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3. Prospective multicenter non-interventional real-world study to assess the patterns of use, effectiveness and safety of follitropin delta in routine clinical practice (the PROFILE study)

Author

Blockeel, Christophe, Griesinger, Georg, Rago, Rocco, Larsson, Per, Sonderegger, Yum Lina Yip, Rivière, Stéphane, Laven, Joop S.E., Blockeel, Christophe, Griesinger, Georg, Rago, Rocco, Larsson, Per, Sonderegger, Yum Lina Yip, Rivière, Stéphane, and Laven, Joop S.E.

Abstract

Objective: To observe the real-world utilization patterns, effectiveness and safety profile of follitropin delta in women ≥18 years naïve to ovarian stimulation undergoing in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI). Design: Prospective, multinational, multicenter, observational study. All IVF/ICSI treatment protocols were conducted according to routine clinical practice, including undertaking fresh/frozen transfers. Outcomes included use of dosing algorithm, follitropin delta dosing patterns, ovarian response, pregnancy rates and adverse drug reactions (ADRs). Results: The first ovarian stimulation cycle using follitropin delta was initiated in 944 women. Mean baseline demographics were: age, 33.5 ± 4.7 years; bodyweight, 67.1 ± 13.6 kg; anti-Müllerian hormone, 20.3 ± 16.1 pmol/L (2.84 ± 2.25 ng/mL). The dosing algorithm was used to calculate the follitropin delta daily starting dose in 893/944 women (94.5%). The mean difference between the calculated and prescribed daily dose was small (0.2 ± 1.40 µg). The mean daily starting follitropin delta dose was 10.4 ± 2.72 µg and the mean total dose administered was 104 µg. Follitropin delta dose adjustments were reported for 57/944 (6.0%) women. The mean number of retrieved oocytes was 10.1 ± 7.03. Ongoing pregnancy at 10–11 weeks was reported for 255 women (27.0% per initiated cycle and 43.1% per fresh transfer [n=592]). Cumulative ongoing pregnancy rate after fresh and/or frozen transfer was 36.4% (344/944). Four women discontinued follitropin delta due to ADRs. Ovarian hyperstimulation syndrome (OHSS) was the most frequently reported ADR (n=37 [3.9%]); most cases of OHSS were of mild or moderate intensity (n=30 [3.2%]). Conclusions: This large real-world study of follitropin delta utilization patterns confirms its good pregnancy rates while minimizing OHSS risk during first ovarian stimulation cycle.

Published
2022

8. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Author

Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, and Lecharny, Alain

Published
2005

12. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Author

Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, Lecharny, Alain, Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, and Lecharny, Alain

Abstract

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

Published
2017

13. i4Life: Standardising the World's Biodiversity Catalogue

Author

Culham, Alastair, Sitko, Magdalena, Roskov, Yuri, Didžiulis, Viktoras, Kwok Cheung, Kunze, Thomas, Schalk, Peter, Addink, Wouter, Döring, Markus, Cochrane, Guy, Rivière, Stéphane, Robert, Vincent, Wieslaw Bogdanowicz, Hilton-Taylor, Craig, Berendsohn, Walter, Güntsch, Anton, Jones, Andrew, White, Richard, and Bourgoin, Thierry

Published
2013
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14. algoML : un format XML pour l'apprentissage de l'algorithmique et la programmation

Author

Rivière, Stéphane, Zampieri, Karine, Amerein-Stolner, Béatrice, Laboratoire de Mathématiques Informatique et Applications (LMIA), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Georges-Louis Baron, Éric Bruillard, and Vassilis Komis.

Subjects
programmation, Technologie de l'information, Matériel didactique, Teacher, [SHS.EDU]Humanities and Social Sciences/Education, Multimedia systems in education, Nouvelles technologies de l'information et de la communication, enseignement, Information technology, XML, Information and communications technology, Computer-assisted education, Computer-assisted instruction, Social sciences, Education, Education et informatique, Sciences de l'éducation, Educational technologies, Teaching materials, Enseignement assisté par ordinateur, informatique, Interactive multimedia, Teaching -- Aids and devices, Teaching (Principles and practice), algorithmique
Abstract

Nous présentons algoML, un format XML destiné à représenter des algorithmes et des programmes de façon indépendante d'une notation de pseudo-langage ou d'un langage de programmation particulier, format que nous avons développé dans le cadre de ressources en ligne dans le domaine de l'algorithmique pour l'UNT (Université Numérique Thématique) Unisciel. Nous avons conçu ce format pour qu'il puisse être utilisé dans de nombreux contextes différents, que ce soit au niveau des langages utilisés par les applications (pseudo-langages de haut niveau, langages de programmation existants) ou au niveau des applications elles-mêmes (cours d'algorithmique avec sortie dans différents langages, environnement visuel de programmation avec un langage propre...). Nous avons aussi conçu ce format pour qu'il puisse être traité facilement avec les outils XML standards, notamment le langage de transformation XSLT, sans avoir de connaissance particulière en compilation.

Published
2011

15. Walking in the visibility complex with applications to visibility polygons and dynamic visibility

Author

Rivière, Stéphane, Models, Algorithms and Geometry for Computer Generated Image Graphics (iMAGIS), Laboratoire d'informatique GRAphique, VIsion et Robotique de Grenoble (GRAVIR - IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, and Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
[INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR]
Abstract

International audience; The visibility complex is a data structure that encodes all visibility relations between objects of a scene in the plane. However, in some applications only a subset of these informations is relevant at a time, in particular visibility informations about rays issued from (resp. going to) a given object O. We first consider the set of faces of the complex representing rays issued from a given object. We define an order on these faces and show, once the visibility complex is computed, how to visit all of them with no additional data structure in optimal time O(kf ), where kf is the number of faces visited. Then we show howto use this walk to perform a topological sweep of the vertices incident to these faces in optimal time O(kv), where kv is the number of these vertices, still with no additional data structure. We next consider the set of faces of the complex representing rays issued from the “blue sky” and passing through a line segment s which is outside the convex hull of the scene. We show that the previous algorithms can be adapted simply in this new context, and we use these walks for two applications. First, we show how to compute the visibility polygon of a line segment s = (p, q) outside the convex hull of the scene in O(vis(s)+tv(p)+tv(q)) time, where vis(s) is the size of the visibility polygon and tv(p) (resp. tv(q)) is the time to compute the view around p (resp. q). Second, we show how to maintain the view around a point moving from p to q. Once the view around p is computed, the algorithm has a total running time O(max(v(p), v(p, q))), where v(p) is the size of the view around p and v(p, q) the number of changes of visibility along (p, q). This algorithm is an alternative to those we have described in [Riv97b].

Published
1997

16. Dealing with degeneracies and numerical imprecisions when computing visibility graphs

Author

Rivière, Stéphane, Models, Algorithms and Geometry for Computer Generated Image Graphics (iMAGIS), Laboratoire d'informatique GRAphique, VIsion et Robotique de Grenoble (GRAVIR - IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, and Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
[INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR]
Abstract

International audience; Most algorithms in computational geometry assume that the input is in ”general position”, that is that no degenerate cases occur (such as three aligned points , or three convergent lines . . . ). But in practice, when the size of the input becomes significant, degenerate configurations occur and programs fail. Things get worse when the program must face imprecise computations. Some general tools have been developed to cope with these problems. For solving degeneracies symbolic perturbation schemes are employed (e.g. [EM90], [Yap90]) : coordinates of input are symbolically perturbed so that degeneracies are removed. Other techniques such as the epsilon geometry ([GSS89]) do the actual geometric computations but consider that the results have an imprecision up to ε and decisions made on these results take this imprecision into account. Finally techniques are developed to do exact computations (e.g. [FV93]) and avoid imprecision problems. These general techniques can be used as ”black boxes” for geometric computation in algorithms. This has the advantage that it can be applied to a large range of algorithms, but these black boxes have in general an extra cost which can reduce the performance of the program. We consider here two algorithms for computing visibility graphs and study how to apply the idea of symbolic perturbation, not for black boxes creation, but for direct modifications of the algorithm, making it robust.

Published
1996

23. Crystallization and preliminary crystallographic study of a pheromone-binding protein from the cockroach Leucophaea maderae.

Author

Lartigue, Audrey, Rivière, Stéphane, Brossut, Rèmy, Tegoni, Mariella, and Cambillau, Christian

Subjects
*PHEROMONES, *CARRIER proteins, *COCKROACHES, *CRYSTALLIZATION
Abstract

Pheromone-binding proteins (PBPs) are small helical proteins (13-18 kDa} present in various sensory organs of moths and other insect species. An antennal protein from the cockroach Leucophaea maderae (LmaPBP) has been found to share all the hallmarka of the PBP family and is expressed specifically in the female adult antennae, the gender that perceives the sex pheromone. Here, the crystallization of LmaPBP expressed as a recombinant protein in Escherichia coli periplasm is reported. Crystals of LmaPBP were obtained by the sitting-drop vapoour-diffusion method using a nanodrop-dispensing robot. The protein crystallizes in two different crystal forms. Form 1 belongs to space group P1, with unit-cell parameters a = 43.2, b = 45.1, c = 45.7 Å, α = 118.6, β = 93.0, γ = 106.9° . With two molecules in the asymmetric unit, V[SUBM] is 2.7 *Aring;[SUP-1] Da[SUP-1] and the solvent content is 47%. A complete data set has been collected at 1.6 Å resolution on beamline ID14-2 (ESRF, Grenoble). Form 2 was obtained in the presence of the pheromone (3-hydroxy-butan-2-one) and belongs to space group P2[SUB1], with unit-cell parameters a = 38.2, b = 62.2, c = 45.1 Å, β = 93.0°. With two molecules in the asymmetric unit, V[SUBM] is 2.0 Å[SUP3] Da[SUP-1] and the solvent content is 39%. A complete data set has been collected at 1.7 Å resolution on beamline BM14 (ESRF, Grenoble). SeMet expression has been performed with a view to solving the structure by MAD data collection using the Se absorption edge. [ABSTRACT FROM AUTHOR]

Published
2003
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24. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Author

Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, Lecharny, Alain, Aubourg, Sébastien, Brunaud, Véronique, Bruyère, Clémence, Cock, Mark, Cooke, Richard, Cottet, Annick, Couloux, Arnaud, Déhais, Patrice, Deléage, Gilbert, Duclert, Aymeric, Echeverria, Manuel, Eschbach, Aimée, Falconet, Denis, Filippi, Ghislain, Gaspin, Christine, Geourjon, Christophe, Grienenberger, Jean-Michel, Houlné, Guy, Jamet, Elisabeth, Lechauve, Frédéric, Leleu, Olivier, Leroy, Philippe, Mache, Régis, Meyer, Christian, Nedjari, Hafed, Negrutiu, Ioan, Orsini, Valérie, Peyretaillade, Eric, Pommier, Cyril, Raes, Jeroen, Risler, Jean-Loup, Rivière, Stéphane, Rombauts, Stéphane, Rouzé, Pierre, Schneider, Michel, Schwob, Philippe, Small, Ian, Soumayet-Kampetenga, Ghislain, Stankovski, Darko, Toffano, Claire, Tognolli, Michael, Caboche, Michel, and Lecharny, Alain

Abstract

Genomic projects heavily depend on genome annotations and are limited by the current deficiencies in the published predictions of gene structure and function. It follows that, improved annotation will allow better data mining of genomes, and more secure planning and design of experiments. The purpose of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for Arabidopsis nuclear genes and gene products, and to enter them into an added-value database. This re-annotation project is being performed exhaustively on every member of each gene family. Performing a family-wide annotation makes the task easier and more efficient than a gene-by-gene approach since many features obtained for one gene can be extrapolated to some or all the other genes of a family. A complete annotation procedure based on the most efficient prediction tools available is being used by 16 partner laboratories, each contributing annotated families from its field of expertise. A database, named GeneFarm, and an associated user-friendly interface to query the annotations have been developed. More than 3000 genes distributed over 300 families have been annotated and are available at http://genoplante-info.infobiogen.fr/Genefarm/. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot

25. Indexing for Life: improved genetic data resources for conservation.

Author

Rivière, Stéphane

Subjects
*CONSERVATION of natural resources, *PHYLOGENY, *ENVIRONMENTAL protection, *SUSTAINABLE development, *TAXONOMY
Abstract

The article presents information on the improvement in genetic data resources for conservation. Topics discussed include determining conservation priorities for taxon, combination of evolutionary distinctiveness (ED) with extinction risk, and framing phylogenetically informed conservation strategies.

Published
2014
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