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Biomedical subjects

F Achard

Publications and source records attributed to F Achard.

At least 19 recordsLinked to original sources
PubMed2001

XML, bioinformatics and data integration.

MOTIVATION: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML. CONTACT: Emmanuel.Barillot@infobiogen.fr

Computational Biology↗
PubMed2000

XML: a lingua franca for science?

XML is a new language designed to solve one of the biggest problems of the World Wide Web: its main language, HTML, is not extensible. In this article, the authors discuss the current successes and limitations of the World Wide Web, briefly explain the basics of XML and present the benefits of using XML as a data-exchange language. Finally, they discuss real-life applications that have been developed using XML, with a focus on biology.

Internet↗
PubMed1999

DBcat: a catalog of biological databases.

The DBcat (http://www.infobiogen.fr/services/dbcat) is a comprehensive catalog of biological databases, maintained and curated on a daily basis at GIS Infobiogen. It contains more than 400 databases classified by application domains. The DBcat is a structured flat file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for downloading from Infobiogen anonymous ftp server.

Biology↗
PubMed1999

Virgil database for rich links (1999 update).

With so many databases available for research in the Human Genome Project, it is crucial to efficiently relate information from different resources. For that purpose, we maintain Virgil, a database of rich links for data browsing, data analysis and database interconnection. Virgil current version contains more than 40 000 rich links from five major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/

Animals↗
PubMed1998

Virgil: a database of rich links between GDB and GenBank.

Database interconnection requires the development of links between related objects from different databases. We built a database of links, called Virgil, to manage and distribute rich (documented) links between GDB genes and GenBank human sequences. Virgil contains 18 667 unique links. In addition to a simple Web form for ad-hoc queries, we propose a generic Web interface and a prototype CORBA server for link distribution. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/home. html

Computer Communication Networks↗
PubMed1998

GenXref. VI: Automatic generation of links between two heterogeneous databases.

MOTIVATION: A large proportion of the information found in public databases is not sufficiently cross-referenced. We developed genXref, an automated system for link inference, because embarking on a manual cross-referencing of genome data would require too much expensive human expertise. It uses information retrieval technology to generate links between objects of heterogeneous databases. RESULTS: GenXref was used to generate links between GDB genes and Genbank human sequences. It resulted in > 10,000 links with a precision of 83% and a recall of approximately 32%.

Abstracting and Indexing↗
PubMed1998

The new Virgil database: a service of rich links.

MOTIVATION: Links between biological objects are frequently used by researchers in biology. However, many of the links found in public databases are insufficiently documented and difficult to retrieve. Virgil introduces the idea of a rich link, i.e. the link itself and the related pieces of information. Virgil was developed to collect, manage and distribute such links. RESULTS: At the moment, Virgil is a prototype database that contains rich links between GDB genes and Genbank sequences. The Virgil data model is rich enough to describe comprehensively a link between two biological objects. Two different means to access the information were developed: a schema-driven Web interface and a CORBA server. AVAILABILITY: http://www.infobiogen. fr/services/virgil/home.html CONTACT: Frederic.Achard@infobiogen.fr

Computer Communication Networks↗
PubMed1997

Eicosapentaenoic and docosahexaenoic acids reduce PGH synthase 1 expression in bovine aortic endothelial cells.

To enlighten the mechanism of inhibition of prostacyclin (PGI2) production by n-3 fatty acids, eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, cultured endothelial cells were incubated with albumin bound-EPA or -DHA for 22 h. Under these conditions, PGI2 formation in response to bradykinin, calcium ionophore or exogenous arachidonic acid was equally inhibited by 50%, suggesting that the inhibition might occur downstream the phospholipase step, likely at the level of PGH synthase and/or PGI2 synthase activities. Western blot analysis indicated that the mass of the constitutive isoform of PGH synthase (PGH synthase 1), but not PGI2 synthase, was significantly reduced in n-3 fatty acid-enriched cells. In subsequent experiments, PGH synthase 1 mRNA level, measured by northern blotting, was also decreased in n-3 supplemented cells. This reduction was not due to mRNA destabilization. None of these parameters were altered by similar enrichment with oleic acid (OA). These results suggest that EPA and DHA may affect PGH synthase 1 expression, presumably at the transcriptional level.

Animals↗
PubMed1997

Ubiquitous distributed objects with CORBA.

Database interoperation is becoming a bottleneck for the research community in biology. In this paper, we first discuss the question of interoperability and give a brief overview of CORBA. Then, an example is explained in some detail: a simple but realistic data bank of STSs is implemented. The Object Request Broker is the media for communication between an object server (the data bank) and a client (possibly a genome center). Since CORBA enables easy development of networked applications, we meant this paper to provide an incentive for the bioinformatics community to develop distributed objects.

Base Sequence↗
PubMed1996

Docosapentaenoic acid (22:5,n-3): metabolism and effect on prostacyclin production in endothelial cells.

Eicosapentaenoic acid (EPA, 20:5,n-3) and docosahexaenoic acid (DHA, 22:6, n-3), the two main fatty acids of fish oil, have been shown to inhibit prostacyclin production and to be actively interconverted, leading to the accumulation of docosapentaenoic acid (DPA, 22:5,n-3) in endothelial cell phospholipids. We have investigated the effect of supplementing endothelial cells with DPA on their capacity to produce prostacyclin. We found that endothelial cells incubated for 22 h with 25 microM DPA bound to albumin (fatty acid/albumin ratio of 1.3) produced two-fold less prostacyclin compared to control cells when stimulated with endogenous arachidonic acid-mobilizing agents such as bradykinin and calcium ionophore A23187. Since the formation of prostacyclin from 0.1-15 microM exogenous arachidonic acid was also reduced, it is suggested that prostacyclin inhibition observed in DPA-treated cells might not proceed from a reduction of arachidonic acid availability only. Such an inhibition was already observed after 1 h incubation of the cells with DPA, and with 2-20 times lower DPA concentrations. The inhibition might depend on EPA which was formed by retroconversion of DPA.

Animals↗
PubMed1995

Interconversions and distinct metabolic fate of eicosapentaenoic, docosapentaenoic and docosahexaenoic acids in bovine aortic endothelial cells.

The anti-aggregatory activity of endothelial cells being affected by eicosapentaenoic (EPA, 20:5(n-3)) and docosahexaenoic (DHA, 22:6(n-3)) acids, the two main polyunsaturated fatty acids of fish oil, these fatty acids, as well as their intermediary, docosapentaenoic acid (DPA, 22:5(n-3)), were investigated with respect to their metabolism. Primary cultured bovine aortic endothelial cells were supplemented for 22 h at 37 degrees C with either n-3 fatty acid, and the fatty acids of cell media, of cell lipid classes, and of choline and ethanolamine glycerophospholipids (PC and PE) were quantified. Endothelial cells converted each of the three fatty acids into the two others. They were found esterified in cell lipids and partly released in cell media, the respective parts varying according to the fatty acid. For instance, half of the DPA formed from EPA and two third of the EPA formed from DPA were released in the media. Moreover, the DHA formed from EPA and DPA was not esterified but released in media. In addition, the esterified counterparts were found in either PC or PE, depending on whether they were added or formed by conversions. It is concluded that EPA, DPA and DHA are actively interconverted each others, and differ substantially in terms of distribution between media and cells, and within phospholipid classes.

Animals↗
PubMed1995

Cross-reactivity of delta 17-6-keto-PGF1 alpha with 6-keto-PGF1 alpha antibodies.

The cross-reactivity of the PGI3 metabolite, delta 17-6-keto-PGF1 alpha, with antibodies against 6-keto-PGF1 alpha for radioimmunoassays (RIA) has been investigated. Delta 17-6-keto-PGF1 alpha was obtained either from commercial sources or after its purification from endothelial cells. In the latter case, primary cultured bovine aortic endothelial cells were incubated for 20 min at 37 degrees C with 10 microM eicosapentaenoic acid (EPA) in the presence of 2 microM 13-hydroperoxy-octadecadienoic acid, and activator of the EPA cyclooxygenation, and the 6-keto-PGF1 alpha and beta 17-6-keto-PGF1 alpha produced were separated by RP-HPLC. Then, cross-reactivities of the commercial and purified beta 17-6-keto-PGF1 alpha with 6-keto-PGF1 alpha antibodies were determined and found not to exceed 10%. In addition, the amounts of prostacyclin-related compounds detected by direct measurements in media of cells loaded with EPA were compared with those obtained after purification of 6-keto-PGF1 alpha. In accordance with the cross-reactivity data, we found that RIA in media mainly measured 6-keto-PGF1 alpha, the beta 17-6-keto-PGF1 alpha formed being undetected at 90%. It is concluded that 6-keto-PGF1 alpha antibodies generally used for RIA of 6-keto-PGF1 alpha are highly specific since they can discriminate a metabolite bearing an additional double band such as the PGI3 metabolite beta 17-6-keto-PGF1 alpha.

6-Ketoprostaglandin F1 alpha↗
PubMed1994

A gene for hereditary multiple exostoses maps to chromosome 19p.

Hereditary multiple exostoses (EXT) is an autosomal dominant bony disorder characterized by the formation of cartilage-capped juxta-epiphyseal prominences on the long bones. Recently, a disease gene (EXT 1) has been mapped to chromosome 8q23-q24 by linkage analysis in informative families. Here, we report on the genetic mapping of a second locus (EXT 2) to the short arm of chromosome 19 by linkage to a microsatellite DNA marker at the D19S221 locus, which gives additional support to the view that EXT is a genetically heterogeneous condition.

Chromosome Mapping↗
PubMed1993

Platelet inhibitory functions of aortic endothelial cells. Effects of eicosapentaenoic and docosahexaenoic acids.

The endothelial cell platelet inhibitory potential was assessed directly by measuring the platelet inhibition induced by platelet interaction with the cultured aortic endothelial cell. The prostacyclin content of the platelet suspensions after interaction was also quantified. We found that prostacyclin production accounted for the overall platelet inhibitory potential of the aortic cells since: (a) endothelial cells incubated with aspirin, which did not produce prostacyclin, did not inhibit platelets; (b) the prostacyclin content of platelet suspensions after interaction with endothelial cells correlated with the extent of the platelet inhibition; (c) such a platelet inhibition was reproduced by adding synthetic prostacyclin in amount equivalent to that produced by endothelial cells during the interaction. Eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids incorporated into endothelial phospholipids, decreased the ability of the cells to produce prostacyclin and to inhibit platelets, DHA being less effective than EPA.

Animals↗
PubMed1993

Criteria for anatomical compatibility of the total artificial heart: computerized three-dimensional modeling of the cardiovascular anatomy.

A quantitative study of cardiovascular anatomy was performed by obtaining three-dimensional reconstructions from regular computed tomography scan images in 15 patients, all candidates for heart transplantation. Volumetric estimates of the cardiovascular structures were obtained from these three-dimensional reconstructions using data directly related to total artificial heart (TAH) implantations. By using computerized three-dimensional modeling of these structures, reproducible measurements of the parameters defining the shape and the anatomical connections of the intrathoracic space available for TAH implantation could be derived. The results are intended to be used for both technical and clinical applications such as computer-assisted drawing of the pericardial cavity and the anatomical connections (useful for improving the design of TAH) and combined statistical calculations (multiple regressions, cluster algorithm) of the measurement results, which will then enable the best selection to be made among two or three TAH models for each patient.

Aortography↗
PubMed1990

[Enoximone: hemodynamic effect in patients with cardiac insufficiency].

Enoximone, a phosphodiesterase inhibitor, is a positive inotropic agent with direct vasodilator properties. Its acute effects after I.V. administration and the possibility of oral relay were studied in 14 patients (13 men and 1 woman), 40 to 78 years of age (mean 61 years) with Stage IV cardiac failure (NYHA Classification). Eleven patients had dilated cardiomyopathy, 2 had ischemic heart disease and 1 a dilated hypertrophic cardiomyopathy. The haemodynamic inclusion criteria were: cardiac index less than or equal to 2.2 l/mn/m2 and pulmonary capillary pressure greater than or equal to 18 mmHg. Patients with cardiogenic shock and severe renal or hepatic failure were excluded. The drug was administered as a bolus of 1 mg/kg followed by a continuous infusion of 5 to 15 g/kg/mn (average 8.9 +/- 2.6 for 7 to 72 hours; average 27 +/- 16 hours). Haemodynamic effects of I.V. administration: no change in heart rate, slight lowering of blood pressure, very significant reduction in right atrial and pulmonary capillary pressures, of pulmonary artery pressures, of arteriolo-capillary and systemic resistances and marked increase in cardiac output. General tolerance was excellent with no clinical secondary effects and no signs of hepatic, renal or haematological (platelets) toxicity. Cardiac tolerance was also excellent, no aggravation of preexisting arrhythmias. There was no immediate mortality. Oral relay was undertaken in 14 patients with a daily dose of 300 mg in 12 cases, 400 mg in 1 case and 500 mg in 1 case. Six patients underwent control haemodynamic evaluation on the 8th day: there were no signs of the haemodynamic improvement obtained by I.V. administration.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗