Un ensemble de ressources de référence pour l’étude du français : tlfi, frantext et le logiciel stella

Les recherches en traitement automatique des langues nécessitent de vastes ressources de référence : corpus textuels, dictionnaires informatiques, outils de traitement. Cette contribution présente les ressources linguistiques informatisées du laboratoire atilf (Analyse et Traitement Informatique de la Langue Française) accessibles sur la toile ainsi que leur diversité d’exploitation potentielle. Regroupant un ensemble de plus de 3600 textes de langue française réunis dans frantext et divers dictionnaires, lexiques et autres bases de données, ces ressources exploitent les fonctionnalités du logiciel stella, qui correspond à un véritable moteur de recherche dédié aux bases textuelles s’appuyant sur une nouvelle théorie des objets textuels.Progress in linguistic research, especially in the field of automatic treatment, depends on access to a vast array of linguistic resources such as texts, dictionaries and software. This paper presents the computerized linguistic resources of the atilf Research Laboratory that are available on the Web and discusses the range of their potential uses. Consisting of a set of more than 3600 documents in French in the frantext database, as well as various dictionaries, lexicons, and other databases, these resources are accessed using the functions of stella, dedicated search engine software for textual databases based on a new theory of textual objects

A cognitive model for the representation of time in a man-machine dialogue.

This paper develops the foundations of a model for time representation in the framework of a man-machine dialogue system. While we analyse other approaches, especially Allen's interval calculus, we show how the relations that we commonly manipulate in everyday reasoning can in fact be reduced to two fondamental ones : succession and inclusion. By the way, we insist on the fact that a temporal model intended to reproduce some features of the human cognitive abilities shall include in a common representation linguistic information and conceptual objects. We then present the main characteristics of our temporal model, introducing the concept of coherence zone, and how this one can be used to represent tense information in natural language. Finally, we briefly show the mechanisms that ensure temporal consistency when combining new temporal information to an existing structure, and present the main elements that allow learning and predicting mechanisms within this model

ubiJ, a New Gene Required for Aerobic Growth and Proliferation in Macrophage, Is Involved in Coenzyme Q Biosynthesis in Escherichia coli and Salmonella enterica Serovar Typhimurium.

International audienceUbiquinone (coenzyme Q or Q8) is a redox active lipid which functions in the respiratory electron transport chain and plays a crucial role in energy-generating processes. In both Escherichia coli and Salmonella enterica serovar Typhimurium, the yigP gene is located between ubiE and ubiB, all three being likely to constitute an operon. In this work, we showed that the uncharacterized yigP gene was involved in Q8 biosynthesis in both strains, and we have renamed it ubiJ. Under aerobic conditions, an ubiJ mutant was found to be impaired for Q8 biosynthesis and for growth in rich medium but did not present any defect anaerobically. Surprisingly, the C-terminal 50 amino acids, predicted to interact with lipids, were sufficient to restore Q8 biosynthesis and growth of the ubiJ mutant. Salmonella ubiE and ubiB mutants were impaired in Q8 biosynthesis and in respiration using different electron acceptors. Moreover, ubiE, ubiJ, and ubiB mutants were all impaired for Salmonella intracellular proliferation in macrophages. Taken together, our data establish an important role for UbiJ in Q8 biosynthesis and reveal an unexpected link between Q8 and virulence. They also emphasize that Salmonella organisms in an intracellular lifestyle rely on aerobic respiration to survive and proliferate within macrophages

Augmented venous return for minimally invasive open heart surgery with selective caval cannulation

Objective: Minimally invasive open heart surgery involves limited intrathoracic cannulation sites necessitating cardiopulmonary bypass to be initiated via peripheral access using percutaneous cannulae with the tip placed into the right atrial cavity. However, surgery involving the opening of the right heart obliges the surgeon to maintain the end of the cannulae into the vena cavae. The impeded venous return due to the smaller diameter may be alleviated by inserting a centrifugal pump in the venous line. Methods: Right anterior mini-thoracotomy and exposure of the femoral site were performed before the patient was heparinized. Cannulation of the femoral artery, the inferior vena cava via the femoral vein and the superior vena cava through the mini-thoracotomy was performed and cardiopulmonary bypass was initiated. Venous drainage was augmented with the centrifugal pump. Cardiac arrest was provoked and both vena cavae were snared before performing the intracardiac procedure. Results: Twenty consecutive patients were operated on using this technique (15 males/five females; age: 44.8±14.3 years; bodyweight: 73.5±15.1 kg; body surface area: 1.8±0.2 m2; theoretical blood flow rate: 4.4±0.5 l/min). The cannula sizes were 21.9±2.2 Fr for the femoral artery, 26.5±1.7 Fr for the inferior vena cava and 23.8±2.5 Fr for the superior vena cava. Venous drainage through the single inferior vena cava cannula was 2.1±0.6 l/min (48.8±13.3% of the theoretical flow). Adding the superior vena cava cannula increased the venous flow to 3.1±0.4 l/min (70.7±9.6% of the theoretical value, P<0.005). The use of the centrifugal pump increased the flow to 4.1±0.6 l/min (93.4±8.9% of the theoretical flow, P<0.001) with a mean inlet negative pressure of −69.1±10.2 mmHg. The mean bypass time was 64.0±24.6 min for a mean operative time of 226.3±61.0 min. Minimum venous saturation was 69.4±8.5%. Conclusions: Despite the smaller diameter of the vena cavae compared to the right atrium, and a smaller internal diameter of percutaneous cardiopulmonary bypass cannulae compared to classic ones; the centrifugal pump improves the venous drainage significantly so that minimally invasive open heart procedures can be performed under optimal and safe perfusion condition

Overexpression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the coenzyme Q6 biosynthetic pathway.

International audienceMost of the Coq proteins involved in coenzyme Q (ubiquinone or Q) biosynthesis are interdependent within a multiprotein complex in the yeast Saccharomyces cerevisiae. Lack of only one Coq polypeptide, as in Δcoq strains, results in the degradation of several Coq proteins. Consequently, Δcoq strains accumulate the same early intermediate of the Q(6) biosynthetic pathway; this intermediate is therefore not informative about the deficient biosynthetic step in a particular Δcoq strain. In this work, we report that the overexpression of the protein Coq8 in Δcoq strains restores steady state levels of the unstable Coq proteins. Coq8 has been proposed to be a kinase, and we provide evidence that the kinase activity is essential for the stabilizing effect of Coq8 in the Δcoq strains. This stabilization results in the accumulation of several novel Q(6) biosynthetic intermediates. These Q intermediates identify chemical steps impaired in cells lacking Coq4 and Coq9 polypeptides, for which no function has been established to date. Several of the new intermediates contain a C4-amine and provide information on the deamination reaction that takes place when para-aminobenzoic acid is used as a ring precursor of Q(6). Finally, we used synthetic analogues of 4-hydroxybenzoic acid to bypass deficient biosynthetic steps, and we show here that 2,4-dihydroxybenzoic acid is able to restore Q(6) biosynthesis and respiratory growth in a Δcoq7 strain overexpressing Coq8. The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway

The factors of similarity and association in retroactive inhibition

Thesis (M.A.)--Boston University, 1946. This item was digitized by the Internet Archive

The P174L mutation in human Sco1 severely compromises Cox17-dependent metallation but does not impair copper binding.

International audienceSco1 is a metallochaperone that is required for copper delivery to the Cu(A) site in the CoxII subunit of cytochrome c oxidase. The only known missense mutation in human Sco1, a P174L substitution in the copper-binding domain, is associated with a fatal neonatal hepatopathy; however, the molecular basis for dysfunction of the protein is unknown. Immortalized fibroblasts from a SCO1 patient show a severe deficiency in cytochrome c oxidase activity that was partially rescued by overexpression of P174L Sco1. The mutant protein retained the ability to bind Cu(I) and Cu(II) normally when expressed in bacteria, but Cox17-mediated copper transfer was severely compromised both in vitro and in a yeast cytoplasmic assay. The corresponding P153L substitution in yeast Sco1 was impaired in suppressing the phenotype of cells harboring the weakly functional C57Y allele of Cox17; however, it was functional in sco1delta yeast when the wild-type COX17 gene was present. Pulse-chase labeling of mitochondrial translation products in SCO1 patient fibroblasts showed no change in the rate of CoxII translation, but there was a specific and rapid turnover of CoxII protein in the chase. These data indicate that the P174L mutation attenuates a transient interaction with Cox17 that is necessary for copper transfer. They further suggest that defective Cox17-mediated copper metallation of Sco1, as well as the subsequent failure of Cu(A) site maturation, is the basis for the inefficient assembly of the cytochrome c oxidase complex in SCO1 patients

Functional Characterization of the Eukaryotic Cysteine Desulfurase Nfs1p from Saccharomyces cerevisiae

Previous studies have indicated that the essential protein Nfs1 performs a crucial role in cellular iron-sulfur (Fe/S) protein maturation. The protein is located predominantly in mitochondria, yet low amounts are present in cytosol and nucleus. Here we examined several aspects concerning the molecular function of yeast Nfs1p as a model protein. First, we demonstrated that purified Nfs1p facilitates the in vitro assembly of Fe/S proteins by using cysteine as its specific substrate. Thus, eukaryotic Nfs1 is a functional orthologue of the bacterial cysteine desulfurase IscS. Second, we showed that only the mitochondrial version but not the extramitochondrial version of Nfs1p is functional in generating cytosolic and nuclear Fe/S proteins. Mutation of the nuclear targeting signal of Nfs1p did not affect the maturation of cytosolic and nuclear Fe/S proteins, despite a severe growth defect under this condition. Nfs1p could not assemble an Fe/S cluster on the Isu scaffold proteins when they were located in the yeast cytosol. The lack of function of these central Fe/S cluster assembly components suggests that the maturation of extramitochondrial Fe/S protein does not involve functional copies of the mitochondrial Fe/S cluster assembly machinery in the yeast cytosol. Third, the extramitochondrial version of Nfs1p was shown to play a direct role in the thiomodification of tRNAs. Finally, we identified a highly conserved N-terminal {beta}-sheet of Nfs1p as a functionally essential part of the protein. The implication of these findings for the structural stability of Nfs1p and for its targeting mechanism to mitochondria and cytosol/nucleus will be discussed

A new gene involved in coenzyme Q biosynthesis in Escherichia coli: UbiI functions in aerobic C5-hydroxylation

International audienceCoenzyme Q (ubiquinone or Q) is a redox-active lipid found in organisms ranging from bacteria to mammals in which it plays a crucial role in energy-generating processes. Q biosynthesis is a complex pathway that involves multiple proteins. In this work, we show that the uncharacterized conserved visC gene is involved in Q biosynthesis in Escherichia coli, and we have renamed it ubiI. Based on genetic and biochemical experiments, we establish that the UbiI protein functions in the C5-hydroxylation reaction. A strain deficient in ubiI has a low level of Q and accumulates a compound derived from the Q biosynthetic pathway, which we purified and characterized. We also demonstrate that UbiI is only implicated in aerobic Q biosynthesis and that an alternative enzyme catalyzes the C5-hydroxylation reaction in the absence of oxygen. We have solved the crystal structure of a truncated form of UbiI. This structure shares many features with the canonical FAD-dependent para-hydroxybenzoate hydroxylase and represents the first structural characterization of a monooxygenase involved in Q biosynthesis. Site-directed mutagenesis confirms that residues of the flavin binding pocket of UbiI are important for activity. With our identification of UbiI, the three monooxygenases necessary for aerobic Q biosynthesis in E. coli are known