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Search Results: 1 - 10 of 19158 matches for " Fran?ois-Joseph Chatelon "
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Generalized Blaze Flash, a “Flashover” Behavior for Forest Fires—Analysis from the Firefighter’s Point of View  [PDF]
Franois-Joseph Chatelon, Sophie Sauvagnargues, Gilles Dusserre, Jacques-Henri Balbi
Open Journal of Forestry (OJF) , 2014, DOI: 10.4236/ojf.2014.45059
Abstract: The phenomenon called “flashover” or “eruptive fire” in forest fires is characterized by a sudden change in fire behavior: everything seems to burst into flames instantly and firefighters are overwhelmed by a sort of eruption, spreading at a speed at far several meters per second. Unfortunately it has cost several lives in the past. The reasons for such an accident always create controversy in the research field. Different theories are highlighted and especially two major axes are currently subject to discussion because they are very popular among people involved in fire-fighting. The one with regard to VOCs emissions is the best-known among firemen. Under great heat, during summer or with a fire approaching, plants emit VOCs and the more the temperature grows, the more the amount of VOCs emitted grows. Under specific conditions (essentially topographical, meteorological and atmospheric), the cloud of gas can accumulate in an appropriate zone. The concentration of VOCs may therefore reach the Lower Explosive Limit, triggering the burst of the cloud when in contact with the fire. The second theory depends on physical considerations. An example is based on a convective flow created by the fire itself. When a fire spreads on a slope, it creates an aspiration phenomenon in a way to supply the fire with oxygen. The more this phenomenon is important, the more the flames tilt and increase the rate of speed, needing even more oxygen and thus induced flow. This vicious circle can stabilize or have an erratic behavior to trigger off a fire eruption. This article presents these two theories, and especially the new advances on this research subject.
DIMZAL: A Software Tool to Compute Acceptable Safety Distance  [PDF]
Paul-Antoine Bisgambiglia, Jean-Louis Rossi, Romain Franceschini, Franois-Joseph Chatelon, Paul Antoine Bisgambiglia, Lucile Rossi, Thierry Marcelli
Open Journal of Forestry (OJF) , 2017, DOI: 10.4236/ojf.2017.71002
Abstract: The scope of this work is to present a multidisciplinary study in order to propose a tool called DIMZAL. DIMZAL forecasts fuelbreak safety zone sizes. To evaluate a safety zone and to prevent injury, the Acceptable Safety Distance (ASD) between the fire and firefighters is required. This distance is usually set thanks to a general rule-of-thumb: it should be at least 4 times the maximum flame length. A common assumption considers an empirical relationship between fireline intensity and flame length. In the current work which follows on from an oral presentation held at the VII International Conference on Forest Fire Research in Coimbra in 2014, an alternative way is proposed: a closed physical model is applied in order to quantize the ASD. This model is integrated in a software tool, which uses a simulation framework based on Discrete EVent system Specification formalism (DEVS), a 3D physical real-time model of surface fires developed at the University of Corsica and a mobile application based on a Google SDK to display the results
Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make
Claudine Levasseur,Franois-Joseph Lapointe
Evolutionary Bioinformatics , 2006,
Abstract: Matrix representation with parsimony (MRP) can be used to combine trees in the supertree or the consensus settings. However, despite its popularity, it is still unclear whether MRP is really a consensus method or whether it behaves more like the total evidence approach. Previous simulations have shown that it approximates total evidence trees, whereas other studies have depicted similarities with average consensus trees. In this paper, we assess the hypothesis that MRP is equally related to both approaches. We conducted a simulation study to evaluate the accuracy of total evidence with that or various consensus methods, including MRP. Our results show that the total evidence trees are not significantly more accurate than average consensus trees that accounts for branch lengths, but that both perform better than MRP trees in the consensus setting. The accuracy rate of all methods was similarly affected by the number of taxa, the number of partitions, and the heterogeneity of the data.
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis
Véronique Campbell, Pierre Legendre, Franois-Joseph Lapointe
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-64
Abstract: Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices.Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.In phylogenetic studies, data matrices are assembled and analysed to infer evolutionary relationships among species or higher taxa. Depending on the study, character-state data or distance matrices may be used, and several different types of data may be available to estimate the phylogeny of a particular group [1]. An increasing number of phylogenomic studies are published for data sets including more than 100 genes [2-10]. Whereas character-state data (e.g., nucleotide sequences) are commonly used for parsimony, maximum likelihood or Bayesian analyses, distance methods can be selected as an alternative option to decrease computing time when analysing large data sets, or else, can be used in comparative studies where the primary data are not available.Different approaches have been proposed to analyse the growing amount of information that may originate from different sources. The total evidence approach [11], also called character congruence approach [sensu [12]] or combined analysis [sensu [13]], combines different data sets in a single supermatrix [14-17]. The taxonomic congruence approach [sensu [12]], or consensus approach [13], analyses each matrix separately, and combines the resulting trees a posteriori using a consensus [18-22] or a supertree method [23-26]. The pros and cons of these competing approaches have been debated at length in the literature [7,17,21,22,27-32]. An intermediate approach, referred to as the conditional data combination, consists in testing a priori the level of congruence of
An Application of Supertree Methods to Mammalian Mitogenomic Sequences
Véronique Campbell,Franois-Joseph Lapointe
Evolutionary Bioinformatics , 2010,
Abstract: Two different approaches can be used in phylogenomics: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.
A new effective method for estimating missing values in the sequence data prior to phylogenetic analysis
Abdoulaye Baniré Diallo,Franois-Joseph Lapointe,Vladimir Makarenkov
Evolutionary Bioinformatics , 2006,
Abstract: In this article we address the problem of phylogenetic inference from nucleic acid data containing missing bases. We introduce a new effective approach, called “Probabilistic estimation of missing values” (PEMV), allowing one to estimate unknown nucleotides prior to computing the evolutionary distances between them. We show that the new method improves the accuracy of phylogenetic inference compared to the existing methods “Ignoring Missing Sites” (IMS), “Proportional Distribution of Missing and Ambiguous Bases” (PDMAB) included in the PAUP software [26]. The proposed strategy for estimating missing nucleotides is based on probabilistic formulae developed in the framework of the Jukes-Cantor [10] and Kimura 2-parameter [11] models. The relative performances of the new method were assessed through simulations carried out with the SeqGen program [20], for data generation, and the BioNJ method [7], for inferring phylogenies. We also compared the new method to the DNAML program [5] and “Matrix Representation using Parsimony” (MRP) [13], [19] considering an example of 66 eutherian mammals originally analyzed in [17].
Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, Franois-Joseph Lapointe, Eric Bapteste
Biology Direct , 2011, DOI: 10.1186/1745-6150-6-39
Abstract: We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan BoucherFor a long time, the reconstruction of the tree of life (TOL) was an important goal of evolutionary science [1]. This inclusive hierarchical classification, through its genealogical
Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees
Vladimir Makarenkov, Alix Boc, Jingxin Xie, Pedro Peres-Neto, Franois-Joseph Lapointe, Pierre Legendre
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-250
Abstract: In this article, we discuss the idea of applying weighted bootstrapping to phylogenetic reconstruction by weighting each phylogeny inferred from resampled sequences. Tree weights can be based either on the least-squares (LS) tree estimate or on the average secondary bootstrap score (SBS) associated with each resampled tree. Secondary bootstrapping consists of the estimation of bootstrap scores of the trees inferred from resampled data. The LS and SBS-based bootstrapping procedures were designed to take into account the quality of each "pseudo-replicated" phylogeny in the final tree estimation. A simulation study was carried out to evaluate the performances of the five weighting strategies which are as follows: LS and SBS-based bootstrapping, LS and SBS-based bootstrapping with data normalization and the traditional unweighted bootstrapping.The simulations conducted with two real data sets and the five weighting strategies suggest that the SBS-based bootstrapping with the data normalization usually exhibits larger bootstrap scores and a higher robustness compared to the four other competing strategies, including the traditional bootstrapping. The high robustness of the normalized SBS could be particularly useful in situations where observed sequences have been affected by noise or have undergone massive insertion or deletion events. The results provided by the four other strategies were very similar regardless the noise level, thus also demonstrating the stability of the traditional bootstrapping method.In statistics, bootstrapping is a general purpose parameter estimation approach falling within a broader class of resampling methods [1]. Bootstrapping allows one to assess whether the data distribution has been influenced by stochastic effects. Non-parametric bootstrapping proceeds by generating pseudo-replicates of the observed data. Each of the pseudo-replicated data sets is obtained by random sampling with replacement from the original data set. On the other hand,
Prokaryotic evolution and the tree of life are two different things
Eric Bapteste, Maureen A O'Malley, Robert G Beiko, Marc Ereshefsky, J Peter Gogarten, Laura Franklin-Hall, Franois-Joseph Lapointe, John Dupré, Tal Dagan, Yan Boucher, William Martin
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-34
Abstract: It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.Even before Darwin, biologists used the metaphor of a tree to classify living things [1]. The most prominent historical example, however, is indeed Darwin's "great tree", which extrapolated a family genealogy to the level of species and beyond to describe the historical relationships between living entities. He wrote:The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. .... The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the fo
Reliability of Thyroid Imaging Reporting and Data System (TIRADS) Classification in Differentiating Benign from Malignant Thyroid Nodules  [PDF]
Boniface Moifo, Emmanuel Oben Takoeta, Joshua Tambe, Franois Blanc, Joseph Gonsu Fotsin
Open Journal of Radiology (OJRad) , 2013, DOI: 10.4236/ojrad.2013.33016
Abstract:

Background: Ultrasonography (US) is the best diagnostic tool in the initial assessment of thyroid nodule. Giving its appropriateness and accessibility, ultrasound-based thyroid imaging reporting and data systems (TIRADS) classifications have been developed with main goal to standardize reporting and facilitate communication between practitioners, and to indicate when fine-needle aspiration biopsy (FNAB) should be performed. Objective: To determine the reliability of Russ’ modified TIRADS classification in predicting thyroid malignancy. Materials and Methods: It was a cross sectional study carried out at Centre Hospitalier de Lagny, Marne La Vallée (France). Consecutive records of patients with focal thyroid nodules on ultrasound (US) for which US-guided FNAB was performed and pathology results were available, from January 2007 to August 2012, were selected for review. The risk of malignancy of each TIRADS category was determined and correlation with pathology assessed. Statistical performances of some US features were also assessed. The threshold for statistical significance was set at 0.05. Results: A total of 430 records of patients were eligible. Twenty-three out of 430 (5.3%) nodules were malignant. The risk of malignancy of the TIRADS categories were as follows: TIRADS2 0%, TIRADS3 2.2%, TIRADS4A 5.9%, TIRADS4B 57.9%, TIRADS5 100% (Gamma statistic = 0.85; Spearman correlation = 0.30, Pearson’s R = 0.37, p < 0.001). Some US features were associated with a higher risk of malignancy: irregular contours (OR = 22.4), taller-than-wide shape (OR = 19.5), microcalcifications (OR = 15.2), and marked hypoechogenicity (OR = 12.7). Conclusion: Russ’ modified TIRADS classification is reliable in predicting thyroid malignancy. More evidence is nevertheless necessary for widespread adoption and use.

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