Philippe Grosjean | University of Mons (original) (raw)
Papers by Philippe Grosjean
The total alkalinity variations, due to the important calcification together with the closed syst... more The total alkalinity variations, due to the important calcification together with the closed system design, are now discussed in the text at p13:l-390-396. The paired design allows, at least, for parallel and identical changes in both acidified and control conditions, which is a good point. We claim that such changes occur in many other closed systems with lots of calcifiers... but they are simply not enough documented in many cases. Yet, it is a weak point where much effort is still required to obtain more stabilization of this parameter over time.
Coral Reefs, 2014
High sedimentation rates have been linked to reduced coral health within multiple systems; howeve... more High sedimentation rates have been linked to reduced coral health within multiple systems; however, whether this is a direct result of compromised coral immunity has not been previously investigated. The potential effects of sedimentation on immunity of the hard coral Montipora patula were examined by comparing physiological responses of coral fragments inoculated with sterilized marine sediments and those under control conditions. Sediments were collected from terrestrial runoffaffected reefs in SW Madagascar and applied cyclically for a total of 24 h at a rate observed during precipitationinduced sedimentation events. Coral health was determined 24 h after the onset of the sedimentation stress through measuring metabolic proxies of O 2 budget and lipid ratios. Immune response of the melanin synthesis pathway was measured by quantifying phenoloxidase activity and melanin deposits. Sedimentation induced both immune and metabolic responses in M. patula. Both phenoloxidase activity and melanin deposition were significantly higher in the sediment treatment compared to controls, indicating an induced immune response. Sediment-treated corals also showed a tendency towards increased respiration (during the night) and decreased photosynthesis (during the day) and a significant depletion of energy reserves as compared to controls. These data highlight that short-term (24 h) sedimentation, free of live microorganisms, compromises the health of M. patula. The energetically costly immune response, potentially elicited by residual endotoxins and other inflammatory particles associated with the sterile sediments, likely contributes to the energy depletion. Overall, exposure to sedimentation adversely affects coral health and continued exposure may lead to resource depletion and an increased susceptibility to disease.
Invertebrate Reproduction & Development, 1998
... analysis by means of the maturity index CHRISTINE SPIRLET~>~*, PHILIPPE GROSJEAN~.... more ... analysis by means of the maturity index CHRISTINE SPIRLET~>~*, PHILIPPE GROSJEAN~.~ ... Food availability seems to be more important in controlling gonad size than the timing of gonadal development (De Ridder and Lawrence, 1982). 'corresponding author. Page 2. ...
R package …, 2007
... Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ct... more ... Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu ...
Biofouling, 2005
A turbulent channel flow apparatus was used to determine the adhesion strength of the three perim... more A turbulent channel flow apparatus was used to determine the adhesion strength of the three perimetamorphic stages of the asteroid Asterina gibbosa, i.e. the brachiolaria larvae, the metamorphic individuals and the juveniles. The mean critical wall shear stresses (wall shear stress required to dislodge 50% of the attached individuals) necessary to detach larvae attached by the brachiolar arms (1.2 Pa) and juveniles attached by the tube feet (7.1 Pa) were one order of magnitude lower than the stress required to dislodge metamorphic individuals attached by the adhesive disc (41 Pa). This variability in adhesion strength reflects differences in the functioning of the adhesive organs for these different life stages of sea stars. Brachiolar arms and tube feet function as temporary adhesion organs, allowing repetitive cycles of attachment to and detachment from the substratum, whereas the adhesive disc is used only once, at the onset of metamorphosis, and is responsible for the strong attachment of the metamorphic individual, which can be described as permanent adhesion. The results confirm that the turbulent water channel apparatus is a powerful tool to investigate the adhesion mechanisms of minute organisms.
Aquatic Living Resources, 1998
In the framework of echinoid cultivation, whose objective is to succeed in continuously producing... more In the framework of echinoid cultivation, whose objective is to succeed in continuously producing large amounts of edible sea urchins (Paracentrotus lividus) under controlled conditions (aquaculture), gonadal growth is to be optimized. Among the various parameters influencing the production of roe, the quantity of food distributed was tested for optimization. After a 1-month fast, echinoids were fed artificial food pellets (enriched in soybean and fish proteins) for different periods of time over 48 h, the food thus being available ad libitum for 8, 16, 24, 32, 40, and 48 h; the cycles were repeated for a month. The results show that the quantity of food intake and the gonad index peak after about 35 h of food availability. This suggests food should be distributed discontinuously for optimal gonad production and minimal waste.
Aquaculture, 2000
A starvation and then feeding method was developed to produce about 100% marketable sea urchins, ... more A starvation and then feeding method was developed to produce about 100% marketable sea urchins, Paracentrotus liÕidus, in 3 1r2 months. This method is needed because the reproduction cycle is desynchronized in the conditions imposed during the somatic growth stage in land-based closed systems. The major advantages of starving the animals are resetting the reproductive cycle Ž. to the spent stage gonads almost devoid of sexual cells and stressing the individuals so that they mobilize and restore the nutritive phagocytes, filling them with nutrients. Batches of sea urchins starved 2 months beforehand were fed ad libitum for 45 days with enriched food under eight Ž. Ž combinations of four temperatures 128C, 168C, 208C and 248C and two photoperiods 9 and 17 h. daylight. In our system, the best combination was 248C and 9 h daylight for growth as well as for Ž. gonad quality. The gonadal indices obtained in dry weight were over 9% at 168C and over 12% at 248C, which are better than what is found in the field for this population.
DI-fusion, le Dépôt institutionnel numérique de l'ULB, est l'outil de référencementde l... more DI-fusion, le Dépôt institutionnel numérique de l'ULB, est l'outil de référencementde la production scientifique de l'ULB.L'interface de recherche DI-fusion permet de consulter les publications des chercheurs de l'ULB et les thèses qui y ont été défendues.
ICES Journal of Marine Science, 2007
Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., M... more Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., Mardle, S., Pastoors, M. A., Poos, J. J., Scott, F., and Scott, R. D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. – ICES Journal of Marine Science, 64: 640–646. The FLR framework (Fisheries Library for R) is a development effort directed towards the evaluation of fisheries management strategies. The overall goal is to develop a common framework to facilitate collaboration within and across disciplines (e.g. biological, ecological, statistical, mathematical, economic, and social) and, in particular, to ensure that new modelling methods and software are more easily validated and evaluated, as well as becoming widely available once developed. Specifically, the framework details how to implement and link a variety of fishery, biological, and economic software packages so that alternative management strategies and procedures can be evaluated...
Marine Pollution Bulletin, 2012
Our current view about the relationship between metals and bacteria in marine sediments might be ... more Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT-diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.
Journal of Plankton Research, 2008
2014 Software Evolution Week - IEEE Conference on Software Maintenance, Reengineering, and Reverse Engineering (CSMR-WCRE), 2014
ABSTRACT When writing software, developers are confronted with a trade-off between depending on e... more ABSTRACT When writing software, developers are confronted with a trade-off between depending on existing components and reimplementing similar functionality in their own code. Errors may be inadvertently introduced because of dependencies to unreliable components, and it may take longer time to fix these errors. We study such issues in the context of the CRAN archive, a long-lived software ecosystem consisting of over 5000 R packages being actively maintained by over 2500 maintainers, with different flavors of each package depending on the development status and target operating system. Based on an analysis of package dependencies and package status, we present preliminary results on the sources of errors in these packages per flavor, and the time that is needed to fix these errors.
2015 IEEE 9th International Workshop on Software Clones (IWSC), 2015
Code clone analysis is a very active subject of study, and research on inter-project code clones ... more Code clone analysis is a very active subject of study, and research on inter-project code clones is starting to emerge. In the context of software package repositories specifically, developers are confronted with the choice between depending on code implemented in other packages, or cloning this code in their own package. This article presents an empirical study of identical function clones in the CRAN package archive network, in order to understand the extent of this practice in the R community. Depending on too many packages may hamper maintainability as unexpected conflicts may arise during package updates. Duplicating functions from other packages may reduce maintainability since bug fixes or code changes are not propagated automatically to its clones. We study how the characteristics of cloned functions in CRAN snapshots evolve over time, and classify these clones depending on what has prevented package developers to rely on dependencies instead.
SciViews aims to provide a unique, polymorph object-oriented interface (called "Plug") ... more SciViews aims to provide a unique, polymorph object-oriented interface (called "Plug") to di#erent data analysis software like R, Octave, Scilab, Matlab, Splus, Ox, Mathematica,. . . It is thus possible to develop (Graphical) User Interfaces independently to the calculation kernel and adapt them easily to other systems. Moreover, the same GUI can possibly access several kernels simultaneously.
L'objectif de cette etude est de determiner comment il est possible de coupler des donnees is... more L'objectif de cette etude est de determiner comment il est possible de coupler des donnees issues du FlowCAM analysees a l'aide de Zoo/PhytoImage avec des mesures realisees en cytometrie de flux (a enregistrement des profils optiques - Scanning Flow Cytometry), sur les memes echantillons des systemes d’observation et surveillance en manche et sud Mer du Nord. Dans cette approche preliminaire, nous avons collecte une serie d'echantillons au large des stations du SRN-REPHY d’IFREMER (Dunkerque, Boulogne sur Mer et Baie de Somme) ainsi que sur la radiale de la Baie St Jean (Wimereux-Slack) du LOG. Ces echantillons ont ete numerises avec un FlowCAM et un cytometre de flux de type CytoSense. Les premiers resultats de cette comparaison sont detailles dans le livrable. L'analyse complete grâce au FlowCAM et a Zoo/PhytoImage est detaillee dans le livrable. Afin d'avoir un meilleur point de comparaison entre l'analyse d'image et les profils en cytometrie de flux, ...
The total alkalinity variations, due to the important calcification together with the closed syst... more The total alkalinity variations, due to the important calcification together with the closed system design, are now discussed in the text at p13:l-390-396. The paired design allows, at least, for parallel and identical changes in both acidified and control conditions, which is a good point. We claim that such changes occur in many other closed systems with lots of calcifiers... but they are simply not enough documented in many cases. Yet, it is a weak point where much effort is still required to obtain more stabilization of this parameter over time.
Coral Reefs, 2014
High sedimentation rates have been linked to reduced coral health within multiple systems; howeve... more High sedimentation rates have been linked to reduced coral health within multiple systems; however, whether this is a direct result of compromised coral immunity has not been previously investigated. The potential effects of sedimentation on immunity of the hard coral Montipora patula were examined by comparing physiological responses of coral fragments inoculated with sterilized marine sediments and those under control conditions. Sediments were collected from terrestrial runoffaffected reefs in SW Madagascar and applied cyclically for a total of 24 h at a rate observed during precipitationinduced sedimentation events. Coral health was determined 24 h after the onset of the sedimentation stress through measuring metabolic proxies of O 2 budget and lipid ratios. Immune response of the melanin synthesis pathway was measured by quantifying phenoloxidase activity and melanin deposits. Sedimentation induced both immune and metabolic responses in M. patula. Both phenoloxidase activity and melanin deposition were significantly higher in the sediment treatment compared to controls, indicating an induced immune response. Sediment-treated corals also showed a tendency towards increased respiration (during the night) and decreased photosynthesis (during the day) and a significant depletion of energy reserves as compared to controls. These data highlight that short-term (24 h) sedimentation, free of live microorganisms, compromises the health of M. patula. The energetically costly immune response, potentially elicited by residual endotoxins and other inflammatory particles associated with the sterile sediments, likely contributes to the energy depletion. Overall, exposure to sedimentation adversely affects coral health and continued exposure may lead to resource depletion and an increased susceptibility to disease.
Invertebrate Reproduction & Development, 1998
... analysis by means of the maturity index CHRISTINE SPIRLET~>~*, PHILIPPE GROSJEAN~.... more ... analysis by means of the maturity index CHRISTINE SPIRLET~>~*, PHILIPPE GROSJEAN~.~ ... Food availability seems to be more important in controlling gonad size than the timing of gonadal development (De Ridder and Lawrence, 1982). 'corresponding author. Page 2. ...
R package …, 2007
... Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ct... more ... Author: John Fox [aut, cre], Liviu Andronic [ctb], Michael Ash [ctb], Milan Bouchet-Valat [ctb], Theophilius Boye [ctb], Stefano Calza [ctb], Andy Chang [ctb], Philippe Grosjean [ctb], Richard Heiberger [ctb], Kosar Karimi Pour [ctb], G. Jay Kerns [ctb], Renaud Lancelot [ctb], Matthieu ...
Biofouling, 2005
A turbulent channel flow apparatus was used to determine the adhesion strength of the three perim... more A turbulent channel flow apparatus was used to determine the adhesion strength of the three perimetamorphic stages of the asteroid Asterina gibbosa, i.e. the brachiolaria larvae, the metamorphic individuals and the juveniles. The mean critical wall shear stresses (wall shear stress required to dislodge 50% of the attached individuals) necessary to detach larvae attached by the brachiolar arms (1.2 Pa) and juveniles attached by the tube feet (7.1 Pa) were one order of magnitude lower than the stress required to dislodge metamorphic individuals attached by the adhesive disc (41 Pa). This variability in adhesion strength reflects differences in the functioning of the adhesive organs for these different life stages of sea stars. Brachiolar arms and tube feet function as temporary adhesion organs, allowing repetitive cycles of attachment to and detachment from the substratum, whereas the adhesive disc is used only once, at the onset of metamorphosis, and is responsible for the strong attachment of the metamorphic individual, which can be described as permanent adhesion. The results confirm that the turbulent water channel apparatus is a powerful tool to investigate the adhesion mechanisms of minute organisms.
Aquatic Living Resources, 1998
In the framework of echinoid cultivation, whose objective is to succeed in continuously producing... more In the framework of echinoid cultivation, whose objective is to succeed in continuously producing large amounts of edible sea urchins (Paracentrotus lividus) under controlled conditions (aquaculture), gonadal growth is to be optimized. Among the various parameters influencing the production of roe, the quantity of food distributed was tested for optimization. After a 1-month fast, echinoids were fed artificial food pellets (enriched in soybean and fish proteins) for different periods of time over 48 h, the food thus being available ad libitum for 8, 16, 24, 32, 40, and 48 h; the cycles were repeated for a month. The results show that the quantity of food intake and the gonad index peak after about 35 h of food availability. This suggests food should be distributed discontinuously for optimal gonad production and minimal waste.
Aquaculture, 2000
A starvation and then feeding method was developed to produce about 100% marketable sea urchins, ... more A starvation and then feeding method was developed to produce about 100% marketable sea urchins, Paracentrotus liÕidus, in 3 1r2 months. This method is needed because the reproduction cycle is desynchronized in the conditions imposed during the somatic growth stage in land-based closed systems. The major advantages of starving the animals are resetting the reproductive cycle Ž. to the spent stage gonads almost devoid of sexual cells and stressing the individuals so that they mobilize and restore the nutritive phagocytes, filling them with nutrients. Batches of sea urchins starved 2 months beforehand were fed ad libitum for 45 days with enriched food under eight Ž. Ž combinations of four temperatures 128C, 168C, 208C and 248C and two photoperiods 9 and 17 h. daylight. In our system, the best combination was 248C and 9 h daylight for growth as well as for Ž. gonad quality. The gonadal indices obtained in dry weight were over 9% at 168C and over 12% at 248C, which are better than what is found in the field for this population.
DI-fusion, le Dépôt institutionnel numérique de l'ULB, est l'outil de référencementde l... more DI-fusion, le Dépôt institutionnel numérique de l'ULB, est l'outil de référencementde la production scientifique de l'ULB.L'interface de recherche DI-fusion permet de consulter les publications des chercheurs de l'ULB et les thèses qui y ont été défendues.
ICES Journal of Marine Science, 2007
Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., M... more Kell, L. T., Mosqueira, I., Grosjean, P., Fromentin, J-M., Garcia, D., Hillary, R., Jardim, E., Mardle, S., Pastoors, M. A., Poos, J. J., Scott, F., and Scott, R. D. 2007. FLR: an open-source framework for the evaluation and development of management strategies. – ICES Journal of Marine Science, 64: 640–646. The FLR framework (Fisheries Library for R) is a development effort directed towards the evaluation of fisheries management strategies. The overall goal is to develop a common framework to facilitate collaboration within and across disciplines (e.g. biological, ecological, statistical, mathematical, economic, and social) and, in particular, to ensure that new modelling methods and software are more easily validated and evaluated, as well as becoming widely available once developed. Specifically, the framework details how to implement and link a variety of fishery, biological, and economic software packages so that alternative management strategies and procedures can be evaluated...
Marine Pollution Bulletin, 2012
Our current view about the relationship between metals and bacteria in marine sediments might be ... more Our current view about the relationship between metals and bacteria in marine sediments might be biased because most studies only use ex situ approaches to quantify metals. The aim of the present research was to compare ex situ and in situ methods of metal measurement (DET and DGT-diffusive equilibration or diffusive gradients in thin-films) and relate the results with two commonly used microbiological variables (bacterial biomass and bacterial diversity as revealed by DGGE). No previous studies have used such in situ approaches in microbial ecology. For biomass and most of the investigated trace metals (Ag, Cd, Sn, Cr, Ni, Cu, Pb, and Al) no significant correlations were found. The exceptions were Fe, Mn, Co, and As which behave like micronutrients. For bacterial diversity, no relevant relationships were found. We conclude that in situ methods are more adapted tools for microbial ecologists but that ex situ approaches are still necessary.
Journal of Plankton Research, 2008
2014 Software Evolution Week - IEEE Conference on Software Maintenance, Reengineering, and Reverse Engineering (CSMR-WCRE), 2014
ABSTRACT When writing software, developers are confronted with a trade-off between depending on e... more ABSTRACT When writing software, developers are confronted with a trade-off between depending on existing components and reimplementing similar functionality in their own code. Errors may be inadvertently introduced because of dependencies to unreliable components, and it may take longer time to fix these errors. We study such issues in the context of the CRAN archive, a long-lived software ecosystem consisting of over 5000 R packages being actively maintained by over 2500 maintainers, with different flavors of each package depending on the development status and target operating system. Based on an analysis of package dependencies and package status, we present preliminary results on the sources of errors in these packages per flavor, and the time that is needed to fix these errors.
2015 IEEE 9th International Workshop on Software Clones (IWSC), 2015
Code clone analysis is a very active subject of study, and research on inter-project code clones ... more Code clone analysis is a very active subject of study, and research on inter-project code clones is starting to emerge. In the context of software package repositories specifically, developers are confronted with the choice between depending on code implemented in other packages, or cloning this code in their own package. This article presents an empirical study of identical function clones in the CRAN package archive network, in order to understand the extent of this practice in the R community. Depending on too many packages may hamper maintainability as unexpected conflicts may arise during package updates. Duplicating functions from other packages may reduce maintainability since bug fixes or code changes are not propagated automatically to its clones. We study how the characteristics of cloned functions in CRAN snapshots evolve over time, and classify these clones depending on what has prevented package developers to rely on dependencies instead.
SciViews aims to provide a unique, polymorph object-oriented interface (called "Plug") ... more SciViews aims to provide a unique, polymorph object-oriented interface (called "Plug") to di#erent data analysis software like R, Octave, Scilab, Matlab, Splus, Ox, Mathematica,. . . It is thus possible to develop (Graphical) User Interfaces independently to the calculation kernel and adapt them easily to other systems. Moreover, the same GUI can possibly access several kernels simultaneously.
L'objectif de cette etude est de determiner comment il est possible de coupler des donnees is... more L'objectif de cette etude est de determiner comment il est possible de coupler des donnees issues du FlowCAM analysees a l'aide de Zoo/PhytoImage avec des mesures realisees en cytometrie de flux (a enregistrement des profils optiques - Scanning Flow Cytometry), sur les memes echantillons des systemes d’observation et surveillance en manche et sud Mer du Nord. Dans cette approche preliminaire, nous avons collecte une serie d'echantillons au large des stations du SRN-REPHY d’IFREMER (Dunkerque, Boulogne sur Mer et Baie de Somme) ainsi que sur la radiale de la Baie St Jean (Wimereux-Slack) du LOG. Ces echantillons ont ete numerises avec un FlowCAM et un cytometre de flux de type CytoSense. Les premiers resultats de cette comparaison sont detailles dans le livrable. L'analyse complete grâce au FlowCAM et a Zoo/PhytoImage est detaillee dans le livrable. Afin d'avoir un meilleur point de comparaison entre l'analyse d'image et les profils en cytometrie de flux, ...