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Hommage à Michel Duterde

Annie-France Le Pape, Jean-François Thiebaux, Yvon Lambert, Yves Gigou
2019 VST - Vie sociale et traitements  
Hommage à michel duterde texte rédigé à quatre mains par annie-France le pape, Jean-FranÇois tHiÉbaux, yvon lambert et yves gigou.  ...  À la suite de cet engagement, une commission fut chargée de rédiger un rapport dont les coordinateurs furent Marie et Jean Demay.  ... 
doi:10.3917/vst.143.0129 fatcat:7l2ehyah55asjbdmomjcfzmfre

Predicting plant biomass accumulation from image-derived parameters [article]

Dijun Chen, Rongli Shi, Jean-Michel Pape, Christian Klukas
2016 bioRxiv   pre-print
Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a suitable model to predict plant biomass in the context of high-throughput phenotyping. In the present study, we constructed several models to examine
more » ... quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to three consecutive barley experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model, in particular the cross-experiment performance, is promising to relieve the phenotyping bottleneck in biomass measurement in breeding applications. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of plant biomass outcome. What's more, the methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass.
doi:10.1101/046656 fatcat:zxumqidn7jcw7cxlfz7mx2ak6e

Les plasmas non thermiques

Marc Vandamme, Éric Robert, Stéphanie Lerondel, Jean-Michel Pouvesle, Alain Le Pape
2012 M S.Médecine Sciences  
Le Pape déclarent n'avoir aucun conflit d'intérêts concernant les données publiées dans cet article. 4. Dobrynin D, Wu A, Kalghatgi S, et al.  ... 
doi:10.1051/medsci/2012282013 pmid:22377303 fatcat:23famqenbrarrobcoxginlsvva

3-D Histogram-Based Segmentation and Leaf Detection for Rosette Plants [chapter]

Jean-Michel Pape, Christian Klukas
2015 Lecture Notes in Computer Science  
Recognition and segmentation of plant organs like leaves is one of the challenges in digital plant phenotyping. Here we present a 3-D histogram-based segmentation and recognition approach for top view images of rosette plants such as Arabidopsis thaliana and tobacco. Furthermore a Euclidean-distance-map-based method for the detection of leaves and the corresponding plant leaf segmentation was developed. An approach for the detection of optimal leaf split points for the separation of overlapping
more » ... leaf segments was created. We tested and tuned our algorithms for the Leaf Segmentation Challenge (LSC). The results demonstrate that our method is robust and handles demanding imaging situations and different species with high accuracy.
doi:10.1007/978-3-319-16220-1_5 fatcat:avwdemrnlbbntodmfmqba33wzq

Predicting plant biomass accumulation from image-derived parameters

Dijun Chen, Rongli Shi, Jean-Michel Pape, Kerstin Neumann, Daniel Arend, Andreas Graner, Ming Chen, Christian Klukas
2018 GigaScience  
Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a suitable model to predict plant biomass in the context of high-throughput phenotyping. In the present study, we constructed several models to examine
more » ... quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to three consecutive barley experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model, in particular the cross-experiment performance, is promising to relieve the phenotyping bottleneck in biomass measurement in breeding applications. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of plant biomass outcome. What's more, the methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass. We would like to thank Ingo Mücke for his management of the LemnaTec system operations. We thank Dr. Kerstin Neumann for providing the valuable plant data. We thank Michael Ulrich for performing software tests and helping in data analysis.
doi:10.1093/gigascience/giy001 pmid:29346559 pmcid:PMC5827348 fatcat:xh6v7serfrgitpvzqbwysl4kbi

Analysis of high-throughput plant image data with the information system IAP

Christian Klukas, Jean-Michel Pape, Alexander Entzian
2012 Journal of Integrative Bioinformatics  
SummaryThis work presents a sophisticated information system, the Integrated Analysis Platform (IAP), an approach supporting large-scale image analysis for different species and imaging systems. In its current form, IAP supports the investigation of Maize, Barley and Arabidopsis plants based on images obtained in different spectra.Several components of the IAP system, which are described in this work, cover the complete end-to-end pipeline, starting with the image transfer from the imaging
more » ... structure, (grid distributed) image analysis, data management for raw data and analysis results, to the automated generation of experiment reports.
doi:10.1515/jib-2012-191 fatcat:v3l6l5wlpfhydhvuqk4xw3ggsy

Analysis of high-throughput plant image data with the information system IAP

Christian Klukas, Jean-Michel Pape, Alexander Entzian
2012 Journal of Integrative Bioinformatics  
This work presents a sophisticated information system, the Integrated Analysis Platform (IAP), an approach supporting large-scale image analysis for different species and imaging systems. In its current form, IAP supports the investigation of Maize, Barley and Arabidopsis plants based on images obtained in different spectra. Several components of the IAP system, which are described in this work, cover the complete end-to-end pipeline, starting with the image transfer from the imaging
more » ... ure, (grid distributed) image analysis, data management for raw data and analysis results, to the automated generation of experiment reports.
doi:10.2390/biecoll-jib-2012-191 pmid:22745177 fatcat:cmwfn6vnjzbqrpc4hutx2q2s3i

Outcomes after antiretroviral therapy during the expansion of HIV services in Haiti

Margaret L. McNairy, Patrice Joseph, Michelle Unterbrink, Stanislas Galbaud, Jean-Edouard Mathon, Vanessa Rivera, Deanna Jannat-Khah, Lindsey Reif, Serena P. Koenig, Jean Wysler Domercant, Warren Johnson, Daniel W. Fitzgerald (+2 others)
2017 PLoS ONE  
We report patient outcomes after antiretroviral therapy (ART) initiation in a network of HIV facilities in Haiti, including temporal trends and differences across clinics, during the expansion of HIV services in the country. Methods We assessed outcomes at 12 months after ART initiation (baseline) using routinely collected data on adults (!15 years) in 11 HIV facilities from July 2007-December 2013. Outcomes include death (ascertained from medical records), lost to follow-up (LTF) defined as no
more » ... visit > 365 days from ART initiation, and retention defined as being alive and attending care ! 365 days from ART initiation. Outcomes were compared across calendar year of ART initiation and across facilities. Risk factors for death and LTF were assessed using Cox proportional hazards and competing risk regression models. Results Cumulatively, 9,718 adults initiated ART with median age 37 years (IQR 30-46). Median CD4 count was 254 cells/uL . Twelve months after ART initiation, 4.4% (95% CI 4.0-4.8) of patients died, 21.7% (95% CI 20.9-22.6) were LTF, and 73.9% (95% CI 73.0-74.8) were retained in care. Twelve-month mortality decreased from 13.8% among adults who started ART in 2007 to 4.4% in 2013 (p<0.001). Twelve-month LTF after ART start was 29.2% in 2007, 18.7% in 2008, and increased to 30.1% in 2013 (p<0.001). Overall, twelve-month retention after ART start did not change over time but varied widely across facilities from 61.1% to 86.5%.
doi:10.1371/journal.pone.0175521 pmid:28437477 pmcid:PMC5402937 fatcat:pwqqbs2fibeutmcc65q2itndqu

Cryptosporidiosis Stimulates an Inflammatory Intestinal Response in Malnourished Haitian Children

Beth D. Kirkpatrick, Michelle M. Daniels, Simone Sonia Jean, Jean W. Pape, Christopher Karp, Benjamin Littenberg, Daniel W. Fitzgerald, Howard M. Lederman, James P. Nataro, Cynthia L. Sears
2002 Journal of Infectious Diseases  
The mechanisms by which Cryptosporidium parvum cause persistent diarrhea and increased morbidity and mortality are poorly understood. Three groups of Haitian children !18 months old were studied: case patients, children with diarrhea not due to Cryptosporidium, and healthy control subjects. Compared with both control groups, children with acute cryptosporidiosis were more malnourished (including measures of stunting [ ] and general malnutrition P p . [ ]), vitamin A deficient ( ), and less
more » ... breast-fed ( ). Markers of a P p .01 P p .04 P p .04 proinflammatory immune response, interleukin (IL)-8 and tumor necrosis factor-a receptor I, were significantly elevated in the case population ( and , respectively), as was P p .02 P ! .01 fecal lactoferrin ( ) and the T helper (Th)-2 cytokine IL-13 ( ). The counter-P p .01 P p .03 regulatory cytokine IL-10 was exclusively elevated in the case population ( ). A Th1 P ! .01 cytokine response to infection was not detected. This triple cohort study demonstrates that malnourished children with acute cryptosporidiosis mount inflammatory, Th-2, and counterregulatory intestinal immune responses. The intestinal protozoan Cryptosporidium parvum is a leading cause of acute and persistent diarrhea in persons living in both developing and developed nations [1, 2] . C. parvum is remarkably infectious-an estimated dose of only 30 oocysts causes diarrhea in some hosts [3] . Infection is common in children in underdeveloped countries, where seroprevalence rates can be 190% by age 5 years [4, 5] . Human infection with C. parvum varies broadly in clinical presentation, ranging from asymptomatic colonization to persistent, profuse diarrhea in both im-
doi:10.1086/341296 pmid:12089667 fatcat:n5ijaaid7vdtnfo2s6t4ukdfii

Aerosolized Chemotherapy

Frederic Gagnadoux, Jose Hureaux, Laurent Vecellio, Thierry Urban, Alain Le Pape, Isabelle Valo, Jerome Montharu, Valerie Leblond, Michele Boisdron-Celle, Stephanie Lerondel, Caroline Majoral, Patrice Diot (+2 others)
2008 Journal of Aerosol Medicine  
Gagnadoux, Frédéric [1], Hureaux, José [2], Vecellio, Laurent [3], Urban, Thierry [4], Le Pape, Alain [5], Valo, Isabelle [6], Montharu, Jerome [7], Leblond, Valerie [8], Boisdron-Celle, Michèle [9], Lerondel  ...  , Stephanie [10], Majoral, Caroline [11], Diot, Patrice [12], Racineux, Jean-Louis [13], Lemarie, Etienne [14] Pays Etats-Unis Editeur Mary Ann Liebert Ville New Rochelle Type Article scientifique  ... 
doi:10.1089/jamp.2007.0656 pmid:18518832 fatcat:vzgihzoaujepfdulcpqy3nud4m

Accuracy of unguided and ultrasound guided Coracohumeral ligament infiltrations – a feasibility cadaveric case series

John L. Pape, Mathieu Boudier-Revéret, Jean-Michel Brismée, Kerry K. Gilbert, Detlev Grabs, Stéphane Sobczak
2020 BMC Musculoskeletal Disorders  
Coracohumeral ligament (CHL) thickening, contracture, and fibroplasia have been identified in glenohumeral idiopathic adhesive capsulitis (GHIAC). The CHL is the main structure responsible for the range of motion limitations. Favorable outcomes have been reported with CHL surgical release. Intra-articular glenohumeral joint corticosteroid infiltrations are utilized to disrupt the inflammatory process and reduce pain in GHIAC. The aim of this study was to investigate whether the CHL could be
more » ... rately targeted with a periligamentous infiltration. A convenience sample of 12 unembalmed cadaver shoulders (mean age: 74.5 years, range 66-87 years) without evidence of previous injury or surgery were utilized in this exploratory double factor feasibility cadaveric (unguided and ultrasound (US) guided) case series. Two clinicians trained in musculoskeletal infiltration techniques carried out the infiltrations on each shoulder with colored latex. One clinician infiltrated without guidance, the other with US-guidance. The injecting clinicians were blinded to the others infiltration procedure and the order was randomized. An anatomist blinded to the infiltration order performed a shoulder dissection and recorded the infiltrate location. Percentage calculation for accuracy of infiltration and a chi-square evaluation of the difference between unguided and US-guided infiltrations was applied. An accuracy of 75% was achieved for unguided infiltration and 80% for US-guided infiltration techniques. Chi-squared indicated there was no significant difference (p = 0.82) between the unguided and US-guided techniques. US-guided and unguided infiltrations achieved good accuracy targeting the CHL, suggesting infiltrations can specifically and accurately target the CHL. In vivo investigation using such infiltration techniques are warranted.
doi:10.1186/s12891-020-3153-4 pmid:32111219 pmcid:PMC7049223 fatcat:utt5jgpefvdhrgo344byaf4chq

Concurrent Aerodynamic Optimization of Rotor Blades Using a Nash Game Method

Enric Roca Léon, Arnaud Le Pape, Michel Costes, Jean-Antoine Désidéri, David Alfano
2016 Journal of the American Helicopter Society  
A multi-objective strategy adapted to the aerodynamic concurrent optimization of helicopter rotor blades is developed. The present strategy is based on Nash Games from game theory, where the objective functions are minimized by virtual players involved in a non-cooperative concurrent game. A method is presented to split the design vector into two sub-spaces, defined to be the strategies of the players in charge of the minimization of the primary and the secondary objective functions
more » ... . This split of territory allows the optimization of the secondary function while causing the least possible degradation of the first one. This methodology is applied to the model rotor ER-ATO, seeking to maximize the Figure of Merit in hover while minimizing the required rotor power in forward flight. An initial constrained optimization in hover is conducted using a previously developed adjoint-based technique using the 3D Navier-Stokes solver elsA along with the gradient-based CONMIN algorithm. The chord, twist and sweep distributions of the baseline blade are parametrized using Bézier and cubic splines for a total of 16 design variables. The obtained optimized rotor is then R Rotor radius [m] AHS Log No. xxxx 3 S = πR 2 Rotor disk surface [m 2 ] Z b = 100F z 1 2 ρ∞Sσ(RΩ) 2 Rotor thrust coefficient µ = V ∞ /(ΩR) Advance ratio Ω Rotor rotational speed [rad/s] σ = N b c πR Rotor solidity
doi:10.4050/jahs.61.022009 fatcat:ebwoqq7b2vf5lmp7eoaiz56cqy

Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping

Daniel Arend, Matthias Lange, Jean-Michel Pape, Kathleen Weigelt-Fischer, Fernando Arana-Ceballos, Ingo Mücke, Christian Klukas, Thomas Altmann, Uwe Scholz, Astrid Junker
2016 Scientific Data  
With the implementation of novel automated, high throughput methods and facilities in the last years, plant phenomics has developed into a highly interdisciplinary research domain integrating biology, engineering and bioinformatics. Here we present a dataset of a non-invasive high throughput plant phenotyping experiment, which uses image-and image analysis-based approaches to monitor the growth and development of 484 Arabidopsis thaliana plants (thale cress). The result is a comprehensive
more » ... t of images and extracted phenotypical features. Such datasets require detailed documentation, standardized description of experimental metadata as well as sustainable data storage and publication in order to ensure the reproducibility of experiments, data reuse and comparability among the scientific community. Therefore the here presented dataset has been annotated using the standardized ISA-Tab format and considering the recently published recommendations for the semantical description of plant phenotyping experiments. Design Type time series design • parallel group design Measurement Type(s) phenotype Technology Type(s) image acquisition and analysis Factor Type(s) environmental condition Sample Characteristic(s) Arabidopsis thaliana • shoot system
doi:10.1038/sdata.2016.55 pmid:27529152 pmcid:PMC4986541 fatcat:6w222or54zbdjjvi4gr6sxguju

Radiological dose reconstruction for birds reconciles outcomes of Fukushima with knowledge of dose-effect relationships

Jacqueline Garnier-Laplace, Karine Beaugelin-Seiller, Claire Della-Vedova, Jean-Michel Métivier, Christian Ritz, Timothy A. Mousseau, Anders Pape Møller
2015 Scientific Reports  
We reconstructed the radiological dose for birds observed at 300 census sites in the 50-km northwest area affected by the accident at the Fukushima Daiichi nuclear power plant over 2011-2014. Substituting the ambient dose rate measured at the census points (from 0.16 to 31 μGy h −1 ) with the dose rate reconstructed for adult birds of each species (from 0.3 to 97 μGy h −1 ), we confirmed that the overall bird abundance at Fukushima decreased with increasing total doses. This relationship was
more » ... ectly consistent with exposure levels found in the literature to induce physiological disturbances in birds. Among the 57 species constituting the observed bird community, we found that 90% were likely chronically exposed at a dose rate that could potentially affect their reproductive success. We quantified a loss of 22.6% of the total number of individuals per increment of one unit log 10tansformed total dose (in Gy), over the four-year post-accident period in the explored area. We estimated that a total dose of 0.55 Gy reduced by 50% the total number of birds in the study area over 2011-2014. The data also suggest a significant positive relationship between total dose and species diversity. Exclusion Zone -CEZ 4,9-12 . These analyses were performed taking into account a number of potentially confounding environmental variables such as descriptors of the census conditions (e.g., time, cloud cover, wind, temperature) and of landscape (i.e. cover type such as e.g., farmland, grass, coniferous trees) 4, 6, 7, [9] [10] [11] [12] . Analyses based on Generalized Linear Mixed Models (GLMM) with Poisson distributed data, least squares analyses and non-parametric Spearman rank order correlations showed similar conclusions 6 . Thus the conclusions appeared to be independent of statistical analyses. The most recent analyses of the entire dataset collected in the Fukushima area by Møller et al. 6 showed the abundance of birds decreased with increasing level of ambient radiation, with significant variation among species, and the relationship between abundance and radiation became increasingly negative over time. Among the 154 bird species present in the inventory at Chernobyl and Fukushima, species with small body size and hence relatively high food consumption rates were more negatively impacted by radiation at Fukushima and Chernobyl 7 . Secondary consumers showed stronger negative effects of radiation on abundance than herbivores, and more so at Fukushima than at Chernobyl 7 . There was no overall effect of migration behavior, but migratory species were more negatively impacted in Chernobyl, while residents were more negatively impacted in Fukushima 7 perhaps reflecting the effects of high acute exposures to resident species during the initial phase of the disaster. Species with carotenoid and pheomelanin plumage pigments associated with antioxidant status showed stronger negative effects, especially in Chernobyl compared to Fukushima, while species with eumelanic coloration, which is not related to antioxidant status, did not show such an effect. These differences between Chernobyl and Fukushima may reflect differences in duration of exposure, differences in radioactive isotopes still being present in the radioactive deposits at the census periods, and differences in potential accumulation of mutations since sampled individuals are offspring from a much smaller number of generations in Fukushima than in Chernobyl 7,13 . Recently, Garnier-Laplace et al. 14 proposed a re-assessment of inter-species radio sensitivity emphasizing that organisms in their natural environment from the CEZ appeared to be ca. eight times more sensitive to radiation than they were under laboratory conditions. This is not surprising given that organisms under field conditions may suffer from poor nutrition and/or unfavorable abiotic factors, and parasitism and predation with strong effects on abundance and species diversity, while lab populations are usually kept under optimal conditions, partly as a consequence of legislation related to research ethics. Additionally the duration of exposure is clearly a major feature that distinguishes laboratory and field experiments, since for the same exposure dose rate, the resulting absorbed doses are drastically different with ultimately much higher doses in the field than in the laboratory. Finally, any shift in sensitivity between field and laboratory may be due to the presence of other stressors such as stable contaminants and/or to selection of strains through phenotypic acclimation, DNA methylation, genetic adaptation across generations, or multigenerational phenotypic effects (e.g., maternal effects) 15-17 . On the basis of ecological data describing bird diversity and abundance in the 50-km contaminated area around Fukushima published by Møller et al. 6, 7 , the objectives of the present study were to reconstruct the total dose (and dose rates) of individual birds and to analyse whether this new approach might better explain the intensity and type of observed effects on bird abundance and species diversity. More precisely, we reassessed the entire dataset by substituting the ambient radiation level previously used by Møller et al. 6, 7 by the total doses reconstructed for birds. As noticed by Beresford et al. 18, 19 , the ambient radiation level is assumed to be a biased radiation dose indicator, especially when several species of free-ranging animals may be impacted. For a given contaminated environment, where ambient radiation level is constant, radiological dose rate absorbed by living organisms may vary by several orders of magnitude since animal biodiversity is characterized by a variety of species-specific morphological and ecological features (e.g., types of habitats, diet) that may greatly influence the range of absorbed dose. Any dose (rate) reconstruction needs to assess its two elementary components: the external dose (rate) from the radio-contaminated habitat and the internal dose (rate) from internalization of radionuclides. In this study, both components were assessed on the basis of (i) the stylized morphological and ecological features of the species and (ii) the radioactive concentration of the soil using GPS coordinates from each census point combined with the radioactive contamination maps of the Fukushima area, the latter being based on field monitoring in soils performed by Japanese university scientists, from June-July 2011 20 . We re-analysed the ecological dataset with reconstructed total dose for bird individuals (sum of internal dose and external dose) at census points to investigate its relationship with temporal and spatial records of bird abundance and species richness. We also examined the relationship between absorbed dose and the abundance and diversity of birds and we compared estimated critical radiotoxicity endpoints (e.g., dose giving 50% effects on the abundance) with various radiation effect benchmarks published by international organisations.
doi:10.1038/srep16594 pmid:26567770 pmcid:PMC4645120 fatcat:zskxvu52mfeu7dlbg2247hdvhi

Dose reconstruction supports the interpretation of decreased abundance of mammals in the Chernobyl Exclusion Zone

Karine Beaugelin-Seiller, Jacqueline Garnier-Laplace, Claire Della-Vedova, Jean-Michel Métivier, Hugo Lepage, Timothy A. Mousseau, Anders Pape Møller
2020 Scientific Reports  
We re-analyzed field data concerning potential effects of ionizing radiation on the abundance of mammals collected in the Chernobyl Exclusion Zone (CEZ) to interpret these findings from current knowledge of radiological dose-response relationships, here mammal response in terms of abundance. In line with recent work at Fukushima, and exploiting a census conducted in February 2009 in the CEZ, we reconstructed the radiological dose for 12 species of mammals observed at 161 sites. We used this new
more » ... information rather than the measured ambient dose rate (from 0.0146 to 225 µGy h-1) to statistically analyze the variation in abundance for all observed species as established from tracks in the snow in previous field studies. All available knowledge related to relevant confounding factors was considered in this re-analysis. This more realistic approach led us to establish a correlation between changes in mammal abundance with both the time elapsed since the last snowfall and the dose rate to which they were exposed. This relationship was also observed when distinguishing prey from predators. The dose rates resulting from our re-analysis are in agreement with exposure levels reported in the literature as likely to induce physiological disorders in mammals that could explain the decrease in their abundance in the CEZ. Our results contribute to informing the Weight of Evidence approach to demonstrate effects on wildlife resulting from its field exposure to ionizing radiation.
doi:10.1038/s41598-020-70699-3 pmid:32826946 fatcat:42m2y3ls5jbo5h54jqewncs4vq
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