@article{ISI:000243561600012, title = {The thioredoxin specificity of Drosophila GPx: A paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases}, author = {Matilde Maiorino and Fulvio Ursini and Valentina Bosello and Stefano Toppo and Silvio C. E. Tosatto and Pierlulgi Mauri and Katja Becker and Antonella Roveri and Cristiana Bulato and Louise Benazzi and Antonella de Palma and Leopold Flohe}, journal = {JOURNAL OF MOLECULAR BIOLOGY}, number = {4}, pages = {1033-1046}, volume = {365}, year = {2007}, biburl = {http://www.bibsonomy.org/bibtex/2086745984d33278d13c056778a93cbe8/nutribiochem}, abstract = {Some members of the glutathione peroxidase (GPx) family have been reported to accept thioredoxin as reducing substrate. However, the selenocysteine-containing ones oxidise thioredoxin (Trx), if at all, at extremely slow rates. In contrast, the Cys homolog of Drosophila melanogaster exhibits a clear preference for Trx, the net forward rate constant, k�(+2), for reduction by Trx being 1.5 x 10(6) M-1 s(-1), but only 5.4 M-1 s(-1) for glutathione. Like other CysGPxs with thioredoxin peroxidase activity, Drosophila melanogaster (Dm)GPx oxidized by H2O2 contained an intra-molecular disulfide bridge between the active-site cysteine (C45; C-P) and C91. Site-directed mutagenesis of C91 in DmGPx abrogated Trx peroxidase activity, but increased the rate constant for glutathione by two orders of magnitude. In contrast, a replacement of C74 by Ser or Ala only marginally affected activity and specificity of DmGPx. Furthermore, LCMS/MS analysis of oxidized DmGPx exposed to a reduced Trx C35S mutant yielded a dead-end intermediate containing a disulfide between Trx C32 and DmGPx C91. Thus, the catalytic mechanism of DmGPx, unlike that of selenocysteine (Sec)GPxs, involves formation of an internal disulfide that is pivotal to the interaction with Trx. Hereby C91, like the analogous second cysteine in 2-cysteine peroxiredoxins, adopts the role of a ��resolving" cysteine (C-R). Molecular modeling and homology considerations based on 450 GPxs suggest peculiar features to determine Trx specificity: (i) a nonaligned second Cys within the fourth helix that acts as C-R; (ii) deletions of the subunit interfaces typical of tetrameric GPxs leading to flexibility of the C-R-Containing loop. Based of these characteristics, most of the nonmammalian CysGPxs, in functional terms, are thioredoxin peroxidases. (c) 2006 Elsevier Ltd. All rights reserved.}, issn = {0022-2836}, keywords = {IFZ glutathione_peroxidase mechanism_of_action peroxiredoxin selenocysteine thioredoxin_peroxidase } } @inproceedings{Walker:2001:DLB, title = {Dynamic Load Balancing Model: Preliminary Results for Parallel Pseudo-search Engine Indexers Crawler Mechanisms Using {MPI} and Genetic Programming}, address = {Porto, Portugal}, author = {Reginald L. Walker}, booktitle = {4th International Conference on Vector and Parallel Processing - VECPAR 2000. Selected Papers and Invited Talks}, editor = {J. M. L. M. Palma and J. Dongarra and V. Hernandez}, month = {June}, pages = {61--74}, series = {Lecture Notes in Computer Science}, url = {http://link.springer-ny.com/link/service/series/0558/papers/1981/19810061.pdf}, volume = {1981}, year = {2001}, biburl = {http://www.bibsonomy.org/bibtex/228655d5fb00d49630db5f942749fc638/brazovayeye}, abstract = {Methodologies derived from Genetic Programming (GP) and Knowledge Discovery in Databases (KDD) were used in the parallel implementation of the indexer simulator to emulate the current World Wide Web (WWW) search engine indexers. This indexer followed the indexing strategies that were employed by AltaVista and Inktomi that index each word in each Web document. The insights gained from the initial implementation of this simulator have resulted in the initial phase of the adaption of a biological model. The biological model will offer a basis for future developments associated with an integrated Pseudo-Search Engine. The basic characteristics exhibited by the model will be translated so as to develop a model of an integrated search engine using GP. The evolutionary processes exhibited by this biological model will not only provide mechanisms for the storage, processing, and retrieval of valuable information but also for Web crawlers, as well as for an advanced communication system. The current Pseudo-Search Engine Indexer, capable of organizing limited subsets of Web documents, provides a foundation for the first simulator of this model. Adaptation of the model for the refinement of the Pseudo-Search Engine establishes order in the inherent interactions between the indexer, crawler and browser mechanisms by including the social (hierarchical) structure and simulated behavior of this complex system. The simulation of behavior will engender mechanisms that are controlled and coordinated in their various levels of complexity. This unique model will also provide a foundation for an evolutionary expansion of the search engine as WWW documents continue to grow. The simulator results were generated using Message Passing Interface (MPI) on a network of SUN workstations and an IBM SP2 computer system.}, issn = {0302-9743}, bibdate = {Sat Feb 2 13:03:02 MST 2002}, acknowledgement = {}, coden = {LNCSD9}, keywords = {algorithms, genetic programming } } @inproceedings{conf/aina/AbramowiczHKPZ08, title = {NFP Ontology for Discovery and Sharing Web Services in Distributed Registries.}, author = {Witold Abramowicz and Konstanty Haniewicz and Monika Kaczmarek and Raúl Palma and Dominik Zyskowski}, booktitle = {AINA Workshops}, crossref = {conf/aina/2008w}, pages = {1416-1421}, publisher = {IEEE Computer Society}, url = {http://dblp.uni-trier.de/db/conf/aina/ainaw2008.html#AbramowiczHKPZ08}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/235dea88c1936efc7f4ebe86bbe915b00/dblp}, description = {dblp}, ee = {http://doi.ieeecomputersociety.org/10.1109/WAINA.2008.267}, date = {2008-06-03}, keywords = {dblp } } @inproceedings{conf/icse/SicardBP08, title = {Using components for architecture-based management: the self-repair case.}, author = {Sylvain Sicard and Fabienne Boyer and Noel De Palma}, booktitle = {ICSE}, crossref = {conf/icse/2008}, editor = { Robby}, pages = {101-110}, publisher = {ACM}, url = {http://dblp.uni-trier.de/db/conf/icse/icse2008.html#SicardBP08}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/2307c2bf1922367bff405fd70268cbc52/dblp}, description = {dblp}, date = {2008-05-15}, ee = {http://doi.acm.org/10.1145/1368088.1368103}, isbn = {978-1-60558-079-1}, keywords = {dblp } } @inproceedings{conf/vlsi/PalmaMHBRARM07, title = {A Flexible Design Flow for a Low Power RFID Tag.}, author = {José Carlos S. Palma and César A. M. Marcon and Fabiano Hessel and Eduardo Bezerra and Guilherme Rohde and Luciano Azevedo and Carlos Eduardo Reif and Carolina Metzler}, booktitle = {VLSI-SoC}, crossref = {conf/vlsi/2007soc}, pages = {300-303}, publisher = {IEEE}, url = {http://dblp.uni-trier.de/db/conf/vlsi/vlsisoc2007.html#PalmaMHBRARM07}, year = {2007}, biburl = {http://www.bibsonomy.org/bibtex/28c5479e12616c23a6b3c90e9496d8410/dblp}, description = {dblp}, ee = {http://dx.doi.org/10.1109/VLSISOC.2007.4402517}, date = {2008-05-09}, keywords = {dblp } } @article{journals/sigsoft/Palma03, title = {A tale of two cultures.}, author = {Paul De Palma}, journal = {ACM SIGSOFT Software Engineering Notes}, number = {6}, pages = {4-5}, url = {http://dblp.uni-trier.de/db/journals/sigsoft/sigsoft28.html#Palma03}, volume = {28}, year = {2003}, biburl = {http://www.bibsonomy.org/bibtex/20568fe2ee9258e06ba87411d1e25a399/dblp}, description = {dblp}, ee = {http://doi.acm.org/10.1145/966221.966660}, date = {2008-05-09}, keywords = {dblp } } @inproceedings{conf/vecpar/JuniorLCAS06, title = {Design and Implementation of an Environment for Component-Based Parallel Programming.}, author = {Francisco Heron de Carvalho Junior and Rafael Dueire Lins and Ricardo Cordeiro Corrêa and Gisele Azevedo Araújo and Chanderlie Freire de Santiago}, booktitle = {VECPAR}, crossref = {conf/vecpar/2006}, editor = {Michel J. Daydé and José M. L. M. Palma and Alvaro L. G. A. Coutinho and Esther Pacitti and João Correia Lopes}, pages = {184-197}, publisher = {Springer}, series = {Lecture Notes in Computer Science}, url = {http://dblp.uni-trier.de/db/conf/vecpar/vecpar2006.html#JuniorLCAS06}, volume = {4395}, year = {2006}, biburl = {http://www.bibsonomy.org/bibtex/26eafa7a848c2289aef678d868e0d3ffd/dblp}, description = {dblp}, date = {2008-05-07}, ee = {http://dx.doi.org/10.1007/978-3-540-71351-7_15}, isbn = {978-3-540-71350-0}, keywords = {dblp } } @article{Arnott1999, title = {Information and time-of-usage decisions in the bottleneck model with stochastic capacity and demand}, author = {Richard Arnott and Andr{\'e} de Palma and Robin Lindsey}, journal = {European Economic Review}, month = {Mar}, number = {3}, pages = {525--548}, url = {http://www.sciencedirect.com/science/article/B6V64-3VPJ918-3/1/da0e3ceb7560025b99dccff4e8dd6d6f}, volume = {43}, year = {1999}, biburl = {http://www.bibsonomy.org/bibtex/2d62ce3f06e57a439eadea65a77e1c14b/smicha}, keywords = {Bottlenecks } } @article{Anderson2000b, title = {From local to global competition}, author = {Simon P. Anderson and Andr{\'e} de Palma}, journal = {European Economic Review}, month = {Mar}, number = {3}, pages = {423--448}, url = {http://www.sciencedirect.com/science/article/B6V64-3YKV235-1/1/9841d25f2014f8c593a8e955f531f06f}, volume = {44}, year = {2000}, biburl = {http://www.bibsonomy.org/bibtex/2c6a8a6146349cf35814a0af163825391/smicha}, keywords = {Product differentiation } } @article{Anderson2001b, title = {The efficiency of indirect taxes under imperfect competition}, author = {Simon P. Anderson and Andr{\'e} de Palma and Brent Kreider}, journal = {Journal of Public Economics}, month = {Aug}, number = {2}, pages = {231--251}, url = {http://www.sciencedirect.com/science/article/B6V76-4384RTT-4/1/28e48cc368248d01ee6490be4963a53e}, volume = {81}, year = {2001}, biburl = {http://www.bibsonomy.org/bibtex/2379b57b60074314a38bec5c88df92ed1/smicha}, keywords = {Excise tax } }