Éditeur(s) : HAL CCSD
Résumé : International audience
MOTIVATION: Imaging mass spectrometry (IMS) is a maturating technique of molecular imaging. Confidence in the reproducible quality of IMS data is essential for its integration into routine use. However, the predominant method for assessing quality is visual examination, a time consuming, unstandardized and non-scalable approach. So far, the problem of assessing the quality has only been marginally addressed and existing measures do not account for the spatial information of IMS data. Importantly, no approach exists for unbiased evaluation of potential quality measures. RESULTS: We propose a novel approach for evaluating potential measures by creating a gold-standard set using collective expert judgements upon which we evaluated image-based measures. To produce a gold standard, we engaged 80 IMS experts, each to rate the relative quality between 52 pairs of ion images from MALDI-TOF IMS datasets of rat brain coronal sections. Experts' optional feedback on their expertise, the task and the survey showed that (i) they had diverse backgrounds and sufficient expertise, (ii) the task was properly understood, and (iii) the survey was comprehensible. A moderate inter-rater agreement was achieved with Krippendorff's alpha of 0.5. A gold-standard set of 634 pairs of images with accompanying ratings was constructed and showed a high agreement of 0.85. Eight families of potential measures with a range of parameters and statistical descriptors, giving 143 in total, were evaluated. Both signal-to-noise and spatial chaos-based measures performed highly with a correlation of 0.7 to 0.9 with the gold standard ratings. Moreover, we showed that a composite measure with the linear coefficients (trained on the gold standard with regularized least squares optimization and lasso) showed a strong linear correlation of 0.94 and an accuracy of 0.98 in predicting which image in a pair was of higher quality. AVAILABILITY AND IMPLEMENTATION: The anonymized data collected from the survey and the Matlab source code for data processing can be found at: https://github.com/alexandrovteam/IMS_quality. CONTACT: theodore.alexandrov@embl.de
Bioinformatics (Oxford, England)

hal-01163754
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01163754
DOI : 10.1093/bioinformatics/btv266
PUBMED : 26072506

Éditeur(s) : HAL CCSD Wiley
Résumé : 1. A recent article published by Toledo (2011b) investigates the effects of spatial variations in climate and soil, and of logging disturbance, on tree and forest growth in Bolivia. It concludes that climate is the strongest driver of tree and forest growth and that climate change may therefore have large consequences for forest productivity and carbon sequestration. However, serious methodological and conceptual discrepancies have been found that challenge these conclusions.[br/] 2. Because of an errant coding of time after logging in the regression analysis, and because floristic changes induced by logging could not be incorporated into the analysis, the effect of logging on the average diameter growth is likely to have been strongly underestimated.[br/] 3. Basal area growth was improperly calculated as basal area change, and it displayed surprisingly high values, even among unlogged plots. We hypothesize that either these plots may be actually located in secondary forests recovering from past logging, or measurement biases may have hampered the data set.[br/] 4. Regardless of climategrowth relationships established across these plots, any inference concerning the potential effects of climate change on forest growth would require a specific quantitative assessment.[br/] 5. Synthesis. It is critical to re-assess the relative weight of climate and logging disturbance as driving factors of tree and forest growth, and to find an explanation for the very high basal area increment reported among the unlogged plots. We provide specific recommendations for further analyses of this and similar data sets.
ISSN: 0022-0477

hal-01032432
https://hal.archives-ouvertes.fr/hal-01032432
DOI : 10.1111/j.1365-2745.2011.01895.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Deep-seated gravitational spreading (DSGS) affects the slopes of formerly glaciated mountain ridges. On Mars, DSGS has played a key role in shaping the landforms of the giant Valles Marineris troughs. Though less spectacular, DSGS is common in terrestrial orogens, where understanding its mechanics is critical in the light of the ongoing climate change because it is a potential source of catastrophic landslides in deglaciated valleys. We conducted parametric numerical studies in order to identify important factors responsible for DSGS initiation. DSGS models are computed using an elastoviscoplastic finite element code. Using ADELI's software, we reproduce topographic ridge spreading under the effect of valley unloading. Two types of spreading topographic ridges are investigated, homogeneous or with horizontal rheological layering. We find that gravitational instabilities are enhanced by high slopes, which increase gravitational stress, and low friction and cohesion, which decrease yield stress. In the unlayered ridge, instability is triggered by glacial unloading with plastic strain concentration inside the ridge and at the base of the high slopes. Vertical fractures develop in the upper part of the slope, potentially leading to fault scarps. Ridge homogeneity promotes a deformation mode controlled by uphill-facing normal faulting and basal bulging. In the second case, the ridge encompasses horizontal geological discontinuities that induce rock mass anisotropy. Discontinuity located at the base of the slope accumulates plastic strain, leading to the formation of a sliding plane evolving into a landslide. The presence of a weak layer at ridge base therefore promotes another slope deformation mode ending up with catastrophic failure. Mechanical conditions and slope height being equal, these conclusions can probably be extrapolated to Earth. Compared with Mars, DSGS on Earth is inhibited because terrestrial topographic gradients are lower than in Valles Marineris, an effect counterbalanced by increased gravitational stress, where the intensity of deformation is enhanced because of the Earth gravity potential.
ISSN: 0169-555X

hal-01420007
https://hal.archives-ouvertes.fr/hal-01420007
DOI : 10.1016/j.geomorph.2016.06.011

Éditeur(s) : HAL CCSD Endocrine Society
Résumé : International audience
Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility.
ISSN: 0888-8809

hal-01146846
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146846
DOI : 10.1210/me.2014-1356
PUBMED : 25710594

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : Proceedings of the 59th Annual Gulf and Caribbean Fisheries Institute
Résumé : In most of marine fishes cultured, larvae in their early development are fed with live prey (rotifer and/or artemia). In hatcheries, culture of these preys is labour consuming, needs specific facilities and represent an important part of production cast. On the other hand, world artemia production is subjected to fluctuation of harvest in the wild which could Iimit fish farming industry in the near future. A dried formula adapted to marine fish larvae has been perfected by Ifremer's center of Brest (France) and is distributed by a feeding company since 1999. This artificial microbound diet has been successfully tested on several temperate fishes such as European seabass (Dicentrarchus labrax), Atlantic cod (Gadus morhua) or European seabream (Sparus aurata) in a co-feeding (i.e. artemia and dried diet) strategy. Experiments described here were carried out ta evaluate the performances obtained during total substitution of artemia by this diet in Red drum (Sciaenops ocellatus) larval culture. ln 2004 and 2005, four experiments were conducted on feed technology aspects (experimental or industrial manufacturing), weaning strategy (direct or co-feeding) and feed distribution method (prototypes or classical self feeder) in comparison to the standardized method using live preys. At the end of larval phase (day 15) and at day 30, end of nursery phase (0.6 g), survival relative to control (RTC) was respectively 96.9% and 111.0% in the best treatment. Concerning growth, the weight RTC reached at day 15 and day 30 was respectively 82.8% and 72.4%. However, it is important to note that rearing protocols have to be adapted ta the use of these micro pellets in order toprevent degradation of culture quality. These results show that this new product can be applied on industrial scale in private hatcheries. But further research is needed ta evaluate replacement of rotifers by this dried formula in order to completely eliminate live prey in larval culture of Red drum.
Dans la plupart des poisons marins élevés, les larves sont nourries avec des proies vivantes (rotifères et/ou artémia) au début de leur développement. Dans les écloseries, la culture de ces proies est consommatrice de main d'oeuvre, nécessite des installations spécifiques et entre pour une part importante dans le coût de production. Par ailleurs, la production mondiale d'artémia est dépendante de la fluctuation des récoltes dans le milieu naturel, ce qui pourrait gêner la filière piscicole marine dans un futur proche. Une formulation alimentaire inerte adaptée aux larves de poisson marin a été mise au point par le centre Ifremer de Brest (France) et est commercialisée par un provendier depuis 1999. Ces microparticules artificielles ont été testée avec succès sur plusieurs poissons tempérés comme le bar européen (Dicentrarchus labrax), la morue atlantique (Gadus morha) ou la daurade européenne (Sparus aurata) dans un contexte de co-feeding (i.e. artémia et aliment inerte). Les expériences décrites ici ont été menées afin d'évaluer les performances obtenues lors de la substitution totale des artémia par cet aliment dans l'élevage larvaire de l'ombrine (Sciaenops ocellatus). En 2004 et 2005, quatre expériences ont été menées sur l'aspect technologie alimentaire (fabrication expérimentale ou industrielle), la stratégie de sevrage (direct ou co-feeding) et le mode de distribution de l'aliment (distributeur classique ou prototypes) en comparaison au standard sur proies vivantes. En fin de phase larvaire (jour 15) et au jour 30 après une phase de prégrossissement (0.6g), la survie par rapport au témoin (RTC) était respectivement de 96.9% et 111 .1% dans le meilleur traitement. Concernant la croissance, les poids obtenus aux jours 15 et 30 atteignaient respectivement 82.8% et 72.4%. Cependant il est important de relever que les protocoles d'élevage doivent être adaptés à l'utilisation de ces microparticules afin de prévenir une dégradation de la qualité d'élevage. Ces résultats montrent que ce nouveau produit peut être appliqué à l'échelle industrielle dans les écloseries privées. Cependant, les recherches doivent être poursuivies pour évaluer les possibilités de remplacement des rotifères par ces aliments inertes afin de s'affranchir complètement de l'utilisation de proies vivantes dans l'élevage larvaire de l'ombrine.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-6597.pdf
http://archimer.ifremer.fr/doc/00000/6597/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Thermal acclimation drastically alters thermotolerance of ectotherms, but the mechanisms determining this plastic response are not fully understood. The present study investigates the proteomic response (2D-DIGE) of adult Drosophila melanogaster acclimated at 11, 25 or 31 C. As expected 11 C-acclimation improved cold tolerance and 31 C-acclimation improved heat tolerance. We hypothesized that the marked organismal responses to acclimation could be detected at the proteomic level assuming that changes in the abundance of specific proteins are linked to the physiological changes underlying the phenotypic response. The 31 C-acclimated flies displayed a particular divergent proteomic profile where molecular chaperones made up a large number of the proteins that were modulated during heat acclimation. Many other proteins showed significant modulation during acclimation including proteins involved in iron ion and cell redox homeostasis, carbohydrate and energy metabolism, chromatin remodeling and translation, and contractile machinery. Interestingly the changes in protein abundance were often unrelated to transcriptional activity of the genes coding for the proteins, except for the most strongly expressed proteins (e.g. Hsp70). The 11 C-acclimation evoked weak proteomic response despite the marked effect on the organismal phenotype. Thus the acquired cold tolerance observed here may involve regulatory process such as posttranslational regulation rather than de novo protein synthesis.
ISSN: 0965-1748

hal-00826939
https://hal.archives-ouvertes.fr/hal-00826939
DOI : 10.1016/j.ibmb.2013.01.006
PUBMED : 23416132

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work deals with the problem of finding for a given industrial target the molecule conformation leading to the most efficient crystal polymorph and/or designing unknown crystal packing of new molecules. The originality of the method relies first on constraining the domain of the most probable crystals, before converging towards the predicted packing by a double genetic-refining optimization algorithm. Validation of this approach is discussed on the case study of 46 energetic crystal compounds, using the semi Ab Initio and Molecular Mechanics code GenMol™. This validation shows that all observed structures are retrieved in any circumstances with a relatively high number of good rankings.
ISSN: 0022-0248

hal-00857875
https://hal.archives-ouvertes.fr/hal-00857875
DOI : 10.1016/j.jcrysgro.2009.04.002

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper introduces the information criteria in feature selection framework. Information criteria are integrated in feature selection scheme to select subset candidates. The accuracy of the proposed approach is based on the quality of the probability density approximations of these features. They are obtained using histograms optimized thanks to the adaptive arithmetic coding principles. Tests on simulated data and references are made. Multiple classifiers are used. The correct classification rate shows, the importance of this tools and its ability to select a best subsets. Generally, the subsets produce a good characterization of classes which the data belong.
TAIMA Proceedings

hal-00634754
https://hal.archives-ouvertes.fr/hal-00634754

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A recent study suggested that adenosine signaling pathway could promote hemolysis in patients with sickle cell anemia (SCA). This signaling pathway involves several gene coding enzymes for which variants have been described. In this study, we analyzed the genotype-phenotype relationships between functional polymorphisms or polymorphisms associated with altered expression of adenosine pathway genes, namely adenosine deaminase (ada; rs73598374), adenosine A2b receptor (adora2b; rs7208480), adenylyl cyclase6 (adcy6; rs3730071, rs3730070, rs7300155), and hemolytic rate in SCA patients. One hundred and fifty SCA patients were genotyped for adcy6, ada, and adora2b variants as well as alpha-globin gene, a genetic factor known to modulate hemolytic rate. Hematological and biochemical data were obtained at steady-state. Lactate dehydrogenase, aspartate aminotransferase, reticulocytes and total bilirubin were used to calculate a hemolytic index. Genotype-phenotype relationships were investigated using parametric tests and multivariate analysis. SCA patients carrying at least one allele of adcy6 rs3730070-G exhibited lower hemolytic rate than non-carriers in univariate analysis (p=0.006). The presence of adcy6 rs3730070-G variant was associated with a decreased hemolytic rate in adjusted model for age and alpha-thalassemia (p=0.032). Our results support a protective effect of adcy6 rs3730070-G variant on hemolysis in SCA patients.
ISSN: 1079-9796

hal-01668332
https://hal.univ-antilles.fr/hal-01668332
DOI : 10.1016/j.bcmd.2016.02.006

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
We show first results of 3D simulation of sea currents in a realistic context. We use the full Navier-Stokes equations for incompressible viscous fluid. The problem is solved using a second order incremental projection method associated with the finite volume of the staggered (MAC) scheme for the spatial discretization. After validation on classical cases, it is used in a numerical simulation of the Pointe à Pitre harbour area. The use of the fictious domain method permits us to take into account the complexity of bathymetric data and allows us to work with regular meshes and thus preserves the efficiency essential for a 3D code.
ISSN: 1270-900X
Guidel, France

hal-00728894
https://hal.archives-ouvertes.fr/hal-00728894
DOI : 10.1051/proc/201235025

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background : Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.Results : In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level.Conclusion : The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01149671
http://hal.upmc.fr/hal-01149671
http://hal.upmc.fr/hal-01149671/document
http://hal.upmc.fr/hal-01149671/file/Lichius_2015_Genome_sequencing.pdf
DOI : 10.1186/s12864-015-1526-0

Résumé : AU COURS DE LA THESE, L'ETUDE DU TRANSCRIPTOME DE SOUCHES GARDEL ET SENEGAL VIRULENTES ET ATTENUEES D'E. RUMINANTIUMA ETE REALISEE. UNE ANALYSE DU TRANSCRIPTOME A DIFFERENTS STADES DE DEVELOPPEMENT, A D'ABORD ETE EFFECTUEE POUR LA SOUCHE GARDEL VIRULENTE. AU STADE CORPS RETICULE (FORME INTRACELLULAIRE NON INFECTIEUSE), UNE SUREXPRESSION DES GENES CODANT POUR DES PROTEINES IMPLIQUEES DANS LE METABOLISME, LE TRANSPORT ET L'ECHANGE DE NUTRIMENTS ET DANS LA RESISTANCE AU STRESS OXYDATIF ETAIT OBSERVEE. IL SEMBLERAIT QUEE. RUMINANTIUMMETTE EN PLACE UN PANEL DE MECANISMES POUR SA SURVIE ET SON DEVELOPPEMENT A L'INTERIEUR DE LA CELLULE HOTE. AU STADE CORPS ELEMENTAIRE (FORME EXTRACELLULAlRE INFECTIEUSE), LE GENE DKSA CODANT POUR UN FACTEUR DE TRANSCRIPTION ETAIT SUREXPRIME. CE GENE A ETE MONTRE COMME ETANT IMPLIQUE DANS LA REGULATION DE FACTEURS DE VIRULENCE. IL SEMBLERAIT . DONC, QU'AU STADE CORPS ELEMENTAIRE, IL Y AIT UNE INDUCTION DE MECANISMES DE VIRULENCE. LA COMPARAISON DE L'EXPRESSION DES GENES AU STADE CORPS ELEMENTAIRE ENTRE SOUCHES VIRULENTES ET ATTENUEES A AUSSI ETE EFFECTUEE. NOS RESULTATS ONT MONTRE UNE MODIFICATION IMPORTANTE DE LA MEMBRANE POUR LES SOUCHES VIRULENTES ET ATTENUEES. POUR LES SOUCHES ATTENUEES, IL A ETE MONTRE UNE SUREXPRESSION DES GENES IMPLIQUES DANS LA BIOGENESE MEMBRANAlRE ET UNE SOUS-EXPRESSION·DES PROTEINES DE LA FAMILLE MULTIGENIQUE MAP. CES RESULTATS SUGGERENT QUE LES PROTEINES MAP JOUENT UN ROLE DE LEURRE VIS-A-VIS DE LA REPONSE IMMUNITAIRE PROTECTRICE. DES PROTEINES MEMBRANAlRES HYPOTHETIQUES SONT SUREXPRIMEES A LA FOIS CHEZ LES SOUCHES VIRULENTES ET ATTENUEES. CERTAINES D'ENTRE ELLES SUREXPRIMEES CHEZ LES SOUCHES ATTENUEES SEMBLENT ETRE DE BONS CANDIDATS VACCINAUX ET DEVRAIENT ETRE ETUDIEES
Transcriptomic study of gardel and senegal both virulent and attenuated e. ruminantium strains was conducted during my phd. an analysis of transcriptome at different stages of development has been first conducted for virulent gardel strain. at reticulate body stage (intracellular form non-infectious), over-expression of genes coding for proteins involved in metabolism, transport and exchange of nutrients and resistance to oxidative stress was observed. at this stage of development, e. ruminantium seems to activate mechanisms for its survival and development within the host cell. at elementary body stage, dksa the gene encoding for a transcription factor was over-expressed. this gene has been shown to be involved in the regulation of virulence factors. it seems, therefore, at the elementary body stage, e. ruminantium induces its virulence factors. secondly, we compare the transcriptome of elementary body between virulent and attenuated strains. our results showed an important membrane modification of attenuated and virulent strains. for attenuated strains, we observed an over-expression of genes involved in membrane biogenesis and a diminution of expression of map multigenic family. it seems that map proteins subvert the protective immune response. hypothetical membrane proteins are over-expressed in both virulent and attenuated strains. some over-expressed proteins in attenuated strains seem to be good vaccine candidates and willstudied.

http://www.theses.fr/2012AGUY0562/document

Éditeur(s) : HAL CCSD De Gruyter
Résumé : International audience
This article examines the case of Kali'na, a minority Indigenous language of French Guiana, from the point of view of descriptive categories available in the literature (namely dominated language, minoritized language, endangered language). These terms are discussed, favouring more dynamic categories which focus on processes (minoritization/deminoritization). The article uses both micro- and macrosociolinguistic levels of analysis. At the macro level, indicators are proposed to gauge the minorization of Kali'na as it occurs on the scale of Guiana as a whole, by observing attitudes towards Kali'na language and culture, particularly as expressed in the media and in epilinguistic comments made by speakers. At the local level, we explore the effects of the recognition by the State of a Kali'na township and their influence on language minoritization in the village and more generally at the level of the linguistic community. We also attempt to determine to what extent, as far as interactions are concerned, alternations and code switching between Kali'na and French might constitute indicators of the process of minoritization or deminoritization or of language death currently underway.
ISSN: 0165-2516

halshs-00292394
https://halshs.archives-ouvertes.fr/halshs-00292394
https://halshs.archives-ouvertes.fr/halshs-00292394/document
https://halshs.archives-ouvertes.fr/halshs-00292394/file/2006-leglise-alby-minorization.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : Validation of building energy simulation programs is of major interest to both users and modellers. To achieve such a task, it is essential to apply a methodology based on a priori test and empirical validation. A priori test consists in verifying that models embedded in a program and their implementation are correct. this should be achieved before carrying out experiments. The aim of this report is to present results from the application of the BESTEST procedure to our code. We will emphasise the way it allows to find bugs in our program and also how it permits to qualify models of heat transfer by conduction
World Renewable Energy Congress VI Renewables: The Energy for the 21st Century World Renewable Energy Congress VI 1-7 July 2000 Brighton, UK

ISBN : 978-0-08-043865-8
hal-00767562
https://hal.archives-ouvertes.fr/hal-00767562
https://hal.archives-ouvertes.fr/hal-00767562/document
https://hal.archives-ouvertes.fr/hal-00767562/file/TedWrec2000.pdf

Résumé : De plus en plus, le bruit est considéré comme une véritable pollution. dans le passé, les carrioles, les sabots des chevaux sur les pavés causaient déjà des nuisances aux habitants des villes. dès le xixe siècle, l'évolution de l'industrialisation entraîna une augmentation de la machinerie, qui ne fit qu'augmenter les nuisances sonores. aujourd'hui, le bruit est la cause de nombreuses plaintes. en conséquence, réduire la pollution sonore est devenu une question majeure du fait de ses effets sur la santé humaine. le bruit peut affecter le sommeil, le système cardiovasculaire, le système cérébral, particulièrement le développement cérébral des enfants. il peut causer des déficiences mentales, des problèmes de concentration et des pertes de mémoire. c'est un problème de santé publique. mais le bruit peut aussi entraîner la commission de crimes ou de suicides ! c'est aussi une question d'ordre public.en france, il existe certains dispositifs juridiques de contrôle des émissions sonores et de lutte contre les nuisances, particulièrement depuis la loi « bruit » de 1992. diverses dispositions ont été codifiées dans le code de l'environnement, les classant en fonction des différentes sources de bruit, mais aussi dans d'autres codes, notamment le code de l'urbanisme. il existe une police environnementale du bruit dont le maire et le préfet sont les deux autorités compétentes. tous ces moyens permettent de pallier les problèmes dûs au bruit à court ou à moyen terme.cependant, aujourd'hui, au regard de la préoccupation de développement durable, il convient de penser aux générations futures et de mettre en place des nouveaux moyens de régulation de la pollution sonore, à long terme. le droit de l'urbanisme apparaît comme le moyen privilégié d'atteindre ce but. le bruit pourrait être régulé par une utilisation plus rationnelle des sols… le but de ma recherche est d'analyser quel type de relation existe entre droit du bruit et droit de l'urbanisme et de mettre en évidence vers quelle forme d'urbanisme la société évolue sous l'influence combinée de l'écologie et de la question sonore, notamment à travers les objectifs posés par le grenelle de l'environnement et les lois adoptées en conséquence.
Noise is considered as a real pollution for the quality of life. Law has been requested to respond the multi-form cases of noise pollution. The matter is firstly the concern of environmental law. It is especially treated in a sectorial way. Town planning law also seizes the question, in a diffuse way, as environmental issue, or in a specific way when noise pollutions are directly caused by the use of grounds.However, under the influence of more and more pervasive environmental law, and further to the new legislation resulting from the Grenelle of the environment, town planning law underwent a deep transformation. It has been rewritten on the basis of new environmental objectives and of sustainable development. Town planning law also absorbs many other juridical sectors. Therefore it appears as a global space law and living environment law, allowing to improve the sound context.The perception of noise has changed, as well as its consideration into town planning law. Town planning law can be considered as a favorable measure to develop a more global and unified approach of the very composite legal system against noise pollution.The study of the relationship between noise and town planning highlights new manners to consider noise into space and living environment, differently from the classic approach imposed by environmental law.

http://www.theses.fr/2014AGUY0711/document

Éditeur(s) : HAL CCSD
Résumé : International audience
In two swordtail species of the genus Xiphophorus, the onset of puberty has been shown to be modulated at the P locus by sequence polymorphism and gene copy-number variation affecting the type 4 melanocortin hormone receptor Mc4r. The system works through the interaction of two allelic types, one encoding wild type and the other dominant-negative receptors. We have analyzed the structure and evolution of the P locus in the platyfish Xiphophorus maculatus, where as many as nine alleles of P determining the onset of sexual maturity in males and females, fecundity in females, and adult size in males are located on both the X and Y chromosomes in a region linked to the master sex-determining locus. In this species, mc4r has been amplified to up to 10 copies on both the X and Y chromosomes through recent large serial duplications. Subsequently, mc4r paralogues have diverged considerably into many different subtypes. Certain copies have acquired new untranslated regions through genomic rearrangements, and transposable element insertions and other mutations have accumulated in promoter regions, possibly explaining observed deviations from the classical mc4r transcriptional pattern. In the mc4r-coding sequence, in-frame insertions and deletions as well as nonsense and missense mutations have generated a high diversity of Mc4r-predicted proteins. Most of these variants are expressed in embryos, adults, and/or tumors. Functional receptor characterization demonstrated major divergence in pharmacological behavior for Mc4r receptors encoded by different copies of platyfish mc4r, with differences in constitutive activity as well as binding and stimulation by hormones. The high degree of allelic and copy-number variation observed between individuals can explain the high level of polymorphism for sexual maturation, fecundity, and body size in the platyfish: multiple combinations of Mc4r variants with different biochemical properties might interact to modulate the melanocortin signaling that regulates the hypothalamus-pituitary-gonadal axis.
GENETICS

hal-01544912
https://hal.archives-ouvertes.fr/hal-01544912
DOI : 10.1534/genetics.113.155952

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Vertebrate genomes contain around 20,000 protein-encoding genes, of which a large fraction is still not associated with specific functions. A major task in future genomics will thus be to assign physiological roles to all open reading frames revealed by genome sequencing. Here we show that C2orf62, a highly conserved protein with little homology to characterized proteins, is strongly expressed in testis in zebrafish and mammals, and in various types of ciliated cells during zebrafish development. By yeast two hybrid and GST pull-down, C2orf62 was shown to interact with TTC17, another uncharacterized protein. Depletion of either C2orf62 or TTC17 in human ciliated cells interferes with actin polymerization and reduces the number of primary cilia without changing their length. Zebrafish embryos injected with morpholinos against C2orf62 or TTC17, or with mRNA coding for the C2orf62 C-terminal part containing a RII dimerization/docking (R2D2) - like domain show morphological defects consistent with imperfect ciliogenesis. We provide here the first evidence for a C2orf62-TTC17 axis that would regulate actin polymerization and ciliogenesis.
ISSN: 1932-6203

hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00955242/file/C2orf62_and_TTC17-accepted.pdf
DOI : 10.1371/journal.pone.0086476

Éditeur(s) : HAL CCSD BioScientifica
Résumé : International audience
Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the 'proteomics informed by transcriptomics' technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.
ISSN: 1470-1626

hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/file/Linking%20transcriptomics%20and%20proteomics%20in%20spermatogenesis.pdf
DOI : 10.1530/REP-15-0073

Éditeur(s) : HAL CCSD Lippincott, Williams & Wilkins
Résumé : International audience
Objectives: Lung cancer risk associated with occupational cleaning activities has been investigated in the population-based case-control study ICARE. Methods: Occupational history was collected by standardized interviews. Jobs were first defined according to the International Standard Classification of Occupations (ISCO) codes and then categorized according to activity sectors. Adjusted odds ratios (ORs) were estimated by unconditional logistic regression, separately for women (619 cases and 760 controls) and men (2265 and 2780). Results: Thirty percent of women and 2.3% of men controls ever held a cleaner or care job. Women who worked as housemaids longer than 7 years showed an OR of 1.76 [95% confidence interval (95% CI) 1.09 to 2.87] with respect to controls. Women employed in domestic service sector for a long time had an OR of 2.06 (95% CI 1.15 to 3.66). Conclusion: We confirmed and redefined the association of lung cancer with occupational cleaning, which concerns a considerable proportion of women workers.
ISSN: 1076-2752

hal-01359564
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01359564
DOI : 10.1097/JOM.0000000000000722
PUBMED : 27206119