Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
OBJECTIVES: To investigate whether the glutathione S-transferase polymorphisms GSTM1 and/or GSTT1 contribute to prostate cancer risk in a Caribbean population of African descent in Guadeloupe. METHODS: We performed a hospital-based case-control study with 134 prostate cancer patients and 134 cancer-free, age-matched control subjects. Epidemiologic data were collected using a standard questionnaire. Logistic regression was used to estimate odds ratios (ORs) and compute confidence intervals (CIs). Genotypes were determined by multiplex polymerase chain reaction. RESULTS: The frequency of the GSTM1-positive genotype was 81% in patients and 73% in control subjects, with an adjusted OR of 1.4 (95% CI 0.7 to 2.5). The frequency of the GSTT1-positive genotype was 78% in patients and 63% in control subjects, with an adjusted OR of 2.6 (95% CI 1.4 to 4.9). CONCLUSIONS: A functional GSTT1 polymorphism may be associated with prostate cancer susceptibility in a Caribbean population of African descent.
ISSN: 0090-4295

hal-00688449
https://hal.archives-ouvertes.fr/hal-00688449
DOI : 10.1016/j.urology.2007.02.039
PUBMED : 17572208

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
This article is concerned with a generalization of the hybrid steepest descent method from variational inequalities to the multivalued case. This will be reached by replacing the multivalued operator by its Yosida approximate, which is always Lipschitz continuous. It is worth mentioning that the hybrid steepest descent method is an algorithmic solution to variational inequality problems over the fixed point set of certain nonexpansive mappings and has remarkable applicability to the constrained nonlinear inverse problems like image recovery and MIMO communication systems
ISSN: 0163-0563

hal-00776641
https://hal.univ-antilles.fr/hal-00776641
DOI : 10.1080/01630563.2011.619676

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A variety of atypical plume-like structures and focused upwellings that are not rooted in the lower mantle have recently been discussed, and seismological imaging has shown ubiquitous small-scale convection in the uppermost mantle in regions such as the Mediterranean region, the western US, and around the western Pacific. We argue that the three-dimensional return flow and slab fragmentation associated with complex oceanic subduction trajectories within the upper mantle can generate focused upwellings and that these may play a significant role in regional tectonics. The testable surface expressions of this process are the outside-arc alkaline volcanism, topographic swell, and low-velocity seismic anomalies associated with partial melt. Using three-dimensional, simplified numerical subduction models, we show that focused upwellings can be generated both ahead of the slab in the back-arc region (though -five times further inward from the trench than arc-volcanism) and around the lateral edges of the slab (in the order of 100 km away from slab edges). Vertical mass transport, and by inference the associated decompression melting, in these regions appears strongly correlated with the interplay between relative trench motion and subduction velocities. The upward flux of material from the depths is expected to be most pronounced during the first phase of slab descent into the upper mantle or during slab fragmentation. We discuss representative case histories from the Pacific and the Mediterranean where we find possible evidence for such slab-related volcanism.
ISSN: 0012-821X

hal-00553075
https://hal.archives-ouvertes.fr/hal-00553075
DOI : 10.1016/j.epsl.2010.08.012

Résumé : Aux Antilles, la faible fréquence des coronaropathies pourrait être liée à des facteurs génétiques, ethniques et/ou une distribution spécifique des facteurs de risque cardio-vasculaire (FDRCV). Les propriétés l'ANP (Atrial Natriuretic Peptide) et l'influence de certains polymorphismes de son gène, fréquents dans les populations d'ascendance Africaine pourraient également être en cause. L'analyse des dossiers de 638 patients coronariens consécutifs a mis en évidence une forte prévalence de l'hypertension artérielle et du diabète dans cette population et révélé des différences significatives dans la prévalence des FDRCV entre Afro-Caribéens (AC), Caucasiens et descendants de migrants Indiens. L'analyse angiographique de 420 patients AC a révélé que le diabète était le FDRCV le plus fortement lié à la sévérité des lésions coronaires alors l'obésité apparaissait comme un facteur protecteur. La transfection in vitro, de cellules musculaires lisses artérielles par une construction adénovirale porteuse du gène de l'ANP a entrainé une inhibition de la prolifération et de la migration cellulaire de 31 % et 25% respectivement. In vivo, cet effet s'est traduit par une réduction de 25% de la formation néotimale et de 28% du rapport intima/média dans un modèle d'hyperplasie de carotide de rat. Dans étude transversale incluant 210 sujets diabétiques AC nous avons mis en évidence une association entre le polymorphisme rs5065 (22381>C) du gène de l'ANP et l'existence d'une coronaropatbie. Dans cette étude, l'odds ratio de la présence d'une coronaropathie chez les porteurs de l'allèle mineur de cette mutation (TC/CC) était de 0,50 (0,26- 0,96; P = 0,038).
In Guadeloupe and Martinique, the low frequency ofcoronary artery disease (CAD) could be related to genetic or ethniefactors and/or specifie distribution ofcardiovascular risk factors (CRFs). Atrial Natriuretic Peptide (ANP) properties and influence of sorne of ANP gene polymorphism that are frequent in populations of African descent could also be involved in CAD occurrence. We retrospectively studied 638 consecutive patients with documented CAO and found a high prevalence of hypertension and diabetes in this population. This study also demonstrated significant differences in the prevalence of CRFs between Afro-Caribbean (AC), Caucasians and Indians migrants. The angiographie analysis of420 patients revealed that in AC, diabetes emerged as the strongest CFR related to the severity ofcoronary lesions while obesity appeared as a protective factor. After transfection by an adenoviral construct carrying the ANP gene, vascular smooth muscle cell proliferation stimulated by 10% fetal calf serum was reduced by 31% and migration by 25%. In vivo, in rat carotid artery model ofvascular injury, neointima formation and intima/media ratio was reduced by 25% and 28% respectively. In a cross-sectional study inc1uding 210 AC diabetics we found an association between rs5065 (22381> C) polymorpbism and the presence of coronary artery disease suggesting that the minor allele could have a protective effect against CAD. The odds ratio for the presence ofCAD in carriers ofthe minor allele ofthis mutation (TC / CC) was 0.50 (0.26-0.96, P = 0.038).

http://www.theses.fr/2012AGUY0553/document

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
Tailoring nearest neighbors algorithms to boosting is an important problem. Recent papers study an approach, UNN, which provably minimizes particular convex surrogates under weak assumptions. However, numerical issues make it necessary to experimentally tweak parts of the UNN algorithm, at the possible expense of the algorithm's convergence and performance. In this paper, we propose a lightweight alternative algorithm optimizing proper scoring rules from a very broad set, and establish formal convergence rates under the boosting framework that surprisingly compete with those known for UNN. It is an adaptive Newton-Raphson algorithm, which belongs to the same lineage as the popular Gentle Adaboost. To the best of our knowledge, no such boosting-compliant convergence rates were previously known for these algorithms. We provide experiments on a dozen domains, including the challenging Caltech and SUN computer vision databases. They display that GNNB significantly outperforms UNN, both in terms of convergence rate and quality of the solution obtained, and GNNB provides a simple and efficient contender to techniques that can be used on very large domains, like stochastic gradient descent -- for which little is known to date. Experiments include a divide-and-conquer improvement of GNNB which exploits the link with proper scoring rules optimization.
ISSN: 0162-8828

hal-00958809
https://hal.archives-ouvertes.fr/hal-00958809
https://hal.archives-ouvertes.fr/hal-00958809/document
https://hal.archives-ouvertes.fr/hal-00958809/file/PAMI.pdf
DOI : 10.1109/TPAMI.2014.2307877

Résumé : Nous traiterons successivement des circonstances de l'émergence du Panama depuis la période précolombienne, les premières expéditions espagnoles à la recherche d'un détroit vers les Indes, de l'indépendance du Panama. Dans la première partie, nous traiteront de l'Isthme du Panama comme terre de passage et de son Canal de1880 à 1914, du rêve séculaire à la réalité où, successivement, nous étudierons son destin français, sa position entre intérêts français et aspirations américaines. Les États-Unis et le Panama nous conduiront à traiter de l'installation des Américains, la construction du Canal (1904-1914) ; les traités Carter-Torrijos, entre compromis et ambiguïtés. La deuxième partie traitera des stratégies de développement du Panama; l'importance des facteurs socioéconomiques et la dynamique des structures sociopolitiques seront mises en exergue. L'intégration des Antillais de Guadeloupe et de Martinique dans le cercle communautaire panaméen de 1914 à nos jours. Àcet égard, nous traiterons des apports de la culture antillaise dans la représentation panaméenne, un brassage culturel. En troisième lieu, leur contribution à l'essor de la nation. Il s'agira ici d'étudier les arts et la culture, la musique et les danses, la littérature et la linguistique de même que les revendications culturelles des minorités ethniques. Enfin, nous orienterons nos recherches sur la question de l'unité panaméenne à l'aube du Ille millénaire, l'organisation des diverses communautés et l'installation européenne au Panama.
We will successively deal with the circumstances of the emergence of Panama since the pre-Colum bian period, the first Spanish shipping expeditions in search of a strait towards India, and the independence of Panama. ln the first part, we shall deal with the Isthmus of Panama as a land of passage and with its Channel from 1880 to 1914, from the secular dream to reality where, successively, we shall study its French fate, its position in regards to French interests and American aspiration. The relationship between the United States and Panama will lead us to deal with the settling of the Americans, the construction of the Channel (1904-1914), the "Carter-Torrijos" treaties, between compromises and ambiguities. The second part will deal with strategies of development for Panama; the importance of socioeconomic factors and the dynamics of the sociopolitical structures will be highlighted. The integration of the people of Guadeloupe and Martinique in the Panamanian community circle from 1914 to nowadays. In this respect, we shall treat contributions of the French West Indian culture within the Panamanian representation; the cultural admixture. In the third part, their contribution at the development of the Panamanian nation. The issue will be to study arts and culture, music and dances, Iiterature and Iinguistics as weil as the cultural demands from ethnic minorities. Finally, we shall direct our researches towards the question of Panamanian unity at the dawn of the third millennium, the organization of the diverse communities and the European settling in Panama

http://www.theses.fr/2010AGUY0393/document

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
There appears to be an incompressible high rate of preterm births among populations of African origin irrespective of their geographic location. The objective of this study was to assess the risk factors for preterm birth in a French Caribbean population of African descent, offered medical care comparable to that on the French mainland, but presenting a higher rate of preterm birth. The study was based on a birth cohort at maternity hospitals in Guadeloupe (French West Indies) including 911 singleton pregnancies enrolled during their third trimester check-up visits. Associations between risk factors and the risk of preterm delivery (spontaneous and induced) were assessed using a multivariate Cox model. In addition, prevalences of sociodemographic and medical factors in Guadeloupe were compared with those on the French mainland. 144 women (15.8 %) delivered preterm, medically induced in 52 %. Women delivering preterm were more often over 35 years old (37 %), single (54 %), and had higher prevalence of prior preterm birth (20 %), prior miscarriage (37 %), lupus (3 %), asthma (14 %), gestational hypertension (26 %), gestational diabetes (13 %) and urinary tract infection (24 %) than women with term births. In the whole cohort, these risk factors were also more frequent than in mainland France. Our results suggest highly prevalent medical risk factors for preterm births in Guadeloupe. This observation combined with specific social risk factors (older maternal age, single living) less frequent on the French mainland probably explains a large part of a higher prevalence of preterm births in this population despite similar medical provision.
ISSN: 1092-7875

hal-00860340
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00860340
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00860340/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00860340/file/rouget_mat_child_health-accepted.pdf
DOI : 10.1007/s10995-012-1112-x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The oxygen fugacity and therefore the iron redox state of a melt is known to have a strong influence on the liquid line of descent of magmas and thus on the composition of the coexisting melts and crystals. We present a new method to estimate this critical parameter from electron probe microanalyses of two of the most common minerals of basaltic series, plagioclase and clinopyroxene. This method is not based on stoichiometric calculations, but on the different partitioning behaviour of Fe3+ and Fe2+ between both minerals and a melt phase: plagioclase can incorporate more Fe3+ than Fe2+, while clinopyroxene can incorporate more Fe2+ than Fe3+. For example, the effect of oxidizing a partly molten basaltic system (Fe3+ is stabilized with respect to Fe2+) results in an increase of FeOtotal in plagioclase, but a decrease in the associated clinopyroxene. We propose an equation, based on published partition coefficients, that allows estimating the redox state of a melt from these considerations. An application to a set of experimental and natural data attests the validity of the proposed model. The associated error can be calculated and is on average <1 log unit of the prevailing oxygen fugacity.;In order to reduce the number of different variables influencing the Fe2+/Fe3+ mineral/melt equilibrium, our model is restricted to basaltic series with SiO2<60% that have crystallized at intermediate to low pressure (<0.5 GPa) and under relatively oxidizing conditions (Delta FMQ>0; where FMQ is the fayalite-magnetite-quartz oxygen buffer equilibrium), but it may be parameterized for other conditions. A spreadsheet is provided to assist the use of equations, and to perform the error propagation analysis.
ISSN: 0377-0273

hal-00475550
https://hal.archives-ouvertes.fr/hal-00475550
DOI : 10.1016/j.jvolgeores.2009.11.023

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Bivalve larvae and hydrographic parameters were sampled over a range of spatio-temporal scales in a deep atoll lagoon. Bivalve larvae abundances were very high throughout the year: 18,550 m(-3) in average. Larvae were (i) concentrated at mid-depth with nocturnal ascent and diurnal descent, (ii) heterogeneously dispersed at the lagoon scale, (iii) subject to day-to-day variation in abundance and (iv) transferred between different parts of the lagoon providing evidence of intra-lagoonal connectivity. The primacy of physical factors was seen on large spatial scale with the diluting effect of water renewal and transfers by hydrodynamics. On smaller spatial scale, the primacy of biological processes was recognised, with larval swimming activity leading to dial vertical migration correlated with food concentration. Variations in larval abundance were driven by bivalve reproductive activity correlated with meteorological conditions (i.e. windy periods). Finally, relationship between bivalve larvae patterns and pearl oyster (Pinctada margaritifera) settlement structuring is discussed. (C) 2012 Elsevier Ltd. All rights reserved.
Marine Pollution Bulletin (0025-326X) (Pergamon-elsevier Science Ltd), 2012 , Vol. 65 , N. 10-12 , P. 453-462

Droits : 2012 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00101/21200/20690.pdf
DOI:10.1016/j.marpolbul.2011.12.028
http://archimer.ifremer.fr/doc/00101/21200/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Increasingly, similarity networks are being used for evolutionary analyses of molecular datasets. These networks are very useful, in particular for the analysis of gene sharing, lateral gene transfer and for the detection of distant homologs. Currently, such analyses require some computer programming skills due to the limited availability of user-friendly freely distributed software. Consequently, although appealing, the construction and analyses of these networks remain less familiar to biologists than do phylogenetic approaches. Results: In order to ease the use of similarity networks in the community of evolutionary biologists, we introduce a software program, EGN, that runs under Linux or MacOSX. EGN automates the reconstruction of gene and genome networks from nucleic and proteic sequences. EGN also implements statistics describing genetic diversity in these samples, for various user-defined thresholds of similarities. In the interest of studying the complexity of evolutionary processes affecting microbial evolution, we applied EGN to a dataset of 571,044 proteic sequences from the three domains of life and from mobile elements. We observed that, in Borrelia, plasmids play a different role than in most other eubacteria. Rather than being genetic couriers involved in lateral gene transfer, Borrelia's plasmids and their genes act as private genetic goods, that contribute to the creation of genetic diversity within their parasitic hosts. Conclusion: EGN can be used for constructing, analyzing, and mining molecular datasets in evolutionary studies. The program can help increase our knowledge of the processes through which genes from distinct sources and/or from multiple genomes co-evolve in lineages of cellular organisms.
ISSN: 1471-2148

hal-01544799
https://hal.archives-ouvertes.fr/hal-01544799
DOI : 10.1186/1471-2148-13-146

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Subduction infancy corresponds to the first few million years following subduction initiation, when slabs start their descent into the mantle. It coincides with the transient (yet systematic) transfer of material from the top of the slab to the upper plate, as witnessed by metamorphic soles welded beneath obducted ophiolites. Combining structure–lithology–pressure–temperature–time data from metamorphic soles with flow laws derived from experimental rock mechanics, this study highlights two main successive rheological switches across the subduction interface (mantle wedge vs. basalts, then mantle wedge vs. sediments; at ∼800 °C and ∼600 °C, respectively), during which interplate mechanical coupling is maximized by the existence of transiently similar rheologies across the plate contact. We propose that these rheological switches hinder slab penetration and are responsible for slicing the top of the slab and welding crustal pieces (high- then low-temperature metamorphic soles) to the base of the mantle wedge during subduction infancy. This mechanism has implications for the rheological properties of the crust and mantle (and for transient episodes of accretion/exhumation of HP-LT rocks in mature subduction systems) and highlights the role of fluids in enabling subduction to overcome the early resistance to slab penetration.
ISSN: 0012-821X

hal-01383368
http://hal.upmc.fr/hal-01383368
http://hal.upmc.fr/hal-01383368/document
http://hal.upmc.fr/hal-01383368/file/Agard_2016_Plate_interface.pdf
DOI : 10.1016/j.epsl.2016.06.054

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. The area is characterized by very localized NSextension at a rate of1.5cm/year, the occurrence of frequent and intensive microseismic crises and occasionalmoderate to large earthquakes like in 1995 (Mw=6.1).Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary naturalobservatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studieshave improved our view about fault geometry and mechanics within CRL, but there is still a critical need for a betterknowledge of the structure at depth both for the accuracy of earthquake locations and for mechanical interpretationof the seismicity.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by usingrecently developed methodologies of structural imaging, in order to determine at the same time and with highresolution, the local 3D structure and the earthquake locations.We perform an iterative joint determination of 3D velocity model and earthquake coordinates. In a first step, Pand S velocity models are determined using first arrival time tomography method proposed by Taillandier et al.(2009). It consists in the minimization of the cost function between observed and theoretical arrival times which isachieved by the steepest descent method (e.g. Tarantola 1987). This latter requires computing the gradient of thecost function by using the adjoint state method (Chavent 1974). In a second step, earthquakes are located in thenew velocity model with a non-linear inversion method based on a Bayesian formulation (Gesret et al. 2015). Step1 and 2 are repeated until the cost function no longer decreases.We present preliminary results consisting in: (1) the adjustement of a 1D velocity model that is used as initialmodel of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquakelocation.In addition to the tomographic imaging, we perform a preliminary receiver function analysis of teleseismic datarecorded by the broadband stations of the CRL network. The RF analysis should provide the interface depthsbeneath seismometers and increase the imaging resolution of the upper crustal structures provided by the 3Dtomography. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar aspossible to the observed RF for a subset of data. We compare the identified interfaces with structures imaged bythe tomography.
EGU general assembly 2016
Vienne, Austria

hal-01306224
https://hal-mines-paristech.archives-ouvertes.fr/hal-01306224

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background: Mass breast cancer screening is offered to French women between the ages of 50 and 74. In the French overseas department of Guadeloupe, where the population is of mostly African ancestry, a low age at diagnosis of breast cancer has been reported, as for African-Americans. This raises the question of whether breast cancer is more aggressive in the age group preceding that eligible for mass screening (4049) in Guadeloupe. Methods: We compared the tumor-related prognostic factors, first line therapy and overall survival rates of breast cancer cases diagnosed between the 40-49 and 50-74 age groups, based on reports of the cancer registry of Guadeloupe for the period 2008-2013. Results: The characteristics studied, risk of death after breast cancer (HR 0.84 [95% CI: 0.58-1.22] and overall survival, did not differ significantly between the two groups, except for higher tumor size (28.8 vs 24.0; p = 0.004) in the younger group. Conclusion: These results do not show a pattern of more aggressive breast cancer in the age group preceding that eligible for mass screening in Guadeloupe. (C) 2017 Elsevier Ltd. All rights reserved.
ISSN: 1877-7821

hal-01659244
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01659244
DOI : 10.1016/j.canep.2017.08.004
PUBMED : 29120835

Éditeur(s) : HAL CCSD Elsevier
Résumé : Thanks to Dr M. Blanchard-Desce (UMR CNRS 5255, University of Bordeaux, France), who kindly provided us with fluorescent dye RS19 and the PIXEL, MRIc, flow cytometry and H2P2 platforms (SFR Biosit, UMS CNRS 3480/US INSERM 018, Rennes).
International audience
[1-9-NαC]-crourorb A1 is a cyclic peptide isolated from Croton urucurana Baillon latex, found in midwestern Brazil, that has been shown to exert cytotoxic effects against a panel of cancer cell lines. However, the underlying mechanisms responsible for the crourorb A1-induced cytotoxicity in cancer cells remain unknown. In this study, the effects of crourorb A1 on the viability, apoptosis, cell cycle and migration of Huh-7 (human hepatocarcinoma) cells were investigated. We evaluated the viability of Huh-7 cells treated with crourorb A1 in 2D and 3D collagen cultures and found that cells in 3D culture exhibited increased resistance to crourorb A1 compared to cells in 2D culture (IC50: 62μg/ml versus 35.75μg/ml). Crourorb A1 treatment decreases the viability of Huh-7 cells in a dose- and time-dependent manner and is associated with the induction of apoptosis, in the absence of necrotic cells, through the activation of caspase-3/7 and increased expression of the pro-apoptotic proteins Bak, Bid, Bax, Puma, Bim, and Bad. The effects of crourorb A1 are also associated with G2/M phase cell cycle arrest and increases in cyclin-dependent kinase (CDK1) and cyclin B1 expression. A significant reduction in Huh-7 cell migration induced by crourorb A1 was also observed in the presence of mitomycin C. Finally, we showed that the JNK/MAP pathway, but not ERK signaling, is involved in crourorb A1-induced hepatocarcinoma cell mortality.
ISSN: 0378-4274

hal-01526429
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526429
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526429/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526429/file/de%20Matos%20C%C3%A2ndido-Bacani%20et%20al.%20-%20%5B1%E2%80%939-N%CE%B1C%5D-crourorb%20A1%20isolated%20from%20Croton%20urucura.pdf
DOI : 10.1016/j.toxlet.2017.03.020

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
How reliable are shear wave splitting measurements as a means of determining mantle flow direction? This remains a topic of debate, especially in the context of subduction. The answer hinges on whether our current understanding of mineral physics provides enough to accurately translate between seismic observations and mantle deformation. Here, we present an integrated model to simulate strain-history-dependent texture development and estimate resulting shear wave splitting in subduction environments. We do this for a mantle flow model that, in its geometry, approximates the double-sided Molucca Sea subduction system in Eastern Indonesia. We test a single-sided and a double-sided subduction case. Results are compared to recent splitting measurements of this region by Di Leo et al. (2012a). The setting lends itself as a case study, because it is fairly young and, therefore, early textures from the slab's descent from the near surface to the bottom of the mantle transition zone--which we simulate in our models--have not yet been overprinted by subsequent continuous steady state flow. Second, it allows us to test the significance of the double-sided geometry, i.e., the need for a rear barrier to achieve trench-parallel subslab mantle flow. We demonstrate that although a barrier amplifies trench-parallel subslab anisotropy due to mantle flow, it is not necessary to produce trench-parallel fast directions per se. In a simple model of A-type olivine lattice-preferred orientation and one-sided subduction, trench-parallel fast directions are produced by a combination of simple shear and extension through compression and pure shear in the subslab mantle.
ISSN: 1525-2027

hal-01053506
https://hal.archives-ouvertes.fr/hal-01053506
DOI : 10.1002/2013GC005032

Éditeur(s) : HAL CCSD AGU and the Geochemical Society
Résumé : International audience
We analyze focal mechanisms of shallow-intermediate earthquakes in a NW-SE transect along the western Betic Cordillera and Alboran Sea, and deep earthquakes located in the central Betics to constrain the state of stress at the Gibraltar Arc slow convergence area. Shallow earthquakes (< 40 km) are preferably clustered at the mountain front. A general NW-SE horizontal compression is compatible with the convergence, and NW plunging compression axes are in agreement with frontal thrust activity. Toward the Alboran Sea the earthquakes are progressively deeper, reaching intermediate depths (40-120 km) near the coast and supporting the present-day activity of subduction only in this area. The Iberian continental crust concentrates most of the intermediate seismicity and is forced to partially sink into the mantle, probably through the pull of the oceanic slab. This downdip pull together with the buoyancy of the Iberian continental crust produces the slab curvature, downdip extension in the external arc of the continental slab, and downdip compression in the inner arc. T axes highly dipping to the southeast at 90-120 km depth occur at the oceanic/continental transition. Deep earthquakes (> 620 km) show very similar focal mechanisms, fitting the general slab behavior of resistance to further descent at the 660 km discontinuity. Seismicity features evidence the present-day stress distribution in a context of transition from subduction to continental collision.
ISSN: 1525-2027

hal-00669889
https://hal.archives-ouvertes.fr/hal-00669889
DOI : 10.1029/2011GC003824

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely ``processually equivalent'' entities, ``processually versatile'' entities, and ``stabilized'' entities.
ISSN: 0169-3867

hal-01544796
https://hal.archives-ouvertes.fr/hal-01544796
DOI : 10.1007/s10539-012-9350-2

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Demographic processes and spatial dispersal of Triatoma dimidiata, a triatomine species vector of Chagas disease, are modeled by integrodifference equations to estimate invasion capacity of this species under different ecological conditions. The application of the theory of orthogonal polynomials and the steepest descent method applied to these equations, allow a good approximation of the abundance of the adult female population and the invasion speed. We show that: (1) under the same mean conditions of demography and dispersal, periodic spatial dispersal results in an invasion speed 2.5 times larger than the invasion speed when spatial dispersal is continuous; (2) when the invasion speed of periodic spatial dispersal is correlated to adverse demographic conditions, it is 34.7% higher as compared to a periodic dispersal that is correlated to good demographic conditions. From our results we conclude, in terms of triatomine population control, that the invasive success of T. dimidiata may be most sensitive to the probability of transition from juvenile to adult stage. We discuss our main theoretical predictions in the light of observed data in different triatomines species found in the literature.
ISSN: 0022-5193

hal-01298098
https://hal-univ-perp.archives-ouvertes.fr/hal-01298098
DOI : 10.1016/j.jtbi.2016.01.017

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
BACKGROUND: Deletions of the glutathione S-transferase genes M1 and T1 (GSTM1 and GSTT1) have been studied as potential risk factors for prostate cancer. Conflicting results have been obtained. Moreover, most such studies could not discriminate heterozygous from homozygous carriers of the non-deleted alleles. OBJECTIVE: We investigated whether copy number variation (CNV) of the GSTM1 and/or GSTT1 genes contribute to the risk of prostate cancer in the Caribbean population of African descent of Guadeloupe. METHODS: In a population-based case-control study, we compared 629 prostate cancer patients and 622 control subjects. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Exact copy numbers of GSTM1 and GSTT1 were determined by real-time PCR. RESULTS: A higher copy number of GSTM1 was marginally associated with prostate cancer risk. Men with 2 and 3 or more GSTT1 genes were at higher risk of prostate cancer (OR: 1.55, 95% CI: 1.11-2.16 and OR: 4.89, 95% CI: 1.71-13.99, respectively; Ptrend extless0.001). Men with 3, 4 and 5 or more copies of both GSTM1 and GSTT1 genes were at higher risk of prostate cancer (OR: 2.18, 95% CI: 1.21-3.91, OR: 3.24, 95% CI: 1.63-6.46, and OR: 5.77, 95% CI: 1.40-23.84, respectively; Ptrend extless0.001). CONCLUSIONS: Copy number of GSTT1 and combined GSTM1/GSTT1 appear to be associated with prostate cancer risk in our population study with gene dose relationship. Our results support the hypothesis that variations in copy number of GSTT1 modulate the risk of prostate cancer.
ISSN: 1932-6203

hal-01063905
https://hal.archives-ouvertes.fr/hal-01063905
DOI : 10.1371/journal.pone.0107275
PUBMED : 25198353