubrep_id":"72","day":"08","publication_status":"published","publist_id":"2374","date_created":"2018-12-11T12:05:25Z","year":"2010","ddc":["005"],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2010-04-08T00:00:00Z","volume":4,"oa_version":"Published Version","doi":"10.1186/1752-0509-4-42","publisher":"BioMed Central","date_updated":"2021-01-12T07:52:32Z","publication":"BMC Systems Biology","file":[{"creator":"system","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:29Z","file_id":"5217","date_updated":"2020-07-14T12:46:16Z","file_size":1919130,"file_name":"IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf","access_level":"open_access","checksum":"220239fae76f7b03c4d7f05d74ef426f"}],"quality_controlled":"1","oa":1,"month":"04"},{"abstract":[{"text":"We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe net- works of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the construction of a stochastic hybrid model in which certain discrete random variables of the original Markov chain are approximated by continuous deterministic variables. We compute the solution of the stochastic hybrid model using a numerical algorithm that discretizes time and in each step performs a mutual update of the transient prob- ability distribution of the discrete stochastic variables and the values of the continuous deterministic variables. We im- plemented the algorithm and we demonstrate its usefulness and efficiency on several case studies from systems biology.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3838","title":"Hybrid numerical solution of the chemical master equation","status":"public","has_accepted_license":"1","citation":{"mla":"Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.","ama":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772","chicago":"Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.","apa":"Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid numerical solution of the chemical master equation (pp. 55–65). Presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772","ista":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution of the chemical master equation. CMSB: Computational Methods in Systems Biology, 55–65.","ieee":"T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution of the chemical master equation,” presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy, 2010, pp. 55–65.","short":"T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp. 55–65."},"scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","publisher":"Springer","doi":"10.1145/1839764.1839772","date_updated":"2021-01-12T07:52:33Z","month":"09","oa":1,"file":[{"content_type":"application/pdf","file_id":"5179","date_created":"2018-12-12T10:15:55Z","creator":"system","relation":"main_file","access_level":"open_access","file_name":"IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf","checksum":"81cb6f0babd97151b171d1ce86582831","date_updated":"2020-07-14T12:46:16Z","file_size":671790}],"quality_controlled":"1","date_published":"2010-09-29T00:00:00Z","type":"conference","oa_version":"Submitted Version","ddc":["004"],"language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"ToHe"}],"pubrep_id":"68","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"},{"last_name":"Mikeev","full_name":"Mikeev, Linar","first_name":"Linar"},{"last_name":"Wolf","full_name":"Wolf, Verena","first_name":"Verena"}],"page":"55 - 65","conference":{"location":"Trento, Italy","end_date":"2010-10-01","start_date":"2010-09-29","name":"CMSB: Computational Methods in Systems Biology"},"date_created":"2018-12-11T12:05:27Z","publist_id":"2356","publication_status":"published","day":"29"},{"conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2010-01-17","end_date":"2010-01-19","location":"Madrid, Spain"},"alternative_title":["LNCS"],"page":"163 - 179","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Thibaud","full_name":"Hottelier, Thibaud","last_name":"Hottelier"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"last_name":"Voronkov","full_name":"Voronkov, Andrei","first_name":"Andrei"}],"pubrep_id":"69","day":"01","publist_id":"2357","publication_status":"published","date_created":"2018-12-11T12:05:27Z","ddc":["005"],"language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"ToHe"}],"date_published":"2010-01-01T00:00:00Z","type":"conference","volume":5944,"oa_version":"Submitted Version","date_updated":"2021-01-12T07:52:33Z","doi":"10.1007/978-3-642-11319-2_14","publisher":"Springer","file":[{"creator":"system","relation":"main_file","file_id":"4989","date_created":"2018-12-12T10:13:09Z","content_type":"application/pdf","file_size":251265,"date_updated":"2020-07-14T12:46:16Z","checksum":"da69b13a2d9a7a316c909e09c1090cef","access_level":"open_access","file_name":"IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf"}],"quality_controlled":"1","oa":1,"month":"01","scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","status":"public","citation":{"mla":"Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices. Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.","ama":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14","chicago":"Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov. “Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.","apa":"Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-642-11319-2_14","ista":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944, 163–179.","short":"T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010, pp. 163–179.","ieee":"T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and type inference for matrices,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179."},"intvolume":" 5944","has_accepted_license":"1","title":"Invariant and type inference for matrices","_id":"3839","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a loop property generation method for loops iterating over multi-dimensional arrays. When used on matrices, our method is able to infer their shapes (also called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties, we first transform a nested loop iterating over a multi- dimensional array into an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants for each unnested loop using a generalization of a recurrence-based invariant generation technique. These loop invariants give us conditions on matrices from which we can derive matrix types automatically us- ing theorem provers. Invariant generation is implemented in the software package Aligator and types are derived by theorem provers and SMT solvers, including Vampire and Z3. When run on the Java matrix package JAMA, our tool was able to infer automatically all matrix types describing the matrix shapes guaranteed by JAMA’s API.","lang":"eng"}],"acknowledgement":"The research was supported by the Swiss NSF."},{"month":"01","quality_controlled":"1","acknowledgement":"This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee, Laurent Doyen, and Barbara Jobstmann.","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Classical formalizations of systems and properties are boolean: given a system and a property, the property is either true or false of the system. Correspondingly, classical methods for system analysis determine the truth value of a property, preferably giving a proof if the property is true, and a counterexample if the property is false; classical methods for system synthesis construct a system for which a property is true; classical methods for system transformation, composition, and abstraction aim to preserve the truth of properties. The boolean view is prevalent even if the system, the property, or both refer to numerical quantities, such as the times or probabilities of events. For example, a timed automaton either satisfies or violates a formula of a real-time logic; a stochastic process either satisfies or violates a formula of a probabilistic logic. The classical black-and-white view partitions the world into \"correct\" and \"incorrect\" systems, offering few nuances. In reality, of several systems that satisfy a property in the boolean sense, often some are more desirable than others, and of the many systems that violate a property, usually some are less objectionable than others. For instance, among the systems that satisfy the response property that every request be granted, we may prefer systems that grant requests quickly (the quicker, the better), or we may prefer systems that issue few unnecessary grants (the fewer, the better); and among the systems that violate the response property, we may prefer systems that serve many initial requests (the more, the better), or we may prefer systems that serve many requests in the long run (the greater the fraction of served to unserved requests, the better). Formally, while a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a directed metric on systems and properties, where the distance between a system and a property provides a measure of \"fit\" or \"desirability.\" There are many ways how such distances can be defined. In a linear-time framework, one assigns numerical values to individual behaviors before assigning values to systems and properties, which are sets of behaviors. For example, the value of a single behavior may be a discounted value, which is largely determined by a prefix of the behavior, e.g., by the number of requests that are granted before the first request that is not granted; or a limit value, which is independent of any finite prefix. A limit value may be an average, such as the average response time over an infinite sequence of requests and grants, or a supremum, such as the worst-case response time. Similarly, the value of a set of behaviors may be an extremum or an average across the values of all behaviors in the set: in this way one can measure the worst of all possible average-case response times, or the average of all possible worst-case response times, etc. Accordingly, the distance between two sets of behaviors may be defined as the worst or average difference between the values of corresponding behaviors. In summary, we propagate replacing boolean specifications for the correctness of systems with quantitative measures for the desirability of systems. In quantitative analysis, the aim is to compute the distance between a system and a property (or between two systems, or two properties); in quantitative synthesis, the objective is to construct a system that has minimal distance from a given property. Multiple quantitative measures can be prioritized (e.g., combined lexicographically into a single measure) or studied along the Pareto curve. Quantitative transformations, compositions, and abstractions of systems are useful if they allow us to bound the induced change in distance from a property. We present some initial results in some of these directions. We also give some potential applications, which not only generalize tradiditional correctness concerns in the functional, timed, and probabilistic domains, but also capture such system measures as resource use, performance, cost, reliability, and robustness.","lang":"eng"}],"title":"From boolean to quantitative notions of correctness","publisher":"ACM","date_updated":"2021-01-12T07:52:34Z","doi":"10.1145/1706299.1706319","_id":"3840","oa_version":"None","intvolume":" 45","citation":{"chicago":"Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,” 45:157–58. ACM, 2010. https://doi.org/10.1145/1706299.1706319.","mla":"Henzinger, Thomas A. From Boolean to Quantitative Notions of Correctness. Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:10.1145/1706299.1706319.","ama":"Henzinger TA. From boolean to quantitative notions of correctness. In: Vol 45. ACM; 2010:157-158. doi:10.1145/1706299.1706319","short":"T.A. Henzinger, in:, ACM, 2010, pp. 157–158.","ieee":"T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45, no. 1, pp. 157–158.","apa":"Henzinger, T. A. (2010). From boolean to quantitative notions of correctness (Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages, Madrid, Spain: ACM. https://doi.org/10.1145/1706299.1706319","ista":"Henzinger TA. 2010. From boolean to quantitative notions of correctness. POPL: Principles of Programming Languages vol. 45, 157–158."},"type":"conference","date_published":"2010-01-17T00:00:00Z","volume":45,"status":"public","department":[{"_id":"ToHe"}],"scopus_import":1,"language":[{"iso":"eng"}],"year":"2010","date_created":"2018-12-11T12:05:27Z","day":"17","publist_id":"2354","publication_status":"published","issue":"1","author":[{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"conference":{"start_date":"2010-01-17","name":"POPL: Principles of Programming Languages","location":"Madrid, Spain","end_date":"2010-01-23"},"page":"157 - 158"},{"page":"441 - 452","pubrep_id":"66","author":[{"last_name":"Didier","first_name":"Frédéric","full_name":"Didier, Frédéric"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"publication_status":"published","publist_id":"2349","day":"15","date_created":"2018-12-11T12:05:28Z","language":[{"iso":"eng"}],"ddc":["570"],"year":"2010","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3843"}]},"department":[{"_id":"ToHe"}],"volume":4,"date_published":"2010-11-15T00:00:00Z","type":"journal_article","oa_version":"Submitted Version","publication":"IET Systems Biology","publisher":"Institution of Engineering and Technology","doi":"10.1049/iet-syb.2010.0005","date_updated":"2023-02-23T11:45:08Z","file":[{"relation":"main_file","creator":"system","file_id":"5254","date_created":"2018-12-12T10:17:02Z","content_type":"application/pdf","file_size":222890,"date_updated":"2020-07-14T12:46:16Z","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","access_level":"open_access","file_name":"IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf"}],"quality_controlled":"1","oa":1,"month":"11","issue":"6","scopus_import":1,"file_date_updated":"2020-07-14T12:46:16Z","status":"public","has_accepted_license":"1","citation":{"chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems Biology. Institution of Engineering and Technology, 2010. https://doi.org/10.1049/iet-syb.2010.0005.","mla":"Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” IET Systems Biology, vol. 4, no. 6. Institution of Engineering and Technology, pp. 441–452, 2010.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010) 441–452.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive uniformization of the chemical master equation. IET Systems Biology. Institution of Engineering and Technology. https://doi.org/10.1049/iet-syb.2010.0005","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization of the chemical master equation. IET Systems Biology. 4(6), 441–452."},"intvolume":" 4","_id":"3842","title":"Fast adaptive uniformization of the chemical master equation","abstract":[{"text":"Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"}]