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2001
Baldwin, J., W. C. Voegtli, N. Khidekel, P. Moenne-Loccoz, C. Krebs, AS Pereira, B. A. Ley, BH HUYNH, T. M. Loehr, P. J. Riggs-Gelasco, A. C. Rosenzweig, and J. M. Bollinger. "Rational reprogramming of the R2 subunit of Escherichia coli ribonucleotide reductase into a self-hydroxylating monooxygenase." Journal of the American Chemical Society. 123 (2001): 7017-7030. AbstractWebsite

The outcome of O-2 activation at the diiron(II) cluster in the R2 subunit of Escherichia coli (class I) ribonucleotide reductase has been rationally altered from the normal tyrosyl radical (Y122)(1) production to self-hydroxylation of a phenylalanine side-chain by two amino acid substitutions that leave intact the (histidine)(2)-(carboxylate)(4) ligand set characteristic of the diiron-carboxylate family. Iron ligand Asp (D) 84 was replaced with Glu (E), the amino acid found in the cognate position of the structurally similar diiron-carboxylate protein, methane monooxygenase hydroxylase (MMOH). We previously showed that this substitution allows accumulation of a mu -1,2-peroxodiiron(III) intermediate,(2 3) which does not accumulate in the wild-type (wt) protein and is probably a structural homologue of intermediate P (H-peroxo) in O-2 activation by MMOH.(4) In addition, the near-surface residue Trp (W) 48 was replaced with Phe (F), blocking transfer of the "extra" electron that occurs in wt R2 during formation of the formally Fe(LII)Fe(IV) cluster X.(5-7) Decay of the mu1,2-peroxodiiron(III) complex in R2-W38F/D84E gives an initial brown product, which contains very little YI22(.) and which converts very slowly (t(1/2) similar to 7 h) upon incubation at 0 degreesC to an intensely purple final product. X-ray crystallographic analysis of the purple product indicates that F208 has undergone epsilon -hydroxylation and the resulting phenol has shifted significantly to become st ligand to Fe2 of the diiron cluster. Resonance Raman (RR) spectra of the purple product generated with O-16(2) or O-18(2) show appropriate isotopic sensitivity in bands assigned to O-phenyl and Fe-O-phenyl vibrational modes, confirming that the oxygen of the Fe(III)-phenolate species is derived from Or. Chemical analysis, experiments involving interception of the hydroxylating intermediate with exogenous reductant, and Mossbauer and EXAFS characterization of the brown and purple species establish that F208 hydroxylation occurs during decay of the peroxo complex and formation of the initial brown product. The slow transition to the purple Fe(LII)-phenolate species is ascribed to a ligand rearrangement in which mu -O2- is lost and the F208-derived phenolate coordinates. The reprogramming to F208 monooxygenase requires both amino acid substitutions, as very little epsilon -hydroxyphenylalanine is formed and pathways leading to Y122(.) formation predominate in both R2-D84E and R2-W48F(2-7).

Indelicato, P., G. C. Rodrigues, E. Lindroth, M. A. Ourdane, F. Parente, J. P. Santos, P. Patté, and J. Bieron. "Relativistic and many-body effects on total binding energies of Cesium and other highly-charged ion." Physica Scripta. T92 (2001): 327. Abstract

The determination of atomic masses from highly ionized atoms using Penning Traps requires precise values for electronic binding energies. In the present work, binding energies of several ions (from several elements) are calculated in the framework of two relativistic many-body methods: Relativistic Many-Body Perturbation Theory (RMBPT) and Multi-Configuration Dirac– Fock (MCDF). The ions studied in this work are: Cl (He and Li-like), Se (F and Ne-like), Cs (He, Be, Ne, Al, Cl, Ar, K, Kr, Xe-like and neutral Cs), Hg, Pb and U (Br and Kr-like). Some of them are presented in this paper. Cesium has been treated in more details, allowing for a systematic comparison between MCDF and RMBPT methods. The Cs ions binding energies allow for the determination of atomic Cs mass, which can be used in a QED-independent fine structure constant determination.

Indelicato, P., E. Lindroth, T. Beier, J. Bieron, A. M. Costa, I. Lindgren, J. P. Marques, A. M. Martenson-Pendrill, M. C. Martins, M. A. Ourdane, F. Parente, P. Patté, G. C. Rodrigues, S. Salomonson, and J. P. Santos. "Relativistic Calculations for Trapped Ions." Hyperfine Interactions. 132 (2001): 347-361. AbstractWebsite

We present recent results in the field of total binding energy calculations, Landщ factors, quantum electrodynamics corrections and lifetime that are of interest for ion traps and ion sources. We describe in detail MCDF and RMBPT calculation of ionic binding energies, which are needed for the determination of atomic masses from highly charged ion measurements. We also show new results concerning Landщ factor in 3-electron ions. Finally we describe how relativistic calculations can help understand the physics of heavy ion production ion sources.

Cabrita, A., L. Pereira, D. Brida, A. Lopes, A. Marques, I. Ferreira, E. Fortunato, and R. Martins. "Silicon carbide photodiodes: Schottky and PINIP structures." Applied surface science. 184.1 (2001): 437-442. Abstract
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Cabrita, A., L. Pereira, D. Brida, A. Lopes, A. Marques, I. Ferreira, E. Fortunato, and R. Martins. "{Silicon carbide photodiodes: Schottky and PINIP structures}." Applied Surface Science. 184 (2001): 437-442. AbstractWebsite
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2000
Dias, JM, CA Cunha, S. Teixeira, G. Almeida, C. Costa, J. Lampreia, JJG Moura, I. Moura, and MJ Romao. "Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774." ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY. 56 (2000): 215-217. Abstract
{Nitrite reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is a multihaem (type c) membrane-bound enzyme that catalyzes the dissimilatory conversion of nitrite to ammonia. Crystals of the oxidized form of this enzyme were obtained using PEG and CaCl2 as precipitants in the presence of 3-(decylmethylammonium)propane-1-sulfonate and belong to the space group P2(1)2(1)2(1), With unit-cell parameters a = 78.94
Cidade, M. T., C. R. Leal, M. H. Godinho, and Patrick Navard. "Temperature dependence of the rheological properties of acetoxypropylcellulose in the thermotropic chiral nematic phase." 348.1 (2000): 27-39. Abstract
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Leite, {João Alexandre Carvalho Pinheiro}, and {José Júlio Alves} Alferes. "Dynamic updates of non-monotonic knowledge bases." Journal Of Logic Programming. 45 (2000): 43-70. Abstract
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Leite, {João Alexandre Carvalho Pinheiro}, and {José Júlio Alves} Alferes. "Multi-dimensional Dynamic Logic Programming." Computational Logic in Multi-Agent Systems. 2000. 17-26. Abstract
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Neves-Silva, R., P. O. Shirley, J. M. Lemos, and A. Gonçalves. "Adaptive regulation of superheated steam temperature." IFAC - Control Eng. Practice. 8 (2000): 1405-1415.
Ramos, A. M. P., and V. J. G. Lúcio Punching of prestressed flat slabs: Experimental analysis. Vol. 57. International Workshop on Punching Shear Capacity of RC Flat Slabs, 57. Stockholm: Royal Institute of Technology, 2000. Abstract

The experimental analysis of nine prestressed flat slab models under punching is described and the results are compared with the recommendations of EC2 and MC90. The tests were performed on specimens at a scale 1/3, prestressed with unbonded high strength steel. In the first set, the specimens (AR2 to AR5 and AR7) were only subjected to in-plane compression, to evaluate the effect of the in-plane forces on the punching resistance. The second set of tests (AR8 to AR11) intended to study the effect of the vertical component of the tendon forces near the column in the punching resistance. This work aims to improve the understanding of the behaviour of prestressed flat slabs under punching load and the evaluation of the punching resistance.

Ramos, Antonio, Valter Lucio, and Paul E. Regan. "Repair and Strengthening Methods of Flat Slabs for Punching." International Workshop on Punching Shear Capacity of RC Flat Slabs. Stockholm: Trita-BKN. Bulletin, 2000. 125-133. Abstract

The present work reports experimental research carried out on repair and strengthening methods of flat slabs for punching. The repair and strengthening methods studied are: strengthening using transversal prestress, repair by substitution of the damaged concrete; and strengthening using steel beams as a column head, connected to the column and to the slab with epoxy resin and mechanical expansion anchors. Four experimental test slabs (AR1 to AR4) were produced and tested: two with transversal prestress, one only repaired and one strengthened with a steel column head. The execution process, its efficiency and design, are discussed.

Santos, TO, RB Caetano, J. M. Lemos, and FJ Coito. "Adaptive Regulation of Arc Welding Temperature with Parallel Integral Action." (2000). Abstract
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Santos, TO, RB Caetano, J. M. Lemos, and FJ Coito. "Multipredictive adaptive control of arc welding trailing centerline temperature." Control Systems Technology, IEEE Transactions on. 8 (2000): 159-169. Abstract
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Judeinstein, P., M. C. Lanca, J. Marat-Mendes, and J. Rault. "Pore dimension of water trees in PE: NMR studies." Polymer. 41 (2000): 8151-8154. AbstractWebsite

In PE films aged under electric field the crystallisation of water (and melting of ice) has been studied by quadrupolar NMR, this technique allows one to determine the concentration of water as low as 10(-4). It is shown that the pore dimensions of the tracks forming the water trees of the order of 2.5 nm, are independent of the ageing time. The mobility of water in these water trees and in porous glass, of similar pore dimensions, are compared. (C) 2000 Elsevier Science Ltd. All rights reserved.

Judeinstein, P., M. C. Lanca, J. Marat-Mendes, and J. Rault. "Pore dimension of water trees in PE: NMR studies." Polymer. 41 (2000): 8151-8154. AbstractWebsite

In PE films aged under electric field the crystallisation of water (and melting of ice) has been studied by quadrupolar NMR, this technique allows one to determine the concentration of water as low as 10(-4). It is shown that the pore dimensions of the tracks forming the water trees of the order of 2.5 nm, are independent of the ageing time. The mobility of water in these water trees and in porous glass, of similar pore dimensions, are compared. (C) 2000 Elsevier Science Ltd. All rights reserved.

Lima, Maria Margarida, and Regina Monteiro. "Pressureless Sintering of Alumina-Glass Composites." Ceramics-Processing, Reliability, Tribology and Wear, Volume 12 (2000): 178-183. Abstract
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Wengenack, NL, H. Lopes, MJ Kennedy, P. Tavares, AS Pereira, I. Moura, JJG Moura, and F. Rusnak. "Redox potential measurements of the Mycobacterium tuberculosis heme protein KatG and the isoniazid-resistant enzyme KatG(S315T): Insights into isoniazid activation." Biochemistry. 39 (2000): 11508-11513. AbstractWebsite

Mycobacterium tuberculosis KatG is a multifunctional heme enzyme responsible for activation of the antibiotic isoniazid. A KatG(S315T) point mutation is found in >50% of isoniazid-resistant clinical isolates. Since isoniazid activation is thought to involve an oxidation reaction, the redox potential of KatG was determined using cyclic voltammetry, square wave voltammetry, and spectroelectrochemical titrations. Isoniazid activation may proceed via a cytochrome P450-like mechanism. Therefore, the possibility that substrate binding by KatG leads to an increase in the heme redox potential and the possibility that KatG(S315T) confers isoniazid resistance by altering the redox potential were examined. Effects of the heme spin state on the reduction potentials of KatG and KatG(S315T) were also determined. Assessment of the Fe3+/Fe2+ couple gave a midpoint potential of ca. -50 mV for both KatG and KatG(S315T). In contrast to cytochrome P450s, addition of substrate had no significant effect on either the KatG or KatG(S315T) redox potential. Conversion of the heme to a low-spin configuration resulted in a -150 to -200 mV shift of the KatG and KatG(S315T) redox potentials. These results suggest that isoniazid resistance conferred by KatG(S315T) is not mediated through changes in the heme redox potential. The redox potentials of isoniazid were also determined using cyclic and square wave voltammetry, and the results provide evidence that the ferric KatG and KatG(S315T) midpoint potentials are too low to promote isoniazid oxidation without formation of a high-valent enzyme intermediate such as compounds I and IT or oxyferrous KatG.

Cidade, M. T., C. R. Leal, M. H. Godinho, and Patrick Navard. "Temperature dependence of the rheological properties of acetoxypropylcellulose in the thermotropic chiral nematic phase." Molecular Crystals and Liquid Crystals. 348.1 (2000): 27-39. Abstract
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Wengenack, NL, H. Lopes, MJ Kennedy, P. Tavares, AS Pereira, I. Moura, JJG Moura, and F. Rusnak. "{Redox potential measurements of the Mycobacterium tuberculosis heme protein KatG and the isoniazid-resistant enzyme KatG(S315T): Insights into isoniazid activation}." Biochemistry. 39 (2000): 11508-11513. Abstract
Mycobacterium tuberculosis KatG is a multifunctional heme enzyme responsible for activation of the antibiotic isoniazid. A KatG(S315T) point mutation is found in >50% of isoniazid-resistant clinical isolates. Since isoniazid activation is thought to involve an oxidation reaction, the redox potential of KatG was determined using cyclic voltammetry, square wave voltammetry, and spectroelectrochemical titrations. Isoniazid activation may proceed via a cytochrome P450-like mechanism. Therefore, the possibility that substrate binding by KatG leads to an increase in the heme redox potential and the possibility that KatG(S315T) confers isoniazid resistance by altering the redox potential were examined. Effects of the heme spin state on the reduction potentials of KatG and KatG(S315T) were also determined. Assessment of the Fe3+/Fe2+ couple gave a midpoint potential of ca. -50 mV for both KatG and KatG(S315T). In contrast to cytochrome P450s, addition of substrate had no significant effect on either the KatG or KatG(S315T) redox potential. Conversion of the heme to a low-spin configuration resulted in a -150 to -200 mV shift of the KatG and KatG(S315T) redox potentials. These results suggest that isoniazid resistance conferred by KatG(S315T) is not mediated through changes in the heme redox potential. The redox potentials of isoniazid were also determined using cyclic and square wave voltammetry, and the results provide evidence that the ferric KatG and KatG(S315T) midpoint potentials are too low to promote isoniazid oxidation without formation of a high-valent enzyme intermediate such as compounds I and IT or oxyferrous KatG.
1999
Allain, Ronan, Philippe Taquet, Bernard Battail, Jean Dejax, Philippe Richir, Monette Veran, Franck Limon-Duparcmeur, R. Vacant, O. Mateus, Phouvong Sayarath, Bounxou Khenthavong, and Sitha Phouyavong. "Un nouveau genre de dinosaure sauropode de la formation des Gres superieurs (Aptien-Albien) du Laos." Comptes Rendus de l'Academie des Sciences - Series IIA - Earth and Planetary Science. 329 (1999): 609-616. Abstractallain_taquet_battail_dejax_richir_mateus_et_al_1999_un_nouveau_genre_de_dinosaure_sauropode_de_la_formation_des_gres_superieurs_aptien-albien_du_laos.pdfWebsite

The partly-articulated postcranial remains of two sauropod skeletons recently found in Tang Vay (Savannakhet Province, Laos) are assigned to the species Tangvayosaurus hoffeti (nov. gen., nov. sp.). The derived characters present in the new material confirm the presence of titanosaurs in South East Asia at the end of the Early Cretaceous, but are not consistent with its placement within Titanosaurus genus as first done by Hoffet in 1942. All of the material relative to this species is therefore referred to a new genus: Tangvayosaurus. Tangvayosaurus and the Thai genus Phuwiangosaurus have strong affinities and are considered as primitive titanosaurs.

Allain, Ronan, Philippe Taquet, Bernard Battail, Jean Dejax, Philippe Richir, Monette Véran, Franck Limon-Duparcmeur, Renaud Vacant, Octavio Mateus, Phouvong Sayarath, Bounxou Khenthavong, and Sitha Phouyavong. "Un nouveau genre de dinosaure sauropode de la formation des Grès supérieurs (Aptien-Albien) du Laos." Comptes Rendus de l{\textquotesingle}Académie des Sciences - Series {IIA} - Earth and Planetary Science. 329 (1999): 609-616. AbstractWebsite
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Cunha, José C., João Louren{\c c}o, and Tiago Antão. "An experiment in tool integration: the DDBG parallel and distributed debugger." J. Syst. Archit.. 45 (1999): 897-907. AbstractWebsite
Most known teaching experiences focus on parallel computing courses only, but some teaching experiences on distributed computing courses have also been reported. In this paper we describe a course on Parallel and Distributed Processing that is taught at undergraduate level in the Computer Science degree of our University.This course presents an integrated approach concerning concurrency, parallelism, and distribution issues. It’s a breadth-first course addressing a wide spectrum of abstractions: the theoretical component focus on the fundamental abstractions to model concurrent systems, including process cooperation schemes, concurrent programming models, data and control distribution, concurrency control and recovery in transactional systems, and parallel processing models; the practical component illustrates the design and implementation issues involved in selected topics such as a data and control distribution problem, a distributed transaction-based support system and a parallel algorithm.We also discuss how this approach has been contributing to prepare the student to further actions regarding research and development of concurrent, distributed, or parallel systems.
Cunha, José C., João M. Lourenço, and Tiago Antão. "An experiment in tool integration: the {DDBG} parallel and distributed debugger." J. Syst. Archit.. 45 (1999): 897-907. Abstractjsa99.pdfWebsite

Most known teaching experiences focus on parallel computing courses only, but some teaching experiences on distributed computing courses have also been reported. In this paper we describe a course on Parallel and Distributed Processing that is taught at undergraduate level in the Computer Science degree of our University.This course presents an integrated approach concerning concurrency, parallelism, and distribution issues. It's a breadth-first course addressing a wide spectrum of abstractions: the theoretical component focus on the fundamental abstractions to model concurrent systems, including process cooperation schemes, concurrent programming models, data and control distribution, concurrency control and recovery in transactional systems, and parallel processing models; the practical component illustrates the design and implementation issues involved in selected topics such as a data and control distribution problem, a distributed transaction-based support system and a parallel algorithm.We also discuss how this approach has been contributing to prepare the student to further actions regarding research and development of concurrent, distributed, or parallel systems.

Correia, C., E. Monzani, I. Moura, J. Lampreia, and JJG Moura. "Cross-linking between cytochrome c(3) and flavodoxin from Desulfovibrio gigas." BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 256 (1999): 367-371. Abstract
Tetraheme cytochrome c(3) (13 kDa) and flavodoxin (16 kDa), are small electron transfer proteins that have been used to mimic, in vitro, part of the electron-transfer chain that operates between substract electron donors and respiratory electron accepters partners in Desulfovibrio species (Palma, N., Moura, I., LeGall, J., Van Beeumen, J., Wampler, J., Moura, J. J. G. (1994) Biochemistry 33, 6394-6407). The electron transfer between these two proteins is believed to occur through the formation of a specific complex where electrostatic interaction is the main driving force (Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P.K. and Wampler, J.E. (1988) Biochemistry 27, 2444-2450, Stewart, D., LeGall, J., Moura, I., Moura, J.J.G., Peck, H.D., Xavier, A.V., Weiner, P., Wampler, J. (1989) fur. J. Biochem. 185, 695-700). In order to obtain structural information of the pre-complex, a covalent complex between the two proteins was prepared. A water-soluble carbodiimide {[}EDC (1-ethyl-3(3 dimethylaminopropyl) carbodiimide hydrochloride] was used for the cross linking reaction. The reaction was optimized varying a wide number of experimental parameters such as ionic strength, protein and cross linker concentration, and utilization of different cross linkers and reaction time between the crosslinker and proteins. (C) 1999 Academic Press.