Author: "Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)"' showing total 42 results

Start Over Author "Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)" Topic 03 medical and health sciences

42 results on '"Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)"'

1. Might Interspecific Interactions between Pathogens Drive Host Evolution? The Case of Plasmodium Species and Duffy-Negativity in Human Populations

Author: Franck Prugnolle, François Renaud, Jessica L. Abbate, Virginie Rougeron, Benjamin Roche, Lluis Quintana-Murci, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Health, Emergence, Adaptation and Transmission (MIVEGEC-HEAT), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Prévention et Thérapie Moléculaires des Maladies Infectieuses Humaines, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Plasmodium falciparum, Plasmodium vivax, Host-Parasite Interactions, 03 medical and health sciences, parasitic diseases, Malaria, Vivax, medicine, Malaria, Falciparum, Plasmodium species, Genetics, biology, Coinfection, Host (biology), Negativity effect, Interspecific competition, biology.organism_classification, medicine.disease, Biological Evolution, Virology, 3. Good health, 030104 developmental biology, Infectious Diseases, Human evolution, Parasitology, Duffy Blood-Group System, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Malarial infections have long been recognized as a driver of human evolution, as demonstrated by the influence of Plasmodium falciparum on sickle-cell anemia persistence. Duffy-negativity is another blood disorder thought to have been selected because it confers nearly complete resistance against Plasmodium vivax infection. Recent evidence suggests that the benefits of being Duffy-negative cannot be expected to play a strong selective pressure on humans, whereas its costs cannot be considered as negligible. Here, we suggest that the cross-talk between P. falciparum and P. vivax in coinfected children could represent the most parsimonious explanation of the frequency of Duffy-negativity. We discuss how this new hypothesis could be tested and call for a reconsideration of the evolution of the Duffy-negative group.
Published: 2017

2. Natural Wolbachia infections are common in the major malaria vectors in Central Africa

Author: Martha Nigg, Olivier Duron, Boris Makanga, Diego Ayala, Fabrice Mezeme, Carlo Costantini, Benjamin Roche, Christophe Paupy, Frédéric Simard, Marc F. Ngangue, Ousman Akone-Ella, Franck Prugnolle, Nil Rahola, Pierre Kengne, Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Centre International de Recherches Médicales de Franceville (CIRMF), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: 0106 biological sciences, 0301 basic medicine, disease control, Anopheles gambiae, [SDV]Life Sciences [q-bio], lcsh:Evolution, Zoology, co-evolution, 010603 evolutionary biology, 01 natural sciences, Plasmodium, diversity, 03 medical and health sciences, parasitic diseases, Anopheles, Genetics, medicine, lcsh:QH359-425, co‐evolution, Ecology, Evolution, Behavior and Systematics, reproductive and urinary physiology, ComputingMilieux_MISCELLANEOUS, biology, Phylogenetic tree, Host (biology), Transmission (medicine), biochemical phenomena, metabolism, and nutrition, medicine.disease, biology.organism_classification, 3. Good health, 030104 developmental biology, bacteria, Wolbachia, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Malaria
Abstract: International audience; During the last decade, the endosymbiont bacterium Wolbachia has emerged as a biological tool for vector disease control. However, for long time, it was believed that Wolbachia was absent in natural populations of Anopheles. The recent discovery that species within the Anopheles gambiae complex host Wolbachia in natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity of Wolbachia infection in 25 African Anopheles species in Gabon (Central Africa). Our results revealed the presence of Wolbachia in 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity of Wolbachia strains that infect Anopheles. Co‐evolutionary analysis unveiled patterns of Wolbachia transmission within some Anopheles species, suggesting that past independent acquisition events were followed by co‐cladogenesis. The large diversity of Wolbachia strains that infect natural populations of Anopheles offers a promising opportunity to select suitable phenotypes for suppressing Plasmodium transmission and/or manipulating Anopheles reproduction, which in turn could be used to reduce the malaria burden in Africa.
Published: 2019

3. Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

Author: Benjamin Roche, Géraldine Loot, Lisa Fourtune, Simon Blanchet, Ivan Paz-Vinas, Olivier Rey, Charlotte Veyssière, Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0106 biological sciences, Genotype, Range (biology), Population, Wildlife, Biodiversity, Population genetics, Fresh Water, 010603 evolutionary biology, 01 natural sciences, Copepoda, approximate Bayesian computation, 03 medical and health sciences, Spatio-Temporal Analysis, Genetics, Animals, Colonization, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Models, Genetic, biology, Ecology, Bayesian clustering, Fishes, population genetics, Genetic Variation, populationgenetics, Bayes Theorem, Sequence Analysis, DNA, biology.organism_classification, Tracheliastes polycolpus, spatio-temporal dynamic, Europe, Genetics, Population, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Approximate Bayesian computation, pathogen, Microsatellite Repeats
Abstract: International audience; Emerging pathogens constitute a severe threat for human health and biodiversity. Determining the status (native or non-native) of emerging pathogens, and tracing back their spatio-temporal dynamics, is crucial to understand the eco-evolutionary factors promoting their emergence, to control their spread and mitigate their impacts. However, tracing back the spatio-temporal dynamics of emerging wildlife pathogens is challenging because (i) they are often neglected until they become sufficiently abundant and pose socio-economical concerns and (ii) their geographical range is often little known. Here, we combined classical population genetics tools and approximate Bayesian computation (i.e. ABC) to retrace the dynamics of Tracheliastes polycolpus, a poorly documented pathogenic ectoparasite emerging in Western Europe that threatens several freshwater fish species. Our results strongly suggest that populations of T. polycolpus in France emerged from individuals originating from a unique genetic pool that were most likely introduced in the 1920s in central France. From this initial population, three waves of colonization occurred into peripheral watersheds within the next two decades. We further demonstrated that populations remained at low densities, and hence undetectable, during 10 years before a major demographic expansion occurred, and before its official detection in France. These findings corroborate and expand the few historical records available for this emerging pathogen. More generally, our study demonstrates how ABC can be used to determine the status, reconstruct the colonization history and infer key evolutionary parameters of emerging wildlife pathogens with low data availability, and for which samples from the putative native area are inaccessible.
Published: 2015

4. The macroecology of cancer incidences in humans is associated with large-scale assemblages of endemic infections

Author: Gabriele Sorci, Jean-François Guégan, Camille Jacqueline, Jessica L. Abbate, Benjamin Roche, Frédéric Thomas, Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Universidad Nacional Autónoma de México (UNAM), ANR-14-CE14-0020,STORY,Communautés de pathogènes: une association de malfaiteurs(2014), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Centre de Recherches Ecologiques et Evolutives sur le Cancer ( CREEC ), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle ( MIVEGEC ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Laboratoire de Parasitologie-Mycologie, Montpellier ( MIVEGEC ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ) -Institut de recherche pour le développement [IRD] : UR224-Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Universidad Nacional Autónoma de México ( UNAM ), ANR-14-CE14-0020,STORY,Communautés de pathogènes: une association de malfaiteurs ( 2014 ), and ANR-10-LABX-25-01/10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia ( 2010 )
Subjects: 0301 basic medicine, Microbiology (medical), Endemic Diseases, [SDV.CAN]Life Sciences [q-bio]/Cancer, Microbiology, Biomes, Helicobacter Infections, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, Schistosomiasis haematobia, Environmental health, Neoplasms, Pathogen-cancer interactions, Epidemiology of cancer, Genetics, medicine, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Animals, Humans, Stomach cancer, Molecular Biology, Data mining, Ecology, Evolution, Behavior and Systematics, Human cancer incidences, Bladder cancer, Cancer prevention, biology, Incidence, Cancer, Helicobacter pylori, Hepatitis B, medicine.disease, biology.organism_classification, Hepatitis C, 3. Good health, 030104 developmental biology, Infectious Diseases, Neglected diseases, Host-Pathogen Interactions, Female, Public Health, Public health strategies, Liver cancer, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 8 pages; International audience; It is now well supported that 20% of human cancers have an infectious causation (i.e., oncogenic agents). Accumulating evidence suggests that aside from this direct role, other infectious agents may also indirectly affect cancer epidemiology through interactions with the oncogenic agents within the wider infection community. Here, we address this hypothesis via analysis of large-scale global data to identify associations between human cancer incidence and assemblages of neglected infectious agents. We focus on a gradient of three widely-distributed cancers with an infectious cause: bladder (~2% of recorded cancer cases are due to Shistosoma haematobium), liver (~60% consecutive to Hepatitis B and C infection) and stomach (Helicobacter pylori is associated with ~70% of cases). We analyzed countries in tropical and temperate regions separately, and controlled for many confounding social and economic variables. First, we found that particular assemblages of bacteria are associated with bladder cancer incidences. Second, we observed a specific and robust association between helminths and liver cancer incidences in both biomes. Third, we show that certain assemblages of viruses may facilitate stomach cancer in tropical area, while others protect against its development in temperate countries. Finally, we discuss the implications of our results in terms of cancer prevention and highlight the necessity to consider neglected diseases, especially in tropics, to adapt public health strategies against infectious diseases and cancer.
Published: 2018

5. Detecting dynamic spatial correlation patterns with generalized wavelet coherence and non-stationary surrogate data

Author: Mario Chavez, Bernard Cazelles, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute ( ICM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Pitié-Salpêtrière [APHP]-Centre National de la Recherche Scientifique ( CNRS ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-Université Cadi Ayyad [Marrakech] (UCA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), and HEP, INSPIRE
Subjects: 0301 basic medicine, Spatial correlation, Multivariate statistics, Statistical methods, Computer science, Wavelet coherence, lcsh:Medicine, FOS: Physical sciences, Article, [ PHYS.PHYS.PHYS-DATA-AN ] Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Surrogate data, [PHYS] Physics [physics], 03 medical and health sciences, 0302 clinical medicine, Wavelet, lcsh:Science, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], [STAT.AP]Statistics [stat]/Applications [stat.AP], Multidisciplinary, [ PHYS ] Physics [physics], Series (mathematics), business.industry, Stochastic process, Statistics, lcsh:R, Contrast (statistics), Pattern recognition, Probability and statistics, Nonlinear phenomena, 030104 developmental biology, Physics - Data Analysis, Statistics and Probability, Quantitative Biology - Neurons and Cognition, FOS: Biological sciences, lcsh:Q, Neurons and Cognition (q-bio.NC), Artificial intelligence, business, [PHYS.PHYS.PHYS-DATA-AN] Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], 030217 neurology & neurosurgery, [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an], Data Analysis, Statistics and Probability (physics.data-an)
Abstract: Time series measured from real-world systems are generally noisy, complex and display statistical properties that evolve continuously over time. Here, we present a method that combines wavelet analysis and non-stationary surrogates to detect short-lived spatial coherent patterns from multivari- ate time-series. In contrast with standard methods, the surrogate data used here are realisations of a non-stationary stochastic process, preserving both the amplitude and time-frequency distributions of original data. We evaluate this framework on synthetic and real-world time series, and we show that it can provide useful insights into the time-resolved structure of spatially extended systems., Comment: 8 pages, 7 figures
Published: 2018

6. Dengue modeling in rural Cambodia: statistical performance versus epidemiological relevance

Author: Bernard Cazelles, Richard Paul, Clara Champagne, Rithea Leang, Sowath Ly, Veasna Duong, Centre de Recherche en Économie et Statistique (CREST), Ecole Nationale de la Statistique et de l'Analyse de l'Information [Bruz] (ENSAI)-École polytechnique (X)-École Nationale de la Statistique et de l'Administration Économique (ENSAE Paris)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive, modélisation et santé (GEMS), Unité d'Épidémiologie et de Santé Publique [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité de Virologie / Virology Unit [Phnom Penh], National Dengue Control Program, Ministry of Health of Cambodgia, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), All the authors have been supported by a grant from Agence Nationale de la Recherche for the PANIC project (Targeting PAthogen's NIChe: a new approach for infectious diseases control in low-income countries: ANR-14-CE02-0015-01). The research leading to these results has also received funding from the European Commission Seventh Framework Program FP7 for the DENFREE project under Grant Agreement 282 378. CC and BC are partially supported by the 'Pépiniere interdisciplinaire Eco-Evo-Devo' from the Centre National de la Recherche Scientifique (CNRS). CC is supported by the PhD studentship of the Groupe des Ecoles Nationales d’Economie et Statistique (GENES), We thank the members of the Epidemiology and Public Health unit and the Virology unit in Institut Pasteur in Cambodia for their work during the DENFREE project., ANR-14-CE02-0015,PANIC,Cibler la niche des pathogènes : Une nouvelle approche pour le contrôle des maladies infectieuses dans les pays aux ressources économiques limitées(2014), European Project: 282378,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,DENFREE(2012), Paul, Richard, Appel à projets générique - Cibler la niche des pathogènes : Une nouvelle approche pour le contrôle des maladies infectieuses dans les pays aux ressources économiques limitées - - PANIC2014 - ANR-14-CE02-0015 - Appel à projets générique - VALID, Dengue research Framework for Resisting Epidemics in Europe - DENFREE - - EC:FP7:HEALTH2012-01-01 - 2016-12-31 - 282378 - VALID, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génomique évolutive, modélisation et santé (CNRS-UMR2000), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Rural Population, Disease Vectors, Model selection, MESH: Dengue Virus, law.invention, Dengue fever, Dengue, Mathematical model, 0302 clinical medicine, MESH: Rural Population, law, Statistics, MESH: Animals, MESH: Incidence, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Incidence, Coherence (statistics), Markov Chains, 3. Good health, Transmission (mechanics), symbols, Seasons, Cambodia, Monte Carlo Method, MESH: Bayes Theorem, 030231 tropical medicine, Information Criteria, MESH: Monte Carlo Method, MESH: Disease Vectors, Biology, Bayesian inference, Disease cluster, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, symbols.namesake, MESH: Markov Chains, medicine, Animals, Humans, lcsh:RC109-216, 030304 developmental biology, Models, Statistical, MESH: Humans, Bayes Theorem, Markov chain Monte Carlo, Dengue Virus, medicine.disease, Virology, Vector borne disease, MESH: Seasons, MESH: Models, Statistical
Abstract: Dengue dynamics are shaped by the complex interplay between several factors, including vector seasonality, interaction between four virus serotypes, and inapparent infections. However, paucity or quality of data do not allow for all of these to be taken into account in mathematical models. In order to explore separately the importance of these factors in models, we combined surveillance data with a local-scale cluster study in the rural province of Kampong Cham (Cambodia), in which serotypes and asymptomatic infections were documented. We formulate several mechanistic models, each one relying on a different set of hypotheses, such as explicit vector dynamics, transmission via asymptomatic infections and coexistence of several virus serotypes. Models are confronted with the observed time series using Bayesian inference, through Markov chain Monte Carlo. Model selection is then performed using statistical information criteria, and the coherence of epidemiological characteristics (reproduction numbers, incidence proportion, dynamics of the susceptible classes) is assessed in each model. Our analyses on transmission dynamics in a rural endemic setting highlight that two-strain models with interacting effects better reproduce the long term data, but they are difficult to parameterize when relying on incidence cases only. On the other hand, considering the available data, incorporating vector and asymptomatic components seems of limited added-value when seasonality and underreporting are already accounted for. Keywords: Model selection, Dengue, Vector borne disease, Mathematical model, Cambodia
Published: 2017
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7. Modeling the spread of avian influenza viruses in aquatic reservoirs: A novel hydrodynamic approach applied to the Rhône delta (southern France)

Author: Olivier Boutron, Marion Vittecoq, Matthieu Guillemain, Olivier Bertrand, Benjamin Roche, Thibault Oudart, Hermann Gauduin, Centre de recherche de la Tour du Valat, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Analyse et Traitement Informatique de la Langue Française (ATILF), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Artelia Eau & Environnement [Echirolles], Artelia Eau & Environnement [Lyon], Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Office Nationale de la Chasse et de la Faune Sauvage, and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: 0301 basic medicine, Delta, Environmental Engineering, animal diseases, 030106 microbiology, Population, Wetland, Context (language use), Biology, medicine.disease_cause, Models, Biological, Avian influenza viruses, law.invention, Wild birds, 03 medical and health sciences, law, Water Supply, medicine, Environmental Chemistry, Animals, Natural reservoir, Ecosystem, education, Waste Management and Disposal, ComputingMilieux_MISCELLANEOUS, geography, education.field_of_study, geography.geographical_feature_category, Ecology, virus diseases, 15. Life on land, Pollution, Influenza A virus subtype H5N1, Mallards, 030104 developmental biology, Transmission (mechanics), Ducks, 13. Climate action, Influenza A virus, Influenza in Birds, Wetlands, Hydrodynamics, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Hydrodynamic model, France
Abstract: Wild aquatic birds represent a natural reservoir of avian influenza viruses (AIV) that can be spread to poultry. AIV epizootics were associated with huge economic impacts during the last decades and are still of major concern. Within aquatic bird populations AIV are transmitted either by direct contact or through the ingestion of water that has been contaminated by infected individuals. This second route involving environmental transmission is of utmost importance in AIV dynamics, yet it has received far less attention than direct bird-to-bird contamination. Our objective was to combine a hydrodynamic model with data on mallard abundance and AIV infection rate within the population, so as to characterize virus dissemination within a complex wetland network. We chose the Vaccares hydrosystem as a wetland model since it represents a large part of the Camargue region, which is a major wintering site for a large diversity of aquatic birds including AIV hosts. We aimed to identify the environmental parameters that drive AIV dynamics within this system and the spatio-temporal pattern of dispersion and persistence of viruses. Our results show that in a complex hydrosystem we can expect a great heterogeneity in AIV risk among wetlands. Our simulations underline how a simple "homogeneous box" approach could in the case of deltaic ecosystems minimize the expected risk by diluting it in the whole system. Moreover, such undermining of the risk perception could affect the predictions relative to risk duration. We present a new approach to identify hotspots of virus concentrations within deltaic areas that could take advantage of the duck count data, AIV surveys and hydrodynamic models that may already be available in several major duck wintering areas comprised of complex hydrosystems, such as the large European deltas. Our method could be of particular interest to optimize surveillance strategies in the current context of highly pathogenic AIV diffusion within wild bird populations.
Published: 2017

8. Using parallel computing to improve the scalability of models with BDI agents

Author: Alexis Drogoul, Laurent Vercouter, Mathieu Bourgais, Patrick Taillandier, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Identité et Différenciation de l’Espace, de l’Environnement et des Sociétés (IDEES), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire Homme et Société (IRIHS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Equipe Multi-agent, Interaction, Décision (MIND - LITIS), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), ANR-14-CE22-0002,ACTEUR,Agents Cognitifs Territorialisés pour l'Etude des dynamiques Urbaines et des Risques(2014), Identités et Différenciation de l'Environnement des Espaces et des Sociétés (IDEES), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), ANR: ACTEUR,Agents Cognitifs Territorialisés pour l’Etude des dynamiques Urbaines et des Risques, Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut de Recherche Interdisciplinaire Homme et Société (IRIHS), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0303 health sciences, Computer science, Distributed computing, Modeling Platform, 02 engineering and technology, Execution time, Parallel Computation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Cognitive agent, Cognitive Agent, 03 medical and health sciences, Simulation, Scalability, 0202 electrical engineering, electronic engineering, information engineering, Parallel architecture, [INFO]Computer Science [cs], 020201 artificial intelligence & image processing, [MATH]Mathematics [math], Architecture, 030304 developmental biology
Abstract: International audience; These last years have seen the development of several extensions of modeling platforms to include BDI agents. These extensions have allowed modelers with little knowledge in programming and artificial intelligence to develop their own cognitive agents. However, especially in large-scale simulations, the problem of the computational time required by such complex agents is still an open issue. In order to address this difficulty , we propose a parallel version of the BDI architecture integrated into the GAMA platform. We show through several case studies that this new parallel architecture is much more efficient in terms of execution time, while remaining easy to use even by non-computer scientists.
Published: 2017

9. Global and local environmental changes as drivers of Buruli ulcer emergence

Author: Marine Combe, Camilla Jensen Velvin, Aaron Morris, Andres Garchitorena, Kevin Carolan, Daniel Sanhueza, Benjamin Roche, Pierre Couppié, Jean-François Guégan, Rodolphe Elie Gozlan, Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Royal Veterinary College [London], University of London [London], Harvard Medical School [Boston] (HMS), Brigham and Women's Hospital [Boston], Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Ecosystemes Amazoniens et Pathologie Tropicale (EPat), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Guyane (UG), Service de Dermatologie [Cayenne, Guyanne Française], Centre Hospitalier Andre Rosemon, International Research Programme Future Earth, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), HAL UPMC, Gestionnaire, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: DNA, Bacterial, Conservation of Natural Resources, Epidemiology, Immunology, Animals, Wild, Review, Communicable Diseases, Emerging, Microbiology, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Drug Discovery, aquatic ecosystem, Animals, Humans, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, skin and connective tissue diseases, Buruli Ulcer, climate, Ecosystem, Disease Reservoirs, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 2. Zero hunger, Tropical Climate, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, generalist pathogen, Mycobacterium ulcerans, 030306 microbiology, tropical, Agriculture, Biodiversity, General Medicine, 15. Life on land, 3. Good health, Infectious Diseases, 13. Climate action, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Parasitology, sense organs, Erratum
Abstract: International audience; Many emerging infectious diseases are caused by generalist pathogens that infect and transmit via multiple host species with multiple dissemination routes, thus confounding the understanding of pathogen transmission pathways from wildlife reservoirs to humans. The emergence of these pathogens in human populations has frequently been associated with global changes, such as socio-economic, climate or biodiversity modifications, by allowing generalist pathogens to invade and persist in new ecological niches, infect new host species, and thus change the nature of transmission pathways. Using the case of Buruli ulcer disease, we review how land-use changes, climatic patterns and biodiversity alterations contribute to disease emergence in many parts of the world. Here we clearly show that Mycobacterium ulcerans is an environmental pathogen characterized by multi-host transmission dynamics and that its infectious pathways to humans rely on the local effects of global environmental changes. We show that the interplay between habitat changes (for example, deforestation and agricultural land-use changes) and climatic patterns (for example, rainfall events), applied in a local context, can lead to abiotic environmental changes and functional changes in local biodiversity that favor the pathogen’s prevalence in the environment and may explain disease emergence.
Published: 2017

10. Cancer brings forward oviposition in the fly Drosophila melanogaster

Author: Lucas Léger, François Renaud, Jacques Montagne, Andreu Casali, Camille Jacqueline, Frédéric Thomas, Celine Moreno, Frederic Mery, Aurélie Tasiemski, Céline Boidin-Wichlacz, Dominique Faugere, Beata Ujvari, Audrey Arnal, Dorothée Missé, Benjamin Roche, Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Deakin University, Burwood, Australia, Deakin University [Burwood], Laboratoire Evolution, Génomes et Spéciation [Gif-sur-Yvette] (LEGS), Institut de recherche pour le développement [IRD] : UR072-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Croissance et métabolisme chez la Drosophile (METABO), Département Biologie Cellulaire (BioCell), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute for Research in Biomedicine (IRB Barcelona), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Centre de Recherches Ecologiques et Evolutives sur le Cancer ( CREEC ), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle ( MIVEGEC ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Laboratoire Evolution, Génomes et Spéciation [Gif-sur-Yvette] ( LEGS ), Institut de recherche pour le développement [IRD] : UR072-Centre National de la Recherche Scientifique ( CNRS ), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 ( Evo-Eco-Paléo ), Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Croissance et métabolisme chez la Drosophile ( METABO ), Département Biologie Cellulaire ( BioCell ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0106 biological sciences, 0301 basic medicine, [ SDV.BDLR.RS ] Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, [ SDV.BA.ZI ] Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, media_common.quotation_subject, Period (gene), fecundity, Zoology, life-history strategy, 010603 evolutionary biology, 01 natural sciences, Life history theory, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, reproduction, 03 medical and health sciences, medicine, cancer, Allele, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, media_common, Original Research, Genetics, Ecology, biology, Cancer, biology.organism_classification, medicine.disease, Fecundity, 3. Good health, Genetically modified organism, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Reproduction, Drosophila melanogaster, life‐history strategy
Abstract: International audience; Hosts often accelerate their reproductive effort in response to a parasitic infection, especially when their chances of future reproduction decrease with time from the onset of the infection. Because malignancies usually reduce survival, and hence potentially the fitness, it is expected that hosts with early cancer could have evolved to adjust their life-history traits to maximize their immediate reproductive effort. Despite the potential importance of these plastic responses, little attention has been devoted to explore how cancers influence animal reproduction. Here, we use an experimental setup, a colony of genetically modified flies Drosophila melanogaster which develop colorectal cancer in the anterior gut, to show the role of cancer in altering life-history traits. Specifically, we tested whether females adapt their reproductive strategy in response to harboring cancer. We found that flies with cancer reached the peak period of oviposition significantly earlier (i.e., 2 days) than healthy ones, while no difference in the length and extent of the fecundity peak was observed between the two groups of flies. Such compensatory responses to overcome the fitness-limiting effect of cancer could explain the persistence of inherited cancer-causing mutant alleles in the wild. K E Y W O R D S cancer, fecundity, life-history strategy, reproduction
Published: 2017

11. Sur la vitesse d’extinction d’une population dans un environnement aléatoire

Author: Nicolas Bacaër, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, General Immunology and Microbiology, Reproduction, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], General Medicine, Environment, [SHS.DEMO]Humanities and Social Sciences/Demography, Extinction, Biological, 01 natural sciences, Markov Chains, General Biochemistry, Genetics and Molecular Biology, Death, 010104 statistics & probability, 03 medical and health sciences, 030104 developmental biology, Humans, 0101 mathematics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], General Agricultural and Biological Sciences
Abstract: International audience; On s’intéresse à la vitesse d’extinction d’une population qui vit dans un environnement aléatoire gouverné par une chaîne de Markov en temps continu. Chaque individu meurt ou se reproduit à un taux qui dépend de l’environnement. Lors de la reproduction, on suppose que le nombre de rejetons suit une certaine loi de probabilité, qui dépend également de l’environnement. Dans le cas dit sous-critique où la population s’éteint à coup sûr, on détermine de manière explicite la vitesse d’extinction. En un certain sens, la stochasticité environnementale ralentit l’extinction de la population.
Published: 2017

12. Spectral consensus strategy for accurate reconstruction of large biological networks

Author: Nataliya Sokolovska, Edi Prifti, Séverine Affeldt, Jean-Daniel Zucker, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, Clustering high-dimensional data, Computer science, 030106 microbiology, computer.software_genre, Biochemistry, 03 medical and health sciences, Structural Biology, Humans, Microbiome, Molecular Biology, Network reconstruction, Bacteria, Applied Mathematics, Research, Microbiota, Computational Biology, Computer Science Applications, Gastrointestinal Microbiome, Community-based method, High-dimensional data, 030104 developmental biology, Taxon, Benchmark (computing), Data mining, Noise (video), DNA microarray, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Spectral theory, Biological network, Algorithms, Unsupervised Machine Learning
Abstract: Background The last decades witnessed an explosion of large-scale biological datasets whose analyses require the continuous development of innovative algorithms. Many of these high-dimensional datasets are related to large biological networks with few or no experimentally proven interactions. A striking example lies in the recent gut bacterial studies that provided researchers with a plethora of information sources. Despite a deeper knowledge of microbiome composition, inferring bacterial interactions remains a critical step that encounters significant issues, due in particular to high-dimensional settings, unknown gut bacterial taxa and unavoidable noise in sparse datasets. Such data type make any a priori choice of a learning method particularly difficult and urge the need for the development of new scalable approaches. Results We propose a consensus method based on spectral decomposition, named Spectral Consensus Strategy, to reconstruct large networks from high-dimensional datasets. This novel unsupervised approach can be applied to a broad range of biological networks and the associated spectral framework provides scalability to diverse reconstruction methods. The results obtained on benchmark datasets demonstrate the interest of our approach for high-dimensional cases. As a suitable example, we considered the human gut microbiome co-presence network. For this application, our method successfully retrieves biologically relevant relationships and gives new insights into the topology of this complex ecosystem. Conclusions The Spectral Consensus Strategy improves prediction precision and allows scalability of various reconstruction methods to large networks. The integration of multiple reconstruction algorithms turns our approach into a robust learning method. All together, this strategy increases the confidence of predicted interactions from high-dimensional datasets without demanding computations. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1308-y) contains supplementary material, which is available to authorized users.
Published: 2016

13. Larval nutritional stress affects vector life history traits and human malaria transmission

Author: Thierry Lefèvre, Amélie Vantaux, Anna Cohuet, Olivier Roux, Benjamin Roche, Kounbobr Roch Dabiré, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche en Sciences de la Santé (IRSS), CNRST, Transmission-Interactions-Adaptations hôtes/vecteurs/pathogènes (MIVEGEC-TRIAD), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), This study was funded by the ANR grant 11-PDOC-006-01 to TL., We would like to thank all of the children and their parents who participated in this study, as well as the local authorities for their support, and Andrea Yockey-Dejean for proofreading the paper. We are very grateful to the IRSS staff in Burkina Faso for technical assistance., and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: 0301 basic medicine, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Plasmodium falciparum, Zoology, Insect, MESH: Insect Vectors, Biology, Article, law.invention, Life history theory, 03 medical and health sciences, MESH: Plasmodium falciparum/growth & development, law, Stress, Physiological, Anopheles, parasitic diseases, medicine, Gametocyte, Animals, Humans, MESH: Animals, MESH: Stress, Physiological, Life History Traits, media_common, Larva, Multidisciplinary, MESH: Humans, MESH: Life History Traits, MESH: Anopheles/parasitology, Ecology, fungi, MESH: Anopheles/growth & development, medicine.disease, Fecundity, 3. Good health, Insect Vectors, Malaria, MESH: Larva/parasitology, MESH: Malaria/transmission, 030104 developmental biology, Transmission (mechanics), MESH: Larva/growth & development, Vector (epidemiology), Female, MESH: Female
Abstract: Exposure to stress during an insect’s larval development can have carry-over effects on adult life history traits and susceptibility to pathogens. We investigated the effects of larval nutritional stress for the first time using field mosquito vectors and malaria parasites. In contrast to previous studies, we show that larval nutritional stress may affect human to mosquito transmission antagonistically: nutritionally deprived larvae showed lower parasite prevalence for only one gametocyte carrier; they also had lower fecundity. However, they had greater survival rates that were even higher when infected. When combining these opposing effects into epidemiological models, we show that larval nutritional stress induced a decrease in malaria transmission at low mosquito densities and an increase in transmission at high mosquito densities, whereas transmission by mosquitoes from well-fed larvae was stable. Our work underscores the importance of including environmental stressors towards understanding host–parasite dynamics to improve disease transmission models and control.
Published: 2016

14. Causality Analysis Between Climatic Factors And Dengue Fever Using The Granger Causality

Author: Pham Nguyen Hoang, Ho Tuong Vinh, Marc Choisy, Jean-Daniel Zucker, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Recherche pour le Développement (IRD [France-Nord]), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), PHAM, Nguyen Hoang, and Génétique et évolution des maladies infectieuses (GEMI)
Subjects: EPIDEMIOLOGIE, DENGUE, 030231 tropical medicine, Dengue virus, medicine.disease_cause, Dengue fever, law.invention, 03 medical and health sciences, 0302 clinical medicine, Granger causality, CORRELATION TEMPORELLE, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, dengue fever, 030212 general & internal medicine, Socioeconomics, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, CAUSALITE AU SENS DE GRANGER, Incidence (epidemiology), Tropical disease, medicine.disease, Causality, [STAT] Statistics [stat], 3. Good health, [STAT]Statistics [stat], Geography, Transmission (mechanics), Vietnam, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Close relationship, FACTEUR CLIMATIQUE, Climatology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, climatic drivers, ANALYSE MULTIVARIABLE
Abstract: International audience; Dengue is a mosquito-borne tropical disease caused by one of the four serotypes of dengue virus. There are about 2,5 billion people living in endemic areas. The potential influence of environmental and climatic factors on the transmission of mosquito-borne diseases are expected in many situations but the exact real influences of climatic variables remain uncertain in most of the cases. In the present study, we applied the Granger causality to analyze the relation between climatic variables and the monthly incidences of dengue syndromes in Vietnam for 64 provinces from 1994 to 2010. The experimental results shows a close relationship between climatic factors and dengue incidence in each province and their neighbourhoods.
Published: 2016

15. Explicit Composition Constructs in DSLs - The case of the epidemiological language Kendrick

Author: Thi Mai Anh Bui, Serge Stinckwich, Mikal Ziane, Nick Papoulias, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Modélisation et Vérification (MoVe), Laboratoire d'Informatique de Paris 6 (LIP6), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, Domain-specific language, Computer science, Programming language, Semantics (computer science), business.industry, 030106 microbiology, 06 humanities and the arts, Modular design, 0603 philosophy, ethics and religion, computer.software_genre, Task (project management), Domain (software engineering), 03 medical and health sciences, Digital subscriber line, Decomposition (computer science), [INFO]Computer Science [cs], 060301 applied ethics, Artificial intelligence, Pharo, business, computer, Natural language processing
Abstract: International audience; Domain Specific Languages (DSL) are designed to be syntactically and semantically easier to use than general-purpose languages performing the same task. This is generally achieved by tailoring programming notions and constructs to the domain tasks at hand. Yet there are examples of domain specific problems that demand elaborate constructs (for e.g. aspects in Aspect DSLs) which need to be carefully introduced as to avoid complicating the language. We present such an example in Pharo for the epidemiological language KENDRICK. KENDRICK simplifies the programming of epidemiological simulations by decomposing highly-coupled monolithic models into modular concerns. This decomposition though, is based on a mathematical model that introduces non-trivial composition semantics into the language that need to be carefully integrated. In this work, we address this problem by extending KENDRICK's DSL with explicit composition semantics, entities and operators.
Published: 2016

16. Deep kernel dimensionality reduction for scalable data integration

Author: Jean-Daniel Zucker, Karine Clément, Nataliya Sokolovska, Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and HAL-UPMC, Gestionnaire
Subjects: 0301 basic medicine, Diffusion map, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, High dimensional, 010501 environmental sciences, External Data Representation, computer.software_genre, 01 natural sciences, Theoretical Computer Science, 03 medical and health sciences, Biomedical data, Artificial Intelligence, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, 0105 earth and related environmental sciences, Mathematics, Applied Mathematics, Dimensionality reduction, Heterogeneous data integration, 030104 developmental biology, Kernel (image processing), Scalability, Data mining, computer, Software, Data integration
Abstract: International audience; Dimensionality reduction is used to preserve significant properties of data in a low-dimensional space. In particular , data representation in a lower dimension is needed in applications , where information comes from multiple high dimensional sources. Data integration , however , is a challenge in itself. In this contribution , we consider a general framework to perform dimen-sionality reduction taking into account that data are heterogeneous. We propose a novel approach , called Deep Kernel Dimensionality Reduction which is designed for learning layers of new compact data representations simultaneously . The method can be also used to learn shared representations between modalities. We show by experiments on standard and on real large-scale biomedical data sets that the proposed method embeds data in a new compact meaningful representation , and leads to a lower classification error compared to the state-of-the-art methods .
Published: 2016

17. Separation of Concerns in Epidemiological Modelling

Author: Thi Mai Anh Bui, Nick Papoulias, Mikal Ziane, Tuong Vinh Ho, Benjamin Roche, Serge Stinckwich, Modélisation et Vérification (MoVe), Laboratoire d'Informatique de Paris 6 (LIP6), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Universitaire de Technologie Paris Descartes (IUT - Paris Descartes), Université Paris Descartes - Paris 5 (UPD5), Université Sorbonne Paris Cité (USPC), Université de Caen Normandie (UNICAEN), Normandie Université (NU), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), PHARO, Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Modélisation et Vérification ( MoVe ), Laboratoire d'Informatique de Paris 6 ( LIP6 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA ), Institut Universitaire de Technologie Paris Descartes ( IUT - Paris Descartes ), Université Paris Descartes - Paris 5 ( UPD5 ), Université Sorbonne Paris Cité ( USPC ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie ( UPMC ), and Université Pierre et Marie Curie - Paris 6 ( UPMC )
Subjects: 0301 basic medicine, 021110 strategic, defence & security studies, Domain-specific language, education.field_of_study, [ INFO ] Computer Science [cs], Theoretical computer science, Computer science, separation of concerns, Separation of concerns, 030106 microbiology, Population, 0211 other engineering and technologies, 02 engineering and technology, Automaton, Domain (software engineering), Modeling and simulation, compartmental models, 03 medical and health sciences, domain specific languages, epidemiological modelling, Tensor (intrinsic definition), Econometrics, [INFO]Computer Science [cs], education, Mixing (physics)
Abstract: International audience; Modelling and simulation have been heavily used in epidemiology, for instance to study the transmission of infectious diseases, their pathogenicity and their propagation. A major hindrance to modelling in epidemiology is the mixing of concerns that ought to be separated. The most obvious one is the computer implementation that should not be mixed with domain aspects. But several domain concerns should also be separated from the core epidemiological ones. These include the distribution of the studied populations into spatial regions, age intervals, sexes, species, viral strains... We propose an approach that relies on a mathematical model of the dynamics of a compartment-based population. The separation of domain concerns is provided by expressing each one as a stochastic automaton and combining them with a tensor sum. A DSL, Kendrick, and a tool, support this approach that has been validated on several case studies.
Published: 2016

18. Plant-Mediated Effects on Mosquito Capacity to Transmit Human Malaria

Author: Anna Cohuet, Rakiswendé S. Yerbanga, Louis-Clément Gouagna, Georges Anicet Ouedraogo, Bienvenue K. Yameogo, Jean-Bosco Ouédraogo, Richard J. Hopkins, Kounbobr Roch Dabiré, Domonbabele François de Sales Hien, Benjamin Roche, Rickard Ignell, Frédéric Simard, Abdoulaye Diabaté, Thierry Lefèvre, Institut de Recherche en Sciences de la Santé (IRSS), CNRST, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Transmission-Interactions-Adaptations hôtes/vecteurs/pathogènes (MIVEGEC-TRIAD), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Greenwich, Université Polytechnique Nazi Boni Bobo-Dioulasso (UNB), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Swedish University of Agricultural Sciences (SLU), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, Plasmodium, Epidemiology, Disease Vectors, Gametocytes, Mosquitoes, Animal Cells, Medicine and Health Sciences, Biology (General), Malaria, Falciparum, Protozoans, biology, Anopheles, Malarial Parasites, food and beverages, Agriculture, Plants, 3. Good health, Insects, Sporozoites, Cellular Types, Research Article, S1, Arthropoda, QH301-705.5, Immunology, Zoology, Context (language use), Crops, Microbiology, Fruits, 03 medical and health sciences, Virology, Botany, parasitic diseases, Parasite Groups, Genetics, Gametocyte, medicine, Parasitic Diseases, Animals, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Molecular Biology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Host (biology), fungi, Organisms, Biology and Life Sciences, Plasmodium falciparum, Plant Nectar, Feeding Behavior, Cell Biology, RC581-607, biology.organism_classification, medicine.disease, Tropical Diseases, Invertebrates, Parasitic Protozoans, Insect Vectors, Malaria, 030104 developmental biology, Culicidae, Germ Cells, Vector (epidemiology), Parasitology, Immunologic diseases. Allergy, Apicomplexa, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, Crop Science
Abstract: The ecological context in which mosquitoes and malaria parasites interact has received little attention, compared to the genetic and molecular aspects of malaria transmission. Plant nectar and fruits are important for the nutritional ecology of malaria vectors, but how the natural diversity of plant-derived sugar sources affects mosquito competence for malaria parasites is unclear. To test this, we infected Anopheles coluzzi, an important African malaria vector, with sympatric field isolates of Plasmodium falciparum, using direct membrane feeding assays. Through a series of experiments, we then examined the effects of sugar meals from Thevetia neriifolia and Barleria lupilina cuttings that included flowers, and fruit from Lannea microcarpa and Mangifera indica on parasite and mosquito traits that are key for determining the intensity of malaria transmission. We found that the source of plant sugar meal differentially affected infection prevalence and intensity, the development duration of the parasites, as well as the survival and fecundity of the vector. These effects are likely the result of complex interactions between toxic secondary metabolites and the nutritional quality of the plant sugar source, as well as of host resource availability and parasite growth. Using an epidemiological model, we show that plant sugar source can be a significant driver of malaria transmission dynamics, with some plant species exhibiting either transmission-reducing or -enhancing activities., Author Summary The Anopheles coluzzii mosquito is an effective vector of human Plasmodium falciparum malaria. Besides feeding on blood, females readily feed on natural sources of plant sugars; but how plant diversity affects their ability to transmit malaria parasites is currently unknown. Here we show that mosquito feeding on peridomestic plant- and fruit-derived sugar sources can affect its interaction with P. falciparum, and hence malaria transmission. The planting of anti-Plasmodium plant sugar sources may represent a promising alternative strategy to contribute to the control of malaria.
Published: 2016

19. Imported chikungunya cases in an area newly colonised by Aedes albopictus : mathematical assessment of the best public health strategy

Author: Alexandra Septfons, Frédéric Jourdain, Didier Fontenille, Yvon Perrin, Thomas Sochacki, Frédéric Simard, Henriette de Valk, Marie-Claire Paty, Harold Noel, Benjamin Roche, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Centre national d'expertise des vecteurs, Montpellier (CNEV), Institut de Veille Sanitaire (INVS), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, medicine.medical_specialty, Aedes albopictus, Epidemiology, Cost-Benefit Analysis, 030231 tropical medicine, medicine.disease_cause, Risk Assessment, law.invention, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Cost of Illness, law, Aedes, Virology, Environmental health, Economic cost, Prevalence, Medicine, Animals, Humans, Computer Simulation, Chikungunya, [MATH]Mathematics [math], Proportional Hazards Models, Travel, Models, Statistical, biology, business.industry, Public health, Health Policy, Public Health, Environmental and Occupational Health, Outbreak, biology.organism_classification, 3. Good health, Surgery, Insect Vectors, 030104 developmental biology, Transmission (mechanics), Models, Economic, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Public Health Practice, Chikungunya Fever, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, business
Abstract: International audience; We aimed to identify the optimal strategy that should be used by public health authorities against transmission of chikungunya virus in mainland France. The theoretical model we developed, which mimics the current surveillance system, predicted that without vector control (VC), the probability of local transmission after introduction of viraemic patients was around 2%, and the number of autochthonous cases between five and 15 persons per hectare, depending on the number of imported cases. Compared with this baseline, we considered different strategies (VC after clinical suspicion of a case or after laboratory confirmation, for imported or autochthonous cases): Awaiting laboratory confirmation for suspected imported cases to implement VC had no significant impact on the epidemiological outcomes analysed, mainly because of the delay before entering into the surveillance system. However, waiting for laboratory confirmation of autochthonous cases before implementing VC resulted in more frequent outbreaks. After analysing the economic cost of such strategies, our study suggested implementing VC immediately after the notification of a suspected autochthonous case as the most efficient strategy in settings where local transmission has been proven. Nevertheless, we identified that decreasing reporting time for imported cases should remain a priority.
Published: 2016

20. Host manipulation by cancer cells: Expectations, facts, and therapeutic implications

Author: Benjamin Roche, François Renaud, Camille Jacqueline, Aurélie Tasiemski, Frederic Mery, Tazzio Tissot, Michel Salzet, François Massol, Audrey Arnal, Robert Poulin, Thierry Lefèvre, Frédéric Thomas, Paul W. Ewald, Beata Ujvari, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Zoology, University of Otago [Dunedin, Nouvelle-Zélande], Transmission-Interactions-Adaptations hôtes/vecteurs/pathogènes (MIVEGEC-TRIAD), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U 1192 (PRISM), Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), University of Louisville, Deakin University, Burwood, Australia, Deakin University [Burwood], Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)
Subjects: 0301 basic medicine, Carcinogenesis, Context (language use), Biology, General Biochemistry, Genetics and Molecular Biology, host manipulation, Host-Parasite Interactions, 03 medical and health sciences, Neoplasms, Tumor Microenvironment, Animals, Humans, Sustenance, cancer cell, Cell Proliferation, Clinical Oncology, clinical oncology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Host (biology), Phenotype, cancer progression, 3. Good health, 030104 developmental biology, Immunology, Cancer cell, Tumor Escape, Cancer development, parasitic ecology, Neuroscience, c ancer cell
Abstract: International audience; Similar to parasites, cancer cells depend on their hosts for sustenance, proliferation and reproduction, exploiting the hosts for energy and resources, and thereby impairing their health and fitness. Because of this lifestyle similarity, it is predicted that cancer cells could, like numerous parasitic organisms, evolve the capacity to manipulate the phenotype of their hosts to increase their own fitness. We claim that the extent of this phenomenon and its therapeutic implications are, however, underappreciated. Here, we review and discuss what can be regarded as cases of host manipulation in the context of cancer development and progression. We elaborate on how acknowledging the applicability of these principles can offer novel therapeutic and preventive strategies. The manipulation of host phenotype by cancer cells is one more reason to adopt a Darwinian approach in cancer research.
Published: 2016

21. Cancer and life-history traits: lessons from host–parasite interactions

Author: Marion Vittecoq, Audrey Arnal, Dorothée Missé, Aurélie Tasiemski, Frederic Mery, Tazzio Tissot, Robert Poulin, François Renaud, Christa Beckmann, Beata Ujvari, Céline Boidin-Wichlacz, Benjamin Roche, Péter Biró, Michel Salzet, Frédéric Thomas, François Massol, Deakin University, Burwood, Australia, Deakin University [Burwood], Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Protéomique, Réponse Inflammatoire, Spectrométrie de Masse (PRISM) - U 1192 (PRISM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Centre de recherche de la Tour du Valat, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Department of Zoology, University of Otago [Dunedin, Nouvelle-Zélande], Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0106 biological sciences, 0301 basic medicine, Offspring, Population, Biology, 010603 evolutionary biology, 01 natural sciences, Host-Parasite Interactions, Life history theory, 03 medical and health sciences, Neoplasms, Parasitic Diseases, Animals, Humans, Parasite hosting, education, Genetics, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Biological Evolution, 3. Good health, Paternal Effects, 030104 developmental biology, Infectious Diseases, Tumour development, Infectious disease (medical specialty), Animal Science and Zoology, Parasitology, Evolutionary ecology
Abstract: SUMMARYDespite important differences between infectious diseases and cancers, tumour development (neoplasia) can nonetheless be closely compared to infectious disease because of the similarity of their effects on the body. On this basis, we predict that many of the life-history (LH) responses observed in the context of host–parasite interactions should also be relevant in the context of cancer. Parasites are thought to affect LH traits of their hosts because of strong selective pressures like direct and indirect mortality effects favouring, for example, early maturation and reproduction. Cancer can similarly also affect LH traits by imposing direct costs and/or indirectly by triggering plastic adjustments and evolutionary responses. Here, we discuss how and why a LH focus is a potentially productive but under-exploited research direction for cancer research, by focusing our attention on similarities between infectious disease and cancer with respect to their effects on LH traits and their evolution. We raise the possibility that LH adjustments can occur in response to cancer via maternal/paternal effects and that these changes can be heritable to (adaptively) modify the LH traits of their offspring. We conclude that LH adjustments can potentially influence the transgenerational persistence of inherited oncogenic mutations in populations.
Published: 2016

22. Niche-based host extinction increases prevalence of an environmentally acquired pathogen

Author: Andres Garchitorena, James N. Mills, Gerardo Suzán, Benjamin Roche, Anne-Hélène Prieur-Richard, Elsa Canard, Jean-François Guégan, Kevin Carolan, Gabriel E. García-Peña, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), DIVERSITAS, United Nations Educational, Scientific and Cultural Organization (UNESCO), FutureEarth Programme, United Nations Environment Programme, Universidad Nacional Autónoma de México (UNAM), Emory University [Atlanta, GA], Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), INRAE UMR IGEPP RENNES FRA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Extinction, Ecology, Host (biology), Niche, social sciences, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, humanities, 03 medical and health sciences, 030104 developmental biology, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Pathogen, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Understanding the ecology of environmentally acquired and multi-host pathogens affecting humans and wildlife has been elusive in part because fluctuations in the abundance of host and pathogen species may feed back onto pathogen transmission. Complexity of pathogen-host dynamics emerges from processes driving local extinction of the pathogen, its hosts and non-hosts. While the extinction of species may entail losses in pathogen-host interactions and decrease the proportion of hosts infected by a pathogen (prevalence), some studies suggest the opposite pattern. Niche-based extinction, based on the species tolerance to environmental conditions, may increase prevalence of infection because the pathogen and its hosts persist, while other species go extinct. Hence, understanding prevalence of infection requires disentangling random-and niche-based extinction processes occurring simultaneously. To contribute to this exercise, we analysed the prevalence of an environmentally acquired, multi-host pathogen, Mycobacterium ulcerans (MU), in a unique dataset of 16 communities of freshwater animals, surveyed during 12 months in Akonolinga, Cameroon in equatorial Africa. Two different ecosystems were identified: rivers (lotic) and swamps and flooded areas (lentic). Increased prevalence of MU infection was correlated with niche-based extinction of aquatic host invertebrates and vertebrates in the lentic ecosystems, whereas decreased prevalence was associated with random disassembly of the lotic ecosystems. This finding suggests that random and niche-based extinction of host taxa are key to assessing the effect of local extinction of species on the ecology of environmentally acquired and multi-host pathogens.
Published: 2016

23. Potential impact of sexual transmission on Ebola virus epidemiology: Sierra Leone as a case study

Author: Jessica L. Abbate, Heinz Richner, Christian L. Althaus, Carmen Lía Murall, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Institute of Ecology and Evolution, Departement Evolutionary Ecology, University of Bern, Max Planck Institute for Dynamics and Self-Organization (MPIDS), Max-Planck-Gesellschaft, Institute of Social and Preventive Medicine [Bern] (ISPM), Universität Bern [Bern] (UNIBE), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Universität Bern [Bern]
Subjects: 0301 basic medicine, RNA viruses, Viral Diseases, Spatial Epidemiology, Statistical methods, Epidemiology, Physiology, Virus Replication, Pathology and Laboratory Medicine, medicine.disease_cause, Geographical locations, law.invention, 0302 clinical medicine, law, Medicine and Health Sciences, 030212 general & internal medicine, 0303 health sciences, lcsh:Public aspects of medicine, Incidence, Incidence (epidemiology), Sexually Transmitted Diseases, Viral, General Medicine, Ebolavirus, Body Fluids, 3. Good health, Monte Carlo method, Physical sciences, Africa, Western, Infectious Diseases, Transmission (mechanics), Medical Microbiology, Filoviruses, Viral Pathogens, Viruses, RNA, Viral, Pathogens, Anatomy, Ebola Virus, Research Article, Neglected Tropical Diseases, Microbiology (medical), medicine.medical_specialty, lcsh:Arctic medicine. Tropical medicine, Sexual transmission, lcsh:RC955-962, Sexually Transmitted Diseases, 610 Medicine & health, Statistics (mathematics), Disease cluster, Models, Biological, Microbiology, Ebola Hemorrhagic Fever, Infectious Disease Epidemiology, Sierra Leone, Sierra leone, 03 medical and health sciences, Condom, 360 Social problems & social services, Semen, medicine, Humans, Epidemics, Microbial Pathogens, Viral Hemorrhagic Fevers, Models, Statistical, Ebola virus, Biology and life sciences, Hemorrhagic Fever Viruses, 030306 microbiology, business.industry, Public Health, Environmental and Occupational Health, Organisms, lcsh:RA1-1270, Convalescence, Hemorrhagic Fever, Ebola, Tropical Diseases, Research and analysis methods, 030104 developmental biology, Immunology, Africa, 570 Life sciences, biology, Mathematical and statistical techniques, People and places, business, Mathematics, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract: Background Sexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013–2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus disease (EVD), it remains unclear what threat is posed by rare sexual transmission events that could arise from survivors. Methodology/Principal Findings We devised a compartmental mathematical model that includes sexual transmission from convalescent survivors: a SEICR (susceptible-exposed-infectious-convalescent-recovered) transmission model. We fitted the model to weekly incidence of EVD cases from the 2014–2015 epidemic in Sierra Leone. Sensitivity analyses and Monte Carlo simulations showed that a 0.1% per sex act transmission probability and a 3-month convalescent period (the two key unknown parameters of sexual transmission) create very few additional cases, but would extend the epidemic by 83 days [95% CI: 68–98 days] (p < 0.0001) on average. Strikingly, a 6-month convalescent period extended the average epidemic by 540 days (95% CI: 508–572 days), doubling the current length, despite an insignificant rise in the number of new cases generated. Conclusions/Significance Our results show that reductions in the per sex act transmission probability via abstinence and condom use should reduce the number of sporadic sexual transmission events, but will not significantly reduce the epidemic size and may only minimally shorten the length of time the public health community must maintain response preparedness. While the number of infectious survivors is expected to greatly decline over the coming months, our results show that transmission events may still be expected for quite some time as each event results in a new potential cluster of non-sexual transmission. Precise measurement of the convalescent period is thus important for planning ongoing surveillance efforts., Author Summary Researchers have recently raised suspicion that the Ebola virus can be transmitted sexually from survivors after recovering from the life-threatening acute phase characteristic of Ebola virus disease (EVD). However, the nature of the impact sexual transmission from convalescent survivors may have on disease dynamics remains unknown. Mathematical models are useful for translating empirical uncertainty into a range of possible outcomes. We formalized an epidemiological model that accounts for a secondary route of transmission of EVD through sexual contact with otherwise healthy survivors. We found that while very few additional cases are expected, a 3-month period of convalescent infectivity could extend the 2014–2015 Sierra Leone epidemic by nearly 3 months, and a 6-month convalescent period could double the current length by extending it an additional 18 months. Our results reveal that measures to reduce sexual contact between survivors and susceptible individuals are not likely to have a major impact on the length of time affected public health communities must remain vigilant, and highlight the need for ongoing surveillance efforts.
Published: 2016

24. Study of a virus–bacteria interaction model in a chemostat: application of geometrical singular perturbation theory

Author: Pierre Auger, Flora Cordoleani, Jean-Christophe Poggiale, Tri Nguyen-Huu, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Singular perturbation, General Mathematics, General Physics and Astronomy, Boundary (topology), reduction, Context (language use), Models, Biological, 01 natural sciences, Domain (mathematical analysis), 03 medical and health sciences, Bioreactors, Intersection, Quantitative Biology::Populations and Evolution, invariant manifold, Bacteriophages, 14. Life underwater, 0101 mathematics, Invariant (mathematics), singular perturbation, Ecosystem, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Mathematics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Bacteria, 010102 general mathematics, Mathematical analysis, General Engineering, Interaction model, Phase space, virus-bacteria interaction, Virus Physiological Phenomena
Abstract: This paper provides a mathematical analysis of a virus–marine bacteria interaction model. The model is a simplified case of the model published and used by Middelboe (Middelboe, M. 2000 Microb. Ecol . 40 , 114–124). It takes account of the virus, the susceptible bacteria, the infected bacteria and the substrate in a chemostat. We show that the numerical values of the parameters given by Middelboe allow two different time scales to be considered. We then use the geometrical singular perturbation theory to study the model. We show that there are two invariant submanifolds of dimension two in the four-dimensional phase space and that these manifolds cross themselves on the boundary of the domain of biological relevance. We then perform a rescaling to understand the dynamics in the vicinity of the intersection of the manifolds. Our results are discussed in the marine ecological context.
Published: 2009

25. Analyse d'un modèle décrivant la dynamique d'une population structurée en stade utilisant le jeu faucon-colombe

Author: Pierre Auger, Nguyen Ngoc Doanh, Ali Moussaoui, Département de Mathematiques [Tlemcen], Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], School of Applied Mathematics and Informatics (Hanoi), Hanoi University of Science and Technology (HUST), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Hawk and dove game, Jeux faucon-colombe, media_common.quotation_subject, Population, Biology, 050905 science studies, Competition (biology), 03 medical and health sciences, agrégation des variables, Resource (project management), Resource Acquisition Is Initialization, Econometrics, [INFO]Computer Science [cs], aggregation of variables, [MATH]Mathematics [math], education, Average cost, 030304 developmental biology, media_common, 0303 health sciences, education.field_of_study, population dynamics, Ecology, 05 social sciences, General Medicine, Fecundity, dynamique des populations, Dynamics (music), 0509 other social sciences, Dove
Abstract: The purpose of this paper is to investigate the effects of conflicting tactics of resource acquisition on stage structured population dynamics. We present a population subdivided into two distinct stages (immature and mature). We assume that immature individual survival is density dependent. We also assume that mature individuals acquire resources required to survive and reproduce by using two contrasted behavioral tactics (hawk versus dove). Mature individual survival thus is assumed to depend on the average cost of fights while individual fecundity depends on the average gain in the competition to access the resource. Our model includes two parts: a fast part that describes the encounters and fights involves a game dynamic model based upon the replicator equations, and a slow part that describes the long-term effects of conflicting tactics on the population dynamics. The existence of two time scales let us investigate the complete system from a reduced one, which describes the dynamics of the total immature and mature densities at the slow time scale. Our analysis shows that an increase in resource value may decrease total population density, because it promotes individual (i.e. selfish) behavior. Our results may therefore find practical implications in animal conservation or biological control for instance. Le but de cet article est d'étudier les effets de comportements agressifs dans l'acquisition de ressources sur la dynamique d'une population structurée en deux classes d'âge. Nous considérons une population divisée en deux sous populations distinctes (immatures et adultes matures). Nous supposons que la survie individuelle de la population immature est densité dépendante. Nous supposons également que les individus matures sont en compétition pour acquérir les ressources nécessaires pour leur survie et leur reproduction. Les adultes utilisent deux tactiques comportementales (faucon et colombe). Lors de confrontations entre adultes, la survie d'un individu mature est supposée être affectée par le coût moyen des combats alors que la fécondité dépend du gain moyen obtenu en accédant à la ressource. Notre modèle comprend deux parties : une partie rapide qui décrit les rencontres et les combats basée sur les équations du réplicateur, et une partie lente qui décrit les effets à long terme des tactiques conflictuelles sur la dynamique de la population. L'existence de deux échelles de temps nous permet d'étudier le système complet à partir d'un système réduit, qui décrit la dynamique des densités totales des immatures et des adultes à l'échelle de temps lente. Notre analyse montre que le taux de croissance global de la population dépend de la valeur de la ressource et du coût des combats entre adultes. Nos résultats trouvent des implications pratiques dans la conservation des espèces et le contrôle biologique.
Published: 2015

26. KENDRICK: a Domain Specific Language and Platform for Mathematical Epidemiological Modelling

Author: Bui Thi Mai Anh, Benjamin Roche, Mikal Ziane, Ho Tuong Vinh, Serge Stinckwich, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Modélisation et Vérification (MoVe), Laboratoire d'Informatique de Paris 6 (LIP6), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU), Institut Universitaire de Technologie Paris Descartes (IUT - Paris Descartes), Université Paris Descartes - Paris 5 (UPD5), Université Sorbonne Paris Cité (USPC), IEEE, PHARO, Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA ), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie ( UPMC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ), Institut Universitaire de Technologie Paris Descartes ( IUT - Paris Descartes ), Université Paris Descartes - Paris 5 ( UPD5 ), Université Sorbonne Paris Cité ( USPC ), Modélisation et Vérification ( MoVe ), Laboratoire d'Informatique de Paris 6 ( LIP6 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), and Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Domain-specific language, Theoretical computer science, [ INFO ] Computer Science [cs], Computer science, media_common.quotation_subject, 02 engineering and technology, Mathematical modelling of infectious disease, Adaptability, Bridging (programming), 03 medical and health sciences, domain-specific language, 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], 030304 developmental biology, Reusability, media_common, 0303 health sciences, Mathematical model, business.industry, Simulation modeling, Digital subscriber line, epidemiological modelling, Software engineering, business, compartmental model
Abstract: International audience; Mathematical modelling of infectious diseases often uses simulation models in order to explore transmission mechanisms and to plan potential management strategies to control the epidemics. However, bridging the gap between the conceptual model of epidemiology and its simulation on computer can lead to some issues related to the lack of expressiveness of implemented models and their reusability and adaptability to new circumstances due to detail computer instructions in General-purpose Programming Languages (GPLs). In this paper, we propose to develop a Domain Specific Language (DSL) for expressively specifying mathematical models of epidemiology and to construct a flexible simulation environment for investigating them. We then use our proposed approach to experiment the measles model in different epidemiological aspects. Our platform is also validated through statistical comparisons between time series generated and theoretical expectations, consequently keeping the link with literature on mathematical epidemiology.
Published: 2015

27. Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia

Author: Oliver G. Pybus, Jing Yang, Nuno R. Faria, Bernard Cazelles, Shanqian Huang, Bo Xu, Bing Xu, Qiqi Yang, Huaiyu Tian, Zhe Sun, Beijing Normal University (BNU), Tsinghua University [Beijing] (THU), University of Oxford, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Althouse, B, University of Oxford [Oxford], and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: RNA viruses, 0301 basic medicine, Serotype, Viral Diseases, Aircraft, viruses, Transportation, Dengue virus, Pathology and Laboratory Medicine, medicine.disease_cause, Dengue Fever, Dengue fever, Southeast asia, law.invention, Geographical Locations, Dengue, Database and Informatics Methods, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, Medicine and Health Sciences, Centrality, Economic geography, Spatial diffusion, Asia, Southeastern, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Geography, lcsh:Public aspects of medicine, virus diseases, Thailand, 3. Good health, Phylogeography, Air Travel, Infectious Diseases, Transmission (mechanics), Biogeography, Medical Microbiology, Viral Pathogens, Viruses, Engineering and Technology, RNA, Viral, Pathogens, Sequence Analysis, Network Analysis, Research Article, Neglected Tropical Diseases, Computer and Information Sciences, China, lcsh:Arctic medicine. Tropical medicine, Asia, lcsh:RC955-962, Bioinformatics, India, Research and Analysis Methods, Serogroup, Microbiology, Evolution, Molecular, 03 medical and health sciences, Spatio-Temporal Analysis, Genetics, medicine, Humans, Circulation (currency), Microbial Pathogens, Evolutionary Biology, Population Biology, Flaviviruses, Ecology and Environmental Sciences, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, lcsh:RA1-1270, Dengue Virus, Tropical Diseases, medicine.disease, Virology, 030104 developmental biology, Socioeconomic Factors, People and Places, Earth Sciences, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Americas, Population Genetics
Abstract: The incidence of dengue has grown dramatically in recent decades worldwide, especially in Southeast Asia and the Americas with substantial transmission in 2014–2015. Yet the mechanisms underlying the spatio-temporal circulation of dengue virus (DENV) serotypes at large geographical scales remain elusive. Here we investigate the co-circulation in Asia of DENV serotypes 1–3 from 1956 to 2015, using a statistical framework that jointly estimates migration history and quantifies potential predictors of viral spatial diffusion, including socio-economic, air transportation and maritime mobility data. We find that the spread of DENV-1, -2 and -3 lineages in Asia is significantly associated with air traffic. Our analyses suggest the network centrality of air traffic hubs such as Thailand and India contribute to seeding dengue epidemics, whilst China, Cambodia, Indonesia, and Singapore may establish viral diffusion links with multiple countries in Asia. Phylogeographic reconstructions help to explain how growing air transportation networks could influence the dynamics of DENV circulation., Author summary In the past half century the incidence of dengue fever worldwide has increased 30-fold, with an estimated ~390 million infections per year. The years 2014 and 2015 were characterized by large dengue outbreaks worldwide, which are a threat to public health, especially in Asian countries. Here we use a phylogeographic approach to reconstruct historical virus movement and evaluate multiple potential predictors of the spatial spread of dengue virus (DENV) among Asian countries. We show that air traffic has played a more important role than maritime transport in shaping large-scale geographic dispersal of DENV in Asia. Our study suggests that the patterns of DENV spread result from the interplay between intensity and structure of human mobility through the air transportation network.
Published: 2017

28. Linear vs non-linear learning methods A comparative study for forest above ground biomass, estimation from texture analysis of satellite images

Author: Hippolyte Tapamo, Olivier Monga, Blaise Ngonmang, Pierre Couteron, Adamou Mfopou, Département d'Informatique [Yaoundé], Faculté des Sciences - Yaoundé I, Université de Yaoundé I-Université de Yaoundé I, Laboratoire International de Recherche en Informatique et Mathématiques Appliquées (LIRIMA), Université de Yaoundé I-Université Badji Mokhtar Annaba (UBMA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Joseph Ki-Zerbo [Ouagadougou] (UJZK)-Université d'Antananarivo-Université Gaston Bergé Sénégal-Centre National de la Recherche Scientifique et Technologique (CNRST), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD), Université Pierre et Marie Curie - Paris 6 (UPMC), Faculté des Sciences - Yaoundé, Université de Yaoundé I [Yaoundé]-Université de Yaoundé I [Yaoundé], Université de Yaoundé I [Yaoundé]-Université Badji Mokhtar - Annaba [Annaba] (UBMA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Ouagadougou-Université d'Antananarivo-Université Gaston Bergé Sénégal-Centre National de la Recherche Scientifique et Technologique (CNRST), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique et Technologique (CNRST)-Université Gaston Bergé Sénégal-Université d'Antananarivo-Université Joseph Ki-Zerbo [Ouagadougou] (UJZK)-Université Badji Mokhtar - Annaba [Annaba] (UBMA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Yaoundé I, Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: random forests, [MATH] Mathematics [math], [INFO] Computer Science [cs], 050905 science studies, supervised learning, support vector machines, 03 medical and health sciences, Deforestation, Linear regression, [INFO]Computer Science [cs], [MATH]Mathematics [math], 030304 developmental biology, Remote sensing, computer.programming_language, 0303 health sciences, Dart, Forest inventory, estimation, 05 social sciences, Supervised learning, Aboveground biomass, General Medicine, 15. Life on land, Random forest, Support vector machine, Geography, 13. Climate action, Ordination, regression, 0509 other social sciences, computer, k-nearest neighbor
Abstract: The aboveground biomass estimation is an important question in the scope of Reducing Emission from Deforestation and Forest Degradation (REDD framework of the UNCCC). It is particularly challenging for tropical countries because of the scarcity of accurate ground forest inventory data and of the complexity of the forests. Satellite-borne remote sensing can help solve this problem considering the increasing availability of optical very high spatial resolution images that provide information on the forest structure via texture analysis of the canopy grain. For example, the FOTO (FOurier Texture Ordination) proved relevant for forest biomass prediction in several tropical regions. It uses PCA and linear regression and, in this paper, we suggest applying classification methods such as k-NN (k-nearest neighbors), SVM (support vector machines) and Random Forests to texture descriptors extracted from images via Fourier spectra. Experiments have been carried out on simulated images produced by the software DART (Discrete Anisotropic Radiative Transfer) in reference to information (3D stand mockups) from forests of DRC (Democratic Republic of Congo), CAR (Central African Republic) and Congo. On this basis, we show that some classification techniques may yield a gain in prediction accuracy of 18 to 20%
Published: 2014

29. A model-view/controller approach to support visualization and online data analysis of Agent-based simulations

Author: Jean-Daniel Zucker, Arnaud Grignard, Alexis Drogoul, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: Agent-based model, Computer science, interaction, 02 engineering and technology, computer.software_genre, 03 medical and health sciences, Information visualization, Data visualization, Human–computer interaction, 0202 electrical engineering, electronic engineering, information engineering, complex systems, Reference model, visualization, 030304 developmental biology, online analysis, 0303 health sciences, business.industry, Multi-agent system, Reification (computer science), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, System dynamics, Visualization, IEEE, 020201 artificial intelligence & image processing, Data mining, business, computer, 3D
Abstract: International audience; Agent-based Modeling is playing a key role in an increasing number of approaches addressing modeling complex systems. Historically, such models were focused on describing the system modelled dynamics but not the interaction or visualization of the model itself. The new requirements for high-level realistic visualization and online analysis tools of ABM simulations raise key issues that are yet unsolved: how to visualize interaction between entities and more generally abstracting the key information from the system dynamics. Instead of ad-hoc existing approaches that require reification in the model, we propose an approach dedicated to visualize and discover emerging dynamics from the model. In this approach, the execution of the simulation and its representation is separated and building a visualization is like building a visualization model on top of the reference model. The techniques presented here have been implemented in an Agent-based simulation platform, Gama, and illustrate the new perspective on visualization in Agent-based Modeling.
Published: 2013

30. Online analysis and visualization of agent based models

Author: Arnaud Grignard, Alexis Drogoul, Jean-Daniel Zucker, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Murgante, B. (ed.), Misra, S. (ed.), Carlini, M. (ed.), Torre, C.M. (ed.), Nguyen, H.Q. (ed.), Taniar, D (ed.), Apduhan, B.O. (ed.), and Gervasi, O. (ed.)
Subjects: 0303 health sciences, Computer science, Ecology (disciplines), Complex system, Complexification, interaction, 02 engineering and technology, Agent Based Modeling, Data science, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Visualization, Online analysis, Modeling and simulation, 03 medical and health sciences, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, complex systems, visualization, 030304 developmental biology, online analysis, 3D
Abstract: International audience; Agent-based modeling is used to study many kind of complex systems in different fields such as biology, ecology, or sociology. Visualization of the execution of a such complex systems is crucial in the capacity to apprehend its dynamics. The ever increasing complexification of requirements asked by the modeller has highlighted the need for more powerful tools than the existing ones to represent, visualize and interact with a simulation and extract data online to discover imperceptible dynamics at different spatio-temporal scales. In this article we present our research in advanced visualization and online data analysis developed in GAMA an agent-based, spatially explicit, modeling and simulation platform.
Published: 2013

31. Dietary intervention impact on gut microbial gene richness

Author: Cotillard, Aurélie, Kennedy, Sean P., Kong, Ling Chun, Prifti, Edi, Pons, Nicolas, Le Chatelier, Emmanuelle, Almeida, Mathieu, Quinquis, Benoit, Levenez, Florence, Galleron, Nathalie, Gougis, Sophie, Rizkalla, Salwa, Batto, Jean-Michel, Renault, Pierre, consortium, ANR MicroObes, Doré, Joel, Zucker, Jean-Daniel, Clément, Karine, Ehrlich, Stanislav Dusko, Blottière, Hervé, Leclerc, Marion, Juste, Catherine, de Wouters, Tomas, Lepage, Patricia, Fouqueray, Charlene, Basdevant, Arnaud, Henegar, Cornelieu, Godard, Cindy, Fondacci, Marine, Rohia, Alili, Hajduch, Froogh, Weissenbach, Jean, Pelletier, Eric, Le Paslier, Denis, Gauchi, Jean-Pierre, Gibrat, Jean-François, Loux, Valentin, Carré, Wilfrid, Maguin, Emmanuelle, van de Guchte, Maarten, Jamet, Alexandre, Boumezbeur, Fouad, Layec, Séverine, U872 Centre de Recherche des Cordeliers, Nutriomique, Équipe 7, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH Ile-de-France), Institute of Cardiometabolism and Nutrition, Assistance Publique - Hôpitaux de Paris, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), MetaGenoPolis, Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de Recherche Agronomique, MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA )
Subjects: index, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, obesity, Zoology, 030209 endocrinology & metabolism, Overweight, Gut flora, resistance, 03 medical and health sciences, 0302 clinical medicine, Weight loss, medicine, insulin sensitivity, overweight, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, biology, business.industry, biology.organism_classification, medicine.disease, Obesity, 3. Good health, Biotechnology, Metagenomics, inflammation, Genomic Profile, mass, Enterotype, Species richness, medicine.symptom, business
Abstract: Complex gene-environment interactions are considered important in the development of obesity(1). The composition of the gut microbiota can determine the efficacy of energy harvest from food(2-4) and changes in dietary composition have been associated with changes in the composition of gut microbial populations(5,6). The capacity to explore microbiota composition was markedly improved by the development of metagenomic approaches(7,8), which have already allowed production of the first human gut microbial gene catalogue(9) and stratifying individuals by their gut genomic profile into different enterotypes(10), but the analyses were carried out mainly in nonintervention settings. To investigate the temporal relationships between food intake, gut microbiota and metabolic and inflammatory phenotypes, we conducted diet-induced weight-loss and weight-stabilization interventions in a study sample of 38 obese and 11 overweight individuals. Here we report that individuals with reduced microbial gene richness (40%) present more pronounced dys-metabolism and low-grade inflammation, as observed concomitantly in the accompanying paper(11). Dietary intervention improves low gene richness and clinical phenotypes, but seems to be less efficient for inflammation variables in individuals with lower gene richness. Low gene richness may therefore have predictive potential for the efficacy of intervention.
Published: 2013

32. Richness of human gut microbiome correlates with metabolic markers

Author: Le Chatelier, Emmanuelle, Nielsen, Trine, Qin, Junjie, Prifti, Edi, Hildebrand, Falk, Falony, Gwen, Almeida, Mathieu, Arumugam, Manimozhiyan, Batto, Jean-Michel, Kennedy, Sean, Leonard, Pierre, Li, Junhua, Burgdorf, Kristoffer, Grarup, Niels, Jørgensen, Torben, Brandslund, Ivan, Nielsen, Henrik Bjørn, Juncker, Agnieszka S., Bertalan, Marcelo, Levenez, Florence, Pons, Nicolas, Rasmussen, Simon, Sunagawa, Shinichi, Tap, Julien, Tims, Sebastian, Zoetendal, Erwin G., Brunak, Søren, Clément, Karine, Doré, Joël, Kleerebezem, Michiel, Kristiansen, Karsten, Renault, Pierre, Sicheritz-Ponten, Thomas, de Vos, Willem M., Zucker, Jean-Daniel, Raes, Jeroen, Hansen, Torben, Guedon, Eric, Delorme, Christine, Layec, Séverine, Khaci, Ghalia, van de Guchte, Maarten, Vandemeulebrouck, Gaetana, Jamet, Alexandre, Dervyn, Rozenn, Sanchez, Nicolas, Maguin, Emmanuelle, Haimet, Florence, Winogradski, Yohanan, Cultrone, Antonella, Leclerc, Marion, Juste, Catherine, Blottière, Hervé, Pelletier, Eric, LePaslier, Denis, Artiguenave, François, Bruls, Thomas, Weissenbach, Jean, Turner, Keith, Parkhill, Julian, Antolin, Maria, Manichanh, Chaysavanh, Casellas, Francesc, Boruel, Natalia, Varela, Encarna, Torrejon, Antonio, Guarner, Francisco, Denariaz, Gérard, Derrien, Muriel, van Hylckama Vlieg, Johan E. T., Veiga, Patrick, Oozeer, Raish, Knol, Jan, Rescigno, Maria, Brechot, Christian, M’Rini, Christine, Mérieux, Alexandre, Yamada, Takuji, Bork, Peer, Wang, Jun, Ehrlich, S. Dusko, Pedersen, Oluf, MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Structural Biology, Flanders Institute for Biotechnology, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), European Molecular Biology Laboratory, School of Bioscience and Biotechnology, Southern University of Science and Technology [Shenzhen] (SUSTech), Research Centre for Prevention and Health (RCPH), Department of Public Health [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Capital Region of Denmark, University of Copenhagen = Københavns Universitet (KU), Faculty of Medicine, Institute of Public Health, Aalborg University [Denmark] (AAU), Department of Clinical Biochemistry, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark (SDU), Center for Biological Sequence Analysis & Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark [Lyngby] (DTU), Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), U872 Centre de Recherche des Cordeliers, Nutriomique, Équipe 7, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH Ile-de-France), Institute of Cardiometabolism and Nutrition, Assistance Publique - Hôpitaux de Paris, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], Department of Bacteriology and Immunology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Faculty of Health Sciences, King Abdulaziz University, Center for Sequencing, Aarhus University [Aarhus], Hagedorn Research Institute, Faculty of Health, Département Microbiologie et Chaîne Alimentaire (MICA), European Community (HEALTH-F4-2007-201052) - Lundbeck Foundation Centre for Applied Medical Genomics in Personalized Disease Prediction, Prevention and Care (LuCamp) - ANR MicroObes, the Metagenopolis grant (ANR-11-DPBS-0001 ) - Region Ile de France (CODDIM) - Fondacoeur - Novo Nordisk Foundation, US 1367 MetaGénoPolis, Institut National de la Recherche Agronomique ( INRA ) -MetaGénoPolis ( MGP ) -Microbiologie et Chaîne Alimentaire ( MICA ), Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen ( KU ), Beijing Genomics Institute, Vrije Universiteit [Brussel] ( VUB ), South University of Science and Technology of China, Research Centre for Prevention and Health, Glostrup University Hospital, Aalborg University [Denmark] ( AAU ), UNIVERSITY OF SOUTHERN DENMARK, Technical University of Denmark [Lyngby] ( DTU ), Wageningen University and Research Centre [Wageningen] ( WUR ), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Department of Biology, Department of Bacteriology and Immunology, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA ), Department of Biology / Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Basic Metabolic Research / Institute of Biomedical Science, Département Microbiologie et Chaîne Alimentaire ( MICA ), Institut National de la Recherche Agronomique ( INRA ), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-MetaGénoPolis (MGP), Vrije Universiteit [Brussels] (VUB), Wageningen University and Research Centre [Wageningen] (WUR), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Southern University of Science and Technology (SUSTech), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Capital Region of Denmark, University of Copenhagen = Københavns Universitet (UCPH), Vejle Hospital [Danemark], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: Male, [SDV]Life Sciences [q-bio], body-mass index, Overweight, Weight Gain, Body Mass Index, 0302 clinical medicine, Microbiologie, insulin resistance, Phylogeny, 2. Zero hunger, 0303 health sciences, education.field_of_study, adiposity, Multidisciplinary, reared apart, Ecology, twins, 3. Good health, Europe, 030220 oncology & carcinogenesis, Enterotype, Biological Markers, Female, medicine.symptom, weight-loss, Adult, diet-induced obesity, Population, European Continental Ancestry Group, Zoology, body mass index, wide association, Biology, Microbiology, White People, insulin-resistance, 03 medical and health sciences, Thinness, diet induced obesity, Weight Loss, medicine, Humans, Microbiome, Host-Microbe Interactomics, Obesity, education, 030304 developmental biology, VLAG, Dyslipidemias, disease, Bacteria, [ SDV ] Life Sciences [q-bio], medicine.disease, Diet, Gastrointestinal Tract, Metagenomics, Genes, Bacterial, inflammation, Case-Control Studies, WIAS, Metagenome, Species richness, Insulin Resistance, weight loss, Energy Metabolism, Weight gain, Biomarkers
Abstract: We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previously unknown bacterial species at different proportions; individuals with a low bacterial richness (23% of the population) are characterized by more marked overall adiposity, insulin resistance and dyslipidaemia and a more pronounced inflammatory phenotype when compared with high bacterial richness individuals. The obese individuals among the lower bacterial richness group also gain more weight over time. Only a few bacterial species are sufficient to distinguish between individuals with high and low bacterial richness, and even between lean and obese participants. Our classifications based on variation in the gut microbiome identify subsets of individuals in the general white adult population who may be at increased risk of progressing to adiposity-associated co-morbidities.
Published: 2013

33. Can Human Movements Explain Heterogeneous Propagation of Dengue Fever in Cambodia?

Author: Teurlai, Magali, Huy, Rekol, Cazelles, Bernard, Duboz, Raphaël, Baehr, Christophe, Vong, Sirenda, Gubler, Duane J., Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Nouvelle-Calédonie, Réseau International des Instituts Pasteur (RIIP), National Center for Malaria Control, Parasitology and Entomology, Ministry of Health of Cambodgia, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Asian Institute of Technology [Pathumthani] (AIT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut Pasteur du Cambodge, Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Groupe d'étude de l'atmosphère météorologique (CNRM-GAME), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: Male, Pediatrics, Time Factors, Epidemiology, L73 - Maladies des animaux, Dengue Fever, Disease Outbreaks, Dengue fever, Dengue, 0302 clinical medicine, Mekong river, Medicine, 030212 general & internal medicine, Child, Socioeconomics, Migration, Epidemiological Methods, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, Transients and Migrants, lcsh:Public aspects of medicine, Statistics, 1. No poverty, Spatial epidemiology, Middle Aged, E51 - Population rurale, 3. Good health, Spatial heterogeneity, Infectious Diseases, Child, Preschool, Scale (social sciences), Female, Topography, Medical, Public Health, Cambodia, Genre humain, Research Article, Neglected Tropical Diseases, Disease Ecology, Adult, medicine.medical_specialty, lcsh:Arctic medicine. Tropical medicine, Infectious Disease Control, Adolescent, lcsh:RC955-962, 030231 tropical medicine, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Biostatistics, Infectious Disease Epidemiology, Young Adult, 03 medical and health sciences, Humans, Transmission des maladies, Aged, Geographic area, business.industry, Flavivirus, Public health, Infant, Newborn, Public Health, Environmental and Occupational Health, Infant, lcsh:RA1-1270, medicine.disease, Rural area, business, Mathematics
Abstract: Background Determining the factors underlying the long-range spatial spread of infectious diseases is a key issue regarding their control. Dengue is the most important arboviral disease worldwide and a major public health problem in tropical areas. However the determinants shaping its dynamics at a national scale remain poorly understood. Here we describe the spatial-temporal pattern of propagation of annual epidemics in Cambodia and discuss the role that human movements play in the observed pattern. Methods and Findings We used wavelet phase analysis to analyse time-series data of 105,598 hospitalized cases reported between 2002 and 2008 in the 135 (/180) most populous districts in Cambodia. We reveal spatial heterogeneity in the propagation of the annual epidemic. Each year, epidemics are highly synchronous over a large geographic area along the busiest national road of the country whereas travelling waves emanate from a few rural areas and move slowly along the Mekong River at a speed of ∼11 km per week (95% confidence interval 3–18 km per week) towards the capital, Phnom Penh. Conclusions We suggest human movements – using roads as a surrogate – play a major role in the spread of dengue fever at a national scale. These findings constitute a new starting point in the understanding of the processes driving dengue spread., Author Summary Dengue fever is a mosquito borne viral infection. It has become a major public health problem during the past decades: only 9 countries were affected in the 1970s; dengue is now endemic in more than 100 countries. In the absence of any vaccine or specific treatment, control of dengue fever is currently limited to vector control measures, which are difficult to implement and hardly sustainable, especially in low income countries. To implement efficient control measures, it is crucial to understand the dynamics of propagation of the disease and the key factors underlying these dynamics. In this study, data from 8-year national surveillance in Cambodia were analysed. Dengue fever follows a recurrent pattern of propagation at the national scale. The annual epidemics originate from a few rural areas identified in this work. This study also suggests additional evidence for the role of human movement in the spatial dynamics of the disease, which should be accounted for in control measures. These results differ from the current knowledge about dengue dynamics and are therefore of interest for future research.
Published: 2012

34. Principles and practice of multi-agent systems : 13th International Conference, PRIMA 2010 : Kolkata, India, November 12-15, 2010 : revised selected papers

Author: Jean-Daniel Zucker, Tuong-Vinh Ho, Duc-An Vo, Alexis Drogoul, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Desai, N. (ed.), Liu, A. (ed.), Winikoff, M. (ed.), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: [INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Agent-based model, Theoretical computer science, Computer science, abstraction, 02 engineering and technology, 03 medical and health sciences, 0302 clinical medicine, agent-based modelling language, GAMA platform, 0202 electrical engineering, electronic engineering, information engineering, emergence, sort, Abstraction, Representation (mathematics), Simple (philosophy), business.industry, ACM, simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Visualization, emerging structure, 030220 oncology & carcinogenesis, Obstacle, Boids, 020201 artificial intelligence & image processing, Artificial intelligence, GAML modelling language, business
Abstract: International audience; All modellers have come across, one day, one of these popular toy agent-based models (ABMs), like "Ants", for instance, which depicts the appearance of pheromone trails built by simulated ants. They are simple, but representative of the way "real", more complex, ABMs are designed: in addition to explicitly describe the individual entities used to represent the system, modellers make implicit references to abstractions corresponding to the emerging structures they are tracking in the simulations. Yet, these abstractions are not represented in the models themselves as first-class entities: they are either hidden in ex-post computations or only part of visualization tasks, as if an explicit representation could somehow damage the processes at work in their emergence. This clearly constitutes an obstacle to the development of multi-level models, where emergence is likely to occur at different levels of abstraction of the system: if some of these levels are not represented in the models, the emergence of higher-level structures is not likely to be observed. This paper describes a modelling language that allows a modeller to represent and specify emerging structures in agent-based models. Firstly, to ease the description, we present these structures and their properties in four toy ABMs: Schelling, Boids, Collective Sort and Ants. Then we define the operations that are needed to represent and specify them without sacrificing the properties of the original model. An implementation of these operations in the GAML modelling language (part of the GAMA agent-based platform) is then presented. Finally, two simulations of the Boids model are used to illustrate the expressivity of this language and the multiple advantages it brings in terms of analysis, visualization and modeling of multi-level ABMs.
Published: 2012

35. Basic reproduction ratio for a fishery model in a patchy environment

Author: Gauthier Sallet, Ali Moussaoui, Pierre Auger, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Aboubekr Belkaid - University of Belkaïd Abou Bekr [Tlemcen], Tools and models of nonlinear control theory for epidemiology and immunology (MASAIE), Laboratoire de Mathématiques et Applications de Metz (LMAM), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: 0106 biological sciences, Scale (ratio), Population dynamics, Reproduction (economics), variables, Fishing, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Fisheries, Fish stock, 01 natural sciences, Stability (probability), General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Stock-effort model, Animals, 14. Life underwater, Residence time (statistics), 030304 developmental biology, General Environmental Science, 0303 health sciences, 010604 marine biology & hydrobiology, Applied Mathematics, Reproduction, Sustainable fishery, Aggregation of variables, General Medicine, Models, Theoretical, Time scales, Fishery, Philosophy, Aggregation of, Habitat, Environmental science, General Agricultural and Biological Sciences, Stability
Abstract: We present a dynamical model of a multi-site fishery. The fish stock is located on a discrete set of fish habitats where it is catched by the fishing fleet. We assume that fishes remain on fishing habitats while the fishing vessels can move at a fast time scale to visit the different fishing sites. We use the existence of two time scales to reduce the dimension of the model : we build an aggregated model considering the habitat fish densities and the total fishing effort. We explore a regulation procedure, which imposes an average residence time in patches. Several equilibria exist, a Fishery Free Equilibria (FFEs) as well as a Sustainable Fishery Equilibria (SFEs). We show that the dynamics depends on a threshold which is similar to a basic reproduction ratio for the fishery. When the basic reproduction ratio is less or equal to 1, one of the FFEs is globally asymptotically stable (GAS), otherwise one of the SFEs is GAS. Acta Biotheor, Vol 60, N° 1-2 (2012),pp.167-88,DOI: 10.1007/s10441-012-9155-3.
Published: 2011

36. Stability of differential susceptibility and infectivity epidemic models

Author: Abderrahman Iggidr, A. A. Fall, Gauthier Sallet, Bernard K. Bonzi, Laboratoire d'Analyse Mathématique des Equations (LAME), Université Joseph Ki-Zerbo [Ouagadougou] (UJZK), Tools and models of nonlinear control theory for epidemiology and immunology (MASAIE), Laboratoire de Mathématiques et Applications de Metz (LMAM), Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Université Paul Verlaine - Metz (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Élie Cartan de Lorraine (IECL), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse Numérique et Informatique [Sénégal] (LANI), Université Gaston Berger de Saint-Louis Sénégal (UGB), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Reproductive number, Pure mathematics, Hepatitis B virus, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Stability (learning theory), Basic Reproduction Number, Disease free, Global stability, Biology, 01 natural sciences, Article, 03 medical and health sciences, Basic Reproduction Ratio, Hepatitis B, Chronic, Exponential stability, HBV, Humans, Uniqueness, 0101 mathematics, 030304 developmental biology, Lyapunov methods, Infectivity, 0303 health sciences, Applied Mathematics, Models, Immunological, Agricultural and Biological Sciences (miscellaneous), Differential susceptibility models, 3. Good health, 010101 applied mathematics, Modeling and Simulation, AMS subject classification : 34A34, 34D23, 34D40, 92D30, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Disease Susceptibility, Nonlinear dynamical systems, Mathematical economics, Basic reproduction number, Differential (mathematics)
Abstract: International audience; We introduce classes of differential susceptibility and infectivity epidemic models. These models address the problem of flows between the different susceptible, infectious and infected compartments and differential death rates as well. We prove the global stability of the disease free equilibrium when the basic reproduction ratio [Formula: see text] and the existence and uniqueness of an endemic equilibrium when [Formula: see text] . We also prove the global asymptotic stability of the endemic equilibrium for a differential susceptibility and staged progression infectivity model, when [Formula: see text] . Our results encompass and generalize those of Hyman and Li (J Math Biol 50:626-644, 2005; Math Biosci Eng 3:89-100, 2006).
Published: 2009

37. Atmospheric Moisture Variability and Transmission of Hemorrhagic Fever with Renal Syndrome in Changsha City, Mainland China, 1991–2010

Author: Hong Xiao, Xiujun Li, Huaiyu Tian, Xiao-ling Lin, Bernard Cazelles, Hai-Ning Liu, Jian-Xin Qin, Xixing Zhang, Lidong Gao, Shilu Tong, Hunan University [Changsha] (HNU), Laboratoire Ecologie et évolution, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Shandong University, Queensland University of Technology [Brisbane] (QUT), Hunan provincial center for disease control and prevention, Changsha Municipal Center for Disease Control and Prevention, École normale supérieure - Paris (ENS-PSL), and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)
Subjects: Mainland China, China, Veterinary medicine, lcsh:Arctic medicine. Tropical medicine, Epidemiology, lcsh:RC955-962, Environmental Epidemiology, law.invention, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, Zoonoses, Humans, Medicine, Research article, 030212 general & internal medicine, 030304 developmental biology, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, Disease surveillance, Models, Statistical, Atmospheric moisture, business.industry, lcsh:Public aspects of medicine, Public Health, Environmental and Occupational Health, virus diseases, Humidity, lcsh:RA1-1270, Virology, 3. Good health, Infectious Diseases, Transmission (mechanics), El Niño Southern Oscillation, 13. Climate action, Hemorrhagic Fever with Renal Syndrome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Public Health, Infectious Disease Modeling, business, Environmental Health, Research Article, Hantavirus
Abstract: Background The transmission of hemorrhagic fever with renal syndrome (HFRS) is influenced by environmental determinants. This study aimed to explore the association between atmospheric moisture variability and the transmission of hemorrhagic fever with renal syndrome (HFRS) for the period of 1991–2010 in Changsha, China. Methods and Findings Wavelet analyses were performed by using monthly reported time series data of HFRS cases to detect and quantify the periodicity of HFRS. A generalized linear model with a Poisson distribution and a log link model were used to quantify the relationship between climate and HFRS cases, highlighting the importance of moisture conditions. There was a continuous annual oscillation mode and multi-annual cycle around 3–4 years from 1994 to 1999. There was a significant association of HFRS incidence with moisture conditions and the Multivariate El Niño–Southern Oscillation Index (MEI). Particularly, atmospheric moisture has a significant effect on the propagation of HFRS; annual incidence of HFRS was positively correlated with annual precipitation and annual mean absolute humidity. Conclusions The final model had good accuracy in forecasting the occurrence of HFRS and moisture condition can be used in disease surveillance and risk management to provide early warning of potential epidemics of this disease., Author Summary Hemorrhagic fever with renal syndrome (HFRS), a rodentborne disease caused by Hantaviruses, is characterized by fever, haemorrhage, headache, back pain, abdominal pain, and acute kidney injury. At present, it is endemic in all 31 provinces, autonomous regions, and metropolitan areas in mainland China where human cases account for 90% of the total global cases. Infection rates and population dynamics of hosts are thought to be influenced by climatic factors, especially humidity. Some studies have found that hantaviruses are limited in their spread to high-humidity environments for extended ex vivo stability. Here we provide the evidence that HFRS incidence was strongly associated with moisture conditions, including seasonal variation and annual situation, in Changsha, mainland China, 1991–2010. The results most likely indicate that moisture not only influences growth of food sources that determine rodent population size, thereby affecting the HFRS transmission, but also directly influences rodent activity and hantavirus infectivity. These findings offer insights in understanding possible causes of HFRS transmission, and can be used in disease surveillance and risk management to provide early warning of potential epidemics of this disease.
Published: 2013

38. PCR assay for chromosome 1p deletion in small neuroblastoma samples

Author: Olivier Delattre, Marline Peter, Elise Sonsino, Jean Michon, Yusuke Nakamura, Sylvia Neuenschwander, Gilles Vergnaud, Gilles Thomas, Jean-Michel Zucker, Philippe Vielh, Div. of Hematology/Oncology, Northwestern University, Laboratoire de recherche translationnelle, Direction de la recherche [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Vergnaud, Gilles, Institut Gustave Roussy ( IGR ) -Institut Gustave Roussy ( IGR ), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), École Nationale Supérieure de Techniques Avancées ( Univ. Paris-Saclay, ENSTA ParisTech ), Unité de génétique et biologie des cancers ( U830 ), and Université Paris Descartes - Paris 5 ( UPD5 ) -Institut Curie-Institut National de la Santé et de la Recherche Médicale ( INSERM )
Subjects: Cancer Research, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biology, Polymerase Chain Reaction, law.invention, Loss of heterozygosity, 03 medical and health sciences, chemistry.chemical_compound, Neuroblastoma, 0302 clinical medicine, law, medicine, Humans, Polymerase chain reaction, 030304 developmental biology, 0303 health sciences, Base Sequence, [ SDV ] Life Sciences [q-bio], Chromosome, DNA, Neoplasm, medicine.disease, Primary tumor, Molecular biology, 3. Good health, [SDV] Life Sciences [q-bio], Variable number tandem repeat, Oncology, chemistry, Chromosomes, Human, Pair 1, 030220 oncology & carcinogenesis, Agarose gel electrophoresis, Chromosome Deletion, Ethidium bromide
Abstract: International audience; Deletion of the short arm of chromosome 1 is among the most recurrent cytogenetic alterations found in neuroblastoma and has been associated with short survival. However, this prognostic information, which relies on time-consuming techniques, is not yet routinely exploited. In order to set up a reliable and simple routine test to determine 1p deletion in neuroblastoma, we have used the polymerase chain reaction to genotype neuroblastoma DNA at 2 loci containing a variable number of tandem repeats and located on the distal part of the short arm of chromosome 1. Agarose gel electrophoresis and ethidium bromide staining of the amplification products enable a simple determination of constitutional and tumor genotypes at these loci to be made. A total of 37 samples from 29 patients were studied with this technique. Loss of heterozygosity (LOH) could be identified in 8 cases. In each case the results obtained were in agreement with those achieved by the Southern procedure. This technique will be of particular interest in the pretherapeutic analysis of 1p deletions in small tumor samples obtained by fine-needle aspirates of the primary tumor. It should also enable retrospective studies from paraffin-embedded tumor fragments to be made and provide information for the analysis of tumor heterogeneity in neuroblastoma and in other tumors with 1p deletions.
Published: 1992

39. Natural resistance to cancers: a Darwinian hypothesis to explain Peto’s paradox

Author: Aleah F. Caulin, Michael E. Hochberg, Robert A. Gatenby, Frédéric Thomas, Carlo C. Maley, Dorothée Missé, Benjamin Roche, Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Santa Fe Institute, University of Pennsylvania, Helen Diller Family Comprehensive Cancer Center [San Francisco], University of California [San Francisco] (UC San Francisco), University of California (UC), H. Lee Moffitt Cancer Center and Research Institute, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, University of Pennsylvania [Philadelphia], University of California [San Francisco] (UCSF), University of California, Centre de Recherches Ecologiques et Evolutives sur le Cancer (CREEC), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pathology, medicine.medical_specialty, Cancer Research, Debate, media_common.quotation_subject, Wildlife, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, lcsh:RC254-282, Peto's paradox, 03 medical and health sciences, 0302 clinical medicine, Neoplasms, medicine, Genetics, Animals, Humans, Natural ecosystem, Selection, Genetic, Cancer prevalence, 030304 developmental biology, media_common, 0303 health sciences, Natural selection, Longevity, Models, Theoretical, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Biological Evolution, Immunity, Innate, Natural resistance, Cell Transformation, Neoplastic, Oncology, Evolutionary biology, 030220 oncology & carcinogenesis, Darwinism
Abstract: Background Peto's paradox stipulates that there is no association between body mass (a surrogate of number of cells and longevity) and cancer prevalence in wildlife species. Resolving this paradox is a very promising research direction to understand mechanisms of cancer resistance. As of present, research has been focused on the consequences of these evolutionary pressures rather than of their causes. Discussion Here, we argue that evolution through natural selection may have shaped mechanisms of cancer resistance in wildlife species and that this can result in a threshold in body mass above which oncogenic and tumor suppressive mechanisms should be increasingly purified and positively selected, respectively. Summary We conclude that assessing wildlife species in their natural ecosystems, especially through theoretical modeling, is the most promising way to understand how evolutionary processes can favor one or the other pathway. This will provide important insights into mechanisms of cancer resistance.
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40. An ecological and digital epidemiology analysis on the role of human behavior on the 2014 Chikungunya outbreak in Martinique

Author: Thomas Sochacki, A. Blateau, Renélise Pelagie-Moutenda, Marcel Salathé, Benjamin Roche, Didier Fontenille, Manuel Etienne, André Yébakima, Bernard Cazelles, Frédéric Simard, Martine Ledrans, Lucas Léger, Béatrice Gaillard, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de démoustication, Conseil Général/Direction de la santé et du développement social de la Martinique, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CIRE Antilles-Guyane - Fort de France, Institut de Veille Sanitaire (INVS), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Ecole Polytechnique Fédérale de Lausanne (EPFL), HAL UPMC, Gestionnaire, Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Sorbonne Université (SU)-Universtié Yaoundé 1 [Cameroun]-Université Cadi Ayyad [Marrakech] (UCA)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Institut de Recherche pour le Développement (IRD [France-Nord]), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: medicine.medical_specialty, Operations research, Ecology (disciplines), Science, 030231 tropical medicine, Biology, medicine.disease_cause, Models, Biological, Article, law.invention, Disease Outbreaks, 03 medical and health sciences, 0302 clinical medicine, Spatio-Temporal Analysis, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, Martinique, 030212 general & internal medicine, Chikungunya, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Behavior, Multidisciplinary, Social network, business.industry, Public health, Environmental resource management, Outbreak, Digital epidemiology, 3. Good health, Transmission (mechanics), [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, Chikungunya Fever, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: Understanding the spatio-temporal dynamics of endemic infections is of critical importance for a deeper understanding of pathogen transmission, and for the design of more efficient public health strategies. However, very few studies in this domain have focused on emerging infections, generating a gap of knowledge that hampers epidemiological response planning. Here, we analyze the case of a Chikungunya outbreak that occurred in Martinique in 2014. Using time series estimates from a network of sentinel practitioners covering the entire island, we first analyze the spatio-temporal dynamics and show that the largest city has served as the epicenter of this epidemic. We further show that the epidemic spread from there through two different propagation waves moving northwards and southwards, probably by individuals moving along the road network. We then develop a mathematical model to explore the drivers of the temporal dynamics of this mosquito-borne virus. Finally, we show that human behavior, inferred by a textual analysis of messages published on the social network Twitter, is required to explain the epidemiological dynamics over time. Overall, our results suggest that human behavior has been a key component of the outbreak propagation, and we argue that such results can lead to more efficient public health strategies specifically targeting the propagation process.

41. Interactions between immune challenges and cancer cells proliferation: timing does matter!

Author: Gabriele Sorci, Benjamin Roche, Youssef Bourfia, Hassan Hbid, Camille Jacqueline, Frédéric Thomas, Centre de Recherches Ecologiques et Evolutives sur le Cancer ( CREEC ), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle ( MIVEGEC ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Laboratoire Jacques-Louis Lions ( LJLL ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Mathématiques et Dynamique de Populations, Université Cadi Ayyad [Marrakech], International Center for Mathematical and Computational Modeling of Complex Systems, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 (Cameroun)-University Cadi Ayyad ( UCA ) -UMI IRD, Biogéosciences [Dijon] ( BGS ), AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Fundings provided by the EVOCAN project funded by the Agence Nationale de la Recherche, and the Centre National de la Recherche Scientifique., Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Laboratoire Jacques-Louis Lions (LJLL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Cadi Ayyad [Marrakech] (UCA), Université Pierre et Marie Curie - Paris 6 (UPMC)-UMI IRD-Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique, Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Biogéosciences [UMR 6282] (BGS), and Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, MALADIE, Health, Toxicology and Mutagenesis, medicine.medical_treatment, Medicine (miscellaneous), [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, infectious diseases, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, 0302 clinical medicine, Immune system, INFECTION, Epidemiology of cancer, medicine, cancer, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, Original Research Article, Ecology, Evolution, Behavior and Systematics, IMMUNITE, MODELE MATHEMATIQUE, immunosenescence, immunosuppression, Cancer, Immunosuppression, Immunosenescence, PREVENTION SANITAIRE, biochemical phenomena, metabolism, and nutrition, medicine.disease, CANCER, 3. Good health, 030104 developmental biology, Cancer incidence, 13. Climate action, 030220 oncology & carcinogenesis, Immunology, Cancer cell, [SDV.IMM]Life Sciences [q-bio]/Immunology, Cancer risk, AGENT PATHOGENE
Abstract: Using first a theoretical framework, we show that repeated short immune challenges could impact the accumulation of cancerous cells through continuous perturbation of immune system efficiency. We discuss for a new indirect role for infectious disease in cancer progression., The immune system is a key component of malignant cell control and it is also involved in the elimination of pathogens that threaten the host. Despite our body is permanently exposed to a myriad of pathogens, the interference of such infections with the immune responses against cancer has been poorly investigated. Through a mathematical model, we show that the frequency, the duration and the action (positive or negative) of immune challenges may significantly impact tumor proliferation. First, we observe that a long immunosuppressive challenge increases accumulation of cancerous cells only if it occurs 14 years after the beginning of immunosenescence. However, short immune challenges result in an even greater accumulation of cancerous cells for the same total duration of immunosuppression. Finally, we show that short challenges of immune activation could lead to a slightly decrease in cancerous cell accumulation compared to a long one. Our results predict that frequent and acute immune challenges could have a different and in some extent higher impact on cancer risk than persistent ones even they have been much less studied in cancer epidemiology. These results are discussed regarding the existing empirical evidences and we suggest potential novel indirect role of infectious diseases on cancer incidence which should be investigated to improve prevention strategies against cancer.

42. Can Peto’s paradox be used as the null hypothesis to identify the role of evolution in natural resistance to cancer? A critical review

Author: Beata Ujvari, François Renaud, Benjamin Roche, Hugo Ducasse, François Bonhomme, Frédéric Thomas, Eric Solary, Marion Vittecoq, Florence Bernex, Nelly Pirot, Audrey Arnal, Dorothée Missé, Centre de Recherches Ecologiques et Evolutives sur le Cancer (MIVEGEC-CREEC), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Deakin University, Burwood, Australia, Deakin University [Burwood], Hématopoïèse normale et pathologique, Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche de la Tour du Valat, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), HAL UPMC, Gestionnaire, Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Génétique et évolution des maladies infectieuses (GEMI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Cancer Research, Debate, Carcinogenesis, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Peto's paradox, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Species Specificity, Neoplasms, medicine, Econometrics, Genetics, Animals, Humans, Empirical evidence, Cancer prevalence, 030304 developmental biology, 0303 health sciences, Natural selection, Cancer, medicine.disease, Biological Evolution, Immunity, Innate, 3. Good health, Natural resistance, Cell Transformation, Neoplastic, Oncology, 030220 oncology & carcinogenesis, Identification (biology), Null hypothesis
Abstract: International audience; Background: Carcinogenesis affects not only humans but almost all metazoan species. Understanding the rules driving the occurrence of cancers in the wild is currently expected to provide crucial insights into identifying how some species may have evolved efficient cancer resistance mechanisms. Recently the absence of correlation across species between cancer prevalence and body size (coined as Peto's paradox) has attracted a lot of attention. Indeed, the disparity between this null hypothesis, where every cell is assumed to have an identical probability to undergo malignant transformation, and empirical observations is particularly important to understand, due to the fact that it could facilitate the identification of animal species that are more resistant to carcinogenesis than expected. Moreover it would open up ways to identify the selective pressures that may be involved in cancer resistance. However, Peto's paradox relies on several questionable assumptions, complicating the interpretation of the divergence between expected and observed cancer incidences. Discussions: Here we review and challenge the different hypotheses on which this paradox relies on with the aim of identifying how this null hypothesis could be better estimated in order to provide a standard protocol to study the deviation between theoretical/theoretically predicted and observed cancer incidence. We show that due to the disproportion and restricted nature of available data on animal cancers, applying Peto's hypotheses at species level could result in erroneous conclusions, and actually assume the existence of a paradox. Instead of using species level comparisons, we propose an organ level approach to be a more accurate test of Peto's assumptions. Summary: The accuracy of Peto's paradox assumptions are rarely valid and/or quantifiable, suggesting the need to reconsider the use of Peto's paradox as a null hypothesis in identifying the influence of natural selection on cancer resistance mechanisms.
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