Éditeur(s) : D. Appleton and company D. Appleton and company ( New York )
Résumé : (Statement of Responsibility) By H.M. and P.V.N. Myers.
Narrative of a scientific expedition sent out by the Lyceum of natural histroy of Williams college in the summer of 1867. The present edition includes a brief record of an expedition to Honduras in 1870-1871.
South America
Honduras

000608340
22945394
ADD7471

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
The effects of global change are particularly serious in areas where range shiftsof species are physically constrained such as the Ligurian Sea, which is one ofthe coldest sectors of the Mediterranean. In this basin, historical informationon water temperature (from the sea surface down to 75 m depth) dates backto the 1950s. Early studies also recorded warm-water species occurrence.Thanks to these data we provide the first detailed characterization of watertemperature variation from 1958 up to 2010 in the layer 0–75 m depth. Wecoupled this analysis with the available information on rocky reef epibenthiccommunities (literature review from 1955 to 1964 and field data from 1980 to2010). The analysis of water temperature revealed several patterns of variation:a cooling phase from 1958 to 1980, a phase of rapid warming from 1980 to1990 and a phase of slower warming from 1990 to 2010. Inter-annual variationin temperature increased over the entire period for the water layer down to20 m. Warm-water native and alien species richness increased during thewarming phases. Literature estimates suggest a decrease in warm-water nativespecies richness during the cooling phase. The analysis of quantitative data collectedin the early 1990s and late 2000s indicated a decrease in the cover ofwarm-water native species on shallow rocky reefs and an increase in deeperwaters. We argue that increased inter-annual variation in water temperaturemay disadvantage native warm-water species in shallow waters. Our resultsindicate that the effect of temperature rises in cold, constrained basins may bemore complex than the simple prediction of species changing their geographicalrange according to their thermal limits.
Marine Ecology Progress Series

hal-01239259
https://hal-univ-perp.archives-ouvertes.fr/hal-01239259
DOI : 10.1111/maec.12277

Éditeur(s) : HAL CCSD
Résumé : International audience
Occupational exposure constitutes a common risk factor for lung cancer. We observed molecular alterations in 73% of never-smokers, 35% of men and 8% of women were exposed to at least one occupational carcinogen. We report herein associations between molecular patterns and occupational exposure.BioCAST was a cohort study of lung cancer in never-smokers that reported risk factor exposure and molecular patterns. Occupational exposure was assessed via a validated 71-item questionnaire. Patients were categorised into groups that were unexposed and exposed to polycyclic aromatic hydrocarbons (PAH), asbestos, silica, diesel exhaust fumes (DEF), chrome and paints. Test results were recorded for EGFR, KRAS, HER2, BRAF and PIK3 mutations, and ALK alterations.Overall, 313 out of 384 patients included in BioCAST were analysed. Asbestos-exposed patients displayed a significantly lower rate of EGFR mutations (20% versus 44%, p=0.033), and a higher rate of HER2 mutations (18% versus 4%, p=0.084). ALK alterations were not associated with any occupational carcinogens. The DEF-exposed patients were diagnosed with a BRAF mutation in 25% of all cases. Chrome-exposed patients exhibited enhanced HER2 and PIK3 mutation frequency.Given its minimal effects in the subgroups, we conclude that occupational exposure slightly affects the molecular pattern of lung cancers in never-smokers. In particular, asbestos-exposed patients have a lower chance of EGFR mutations.
European Respiratory Journal

hal-01647080
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01647080
DOI : 10.1183/13993003.00716-2017
PUBMED : 29074543

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Volumetrically minor microsyenites, alkali microgranite and related trachytic dykes intrude early Pliocene OIB-like alkali basaltic and basanitic flows of the Meseta del Lago Buenos Aires in Central Patagonia (47 degrees S-71 degrees 30'W), and occur together with scarce trachytic lava flows. Whole-rock K-Ar ages between 3.98 and 3.08 Ma indicate that the emplacement of these felsic rocks occurred more or less synchronously with that of the post-plateau basaltic sequence that they intrude, during a bimodal mafic-felsic magmatic episode devoid of intermediate compositions. Chemically, these rocks have A(1)-type granitoid affinities and are characterized by high silica and alkali contents (60-68 wt.% SiO2; 8.7-10.8 wt.% Na2O+K2O), major and trace elements patterns evidencing evolution by low-pressure fractional crystallization, and Sr and Nd isotopic signatures similar to those of coeval basalts ((Sr-87/Sr-86)o=0.70488-0.70571; (Nd-143/Nd-144)(o)=0.512603-0.512645). Nevertheless, some of them have the most radiogenic Sr values ever reported for a magmatic rock in the Meseta and even in the whole Neogene Patagonian Plateau Lavas province ((Sr-17/Sr-86)(o)= 0.70556-0.70571; (Nd-143/Nd-144)(o)=0.512603-0.512608). In addition, very high contents of strongly incompatible elements in the most evolved rocks, together with Sr isotopic ratios higher than those of coeval basalts, suggest the occurrence of open-system magmatic processes. Continuous fractional crystallization from a primitive basaltic source, similar to post-plateau coeval basalts, towards alkali granites combined with small rates of assimilation of host Jurassic tuffs (AFC) in a shallow magmatic reservoir, best explains the geochemical and petrographic features of the felsic rocks. Therefore, A(1)-type magmatic rocks can be generated by open-system crystallization of deep asthenospheric melts in back-are tectonic settings. In Central Patagonia, these similar to 3-4 Ma old alkaline intrusions occur aligned along a similar to N160-170 trending lineament, the Zeballos Fault Zone, stacking the morphotectonic front of one segment of the Patagonian Cordillera. Intrusion along this fault zone
ISSN: 0024-4937

hal-00412030
https://hal.archives-ouvertes.fr/hal-00412030
DOI : 10.1016/j.lithos.2007.07.002

Éditeur(s) : HAL CCSD
Résumé : International audience
Background Orodental diseases include several clinically and genetically heterogeneous disorders that can present in isolation or as part of a genetic syndrome. Due to the vast number of genes implicated in these disorders, establishing a molecular diagnosis can be challenging. We aimed to develop a targeted next-generation sequencing (NGS) assay to diagnose mutations and potentially identify novel genes mutated in this group of disorders. Methods We designed an NGS gene panel that targets 585 known and candidate genes in orodental disease. We screened a cohort of 101 unrelated patients without a molecular diagnosis referred to the Reference Centre for Oro-Dental Manifestations of Rare Diseases, Strasbourg, France, for a variety of orodental disorders including isolated and syndromic amelogenesis imperfecta (AI), isolated and syndromic selective tooth agenesis (STHAG), isolated and syndromic dentinogenesis imperfecta, isolated dentin dysplasia, otodental dysplasia and primary failure of tooth eruption. Results We discovered 21 novel pathogenic variants and identified the causative mutation in 39 unrelated patients in known genes (overall diagnostic rate: 39%). Among the largest subcohorts of patients with isolated AI (50 unrelated patients) and isolated STHAG (21 unrelated patients), we had a definitive diagnosis in 14 (27%) and 15 cases (71%), respectively. Surprisingly, COL17A1 mutations accounted for the majority of autosomal-dominant AI cases. Conclusions We have developed a novel targeted NGS assay for the efficient molecular diagnosis of a wide variety of orodental diseases. Furthermore, our panel will contribute to better understanding the contribution of these genes to orodental disease. Trial registration numbers NCT01746121 and NCT02397824
Journal of Medical Genetics

hal-01272929
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01272929
DOI : 10.1136/jmedgenet-2015-103302
PUBMED : 26502894

Éditeur(s) : HAL CCSD
Résumé : National audience
We propose a method to solve the problem of clustering individuals described by mixed variables structured in blocks. It is a hierarchical method with two levels similar to Hierarchical Principal Component Analysis presented by Wold, based on the mixed topology maps (MTM). The first step consists in establishing, for each block of mixed variables, a clustering representing a synthesis of local individuals at the block level. The second step is to re-apply MTM on the weighted results of the first level. We obtain a global clustering of individuals, consensus among the partitions from level 1. The proposed method is illustrated on data from the national survey in the French housing stock carried out in 2003-2005 by the Observatory for Indoor Air Quality (OQAI).
Fouille de Données Complexes, complexité liée aux données multiples et massives (FDC)
bordeaux, France

hal-00748841
https://hal.archives-ouvertes.fr/hal-00748841
https://hal.archives-ouvertes.fr/hal-00748841/document

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Recent field work and review of radiometric data obtained from Neogene lavas and plutonic rocks exposed in the Eastern Central Patagonian Cordillera (46–48ºS), which overlie subducted segments of the South Chile Ridge, suggest important Late Miocene to Pleistocene morphological changes in relation to base level variations and/or tectonic events. We present new field observations from a region south of Lago General Carrera-Buenos Aires, between the main Cordillera and the Meseta del Lago Buenos Aires, demonstrating that normal faulting controlled valley incisions and occurred during lava emplacement at 5–4 Ma and after 3 Ma. We also show that the 12 Ma basaltic flows of the Meseta del Lago Buenos Aires (~2000 m a.s.l.) have been subjected to deep incision, with younger lavas dated at 1.2 Ma partially filling the valleys. These incisions are thought to reflect progressive eastward tilting of the entire meseta. Our new observations, together with additional features from Central Patagonia, strongly suggest that tectonic events led to a regional widespread morphological change after 5 Ma. The coincidence in time and space between the subduction of segments of the South Chile Ridge at 6 and 3 Ma causing opening of a slab window, and strong base level variations in the studied area, suggests a cause-and-effect relationship. In Central Patagonia, compressional tectonics ended well before extensional events reported here. Causes of uplift and further extension are probably completely disconnected. The uplift is purely tectonic in origin and occurred prior to the subduction of the South Chile Ridge. Extension should be a consequence of this subduction.
ISSN: 0954-4879

insu-00272075
https://hal-insu.archives-ouvertes.fr/insu-00272075
DOI : 10.1111/j.1365-3121.2007.00766.x

Éditeur(s) : HAL CCSD
Résumé : International audience
We present a chronological (K-Ar), petrologic and geochemical study (major and trace elements, Sr-Nd isotopes) of Middle Miocene (ca. 16-14 Ma) calc-alkaline rocks (basalts to andesites) extruded in the present-day back-arc region of Central Patagonia (Zeballos Volcanic Sequence (ZVS), 47 S). This magmatism started shortly after mafic plutonism ceased in the arc region (ca. 16 Ma, 200 km west), and ended ca. 2 My before the onset of voluminous slab tear-related back-arc alkaline basaltic magmatism (ca. 12 to Pliocene). The studied calc-alkaline rocks have a typical subduction-related signature (high LILE/HFSE ratios, depletion in Nb, Ta and Ti; Ba/La >20; Ta/Hf <1.5; (Sr-87/Sr-86)(o)=0.70366-0.70402, epsilon(Nd)=+0.1-+3.8). Major and trace elements contents are consistent with their evolution by closed system fractional crystallization of a presumed parental liquid similar in composition to the most basic rock of the suite. Moreover, a strong subducted sediment imprint is recognized (increasing Th/HFSE and decreasing Ce/Pb during differentiation). However, these rocks show striking similarities with volcanic complexes emplaced above areas where a gently dipping slab occurs (high K contents; similar LREE/HREE, Nb/Zr, Ba/Nb; Th/Hf; Th/Ta, Ta/Hf<0.3), particularly the present-day Andean flat-slab region and the Neuquen Basin during the Late Miocene. A comprehensive tectono-magmatic model is here presented to explain the generation and extrusion of these calc-alkaline magmas during the Middle Miocene. The development of a transient low-angle subduction and the resulting eastward migration of the volcanic front are then proposed. Mixing between stored remnants of calc-alkaline magmatism and later primitive alkaline melts is envisioned as the most likely process accounting for the transitional signature (i.e., intermediate between calc-alkaline and alkaline, La/Nb >I; TiO2 <2 wt%) of some basalts extruded synchronously with genuine alkaline lavas in the Neogene Patagonian Plateau Lavas province.
Volcanismo calcoalcalino durante el Mioceno Medio en Patogonia Central (47°S): petrogenesis e implicaciones en la dinamica de placas. En este trabajo se presenta un estudio cronologico (K-Ar), petrologico y geoquimico (elementos mayores y trazas, isotopos de Sr-Nd) de rocas calcoalcalinas (basaltos a andesitas) del Mioceno Medio (16-14 Ma) que ocurren en una posicion de trasarco en Patagonia Central (47°S; Secuencia Volcanica Zeballos, SVZ). Este magmatismo comenzo poco despees de que el plutonismo mafico cesara en la region bajo el arco (ca. 16 Ma, 200 km al oeste), y termino ca. 2 My antes del comienzo de un voluminoso evento magmatico basaltico alcalino desarrollado en el trasarco, relacionado con ventanas astenosfericas, que continuo hasta el Pleistoceno. Las rocas calcoalcalinas estudiadas tienen una quimica tipicamente relacionada con procesos de subduccion (altas razones LILE/HFSE, empobrecimientos en Nb, Ta y Ti; Ba/La>20; Ta/Hf l,5; (87Sr/86Sr)0=0,70366-0,70402, End~O,1±3,8); y sus contenidos de elementos mayores y trazas son consistentes con una evolucion por cristalizacion fraccionada, en un sistema cerrado, desde un liquido parental de composicion similar a la de la roca mas basica del conjunto analizado. Se reconoce, ademas, la influencia de sedimentos subductados en la composicion de estos magmas (aumento de la razon Tb/HFSE y disminucion de la razon Ce/Pb durante la diferenciacion). Sin embargo, estas rocas muestran importantes similitudes composicionales con las de complejos volcanicos emplazados sobre areas donde ocurre subduccion de bajo angulo (altos contenidos de K, similares razones LREF/HREE, Nb/Zr, Ba/Nb; TblHf; TblTa, Ta/Hf O,3), particularmente rocas de la actual region de subduccion plana en Chile central-Argentina y de la cuenca de Neuquen durante el Mioceno Superior. Se propone aqui un modelo tectono-magmatico que explica la generacion y extension de magmas calcoalcalinos en una posicion de trasarco durante el Mioceno Medio en Patagonia mediante el desarrollo de un fenomeno transiente de subduccion de bajo angulo y el consiguiente desplazamiento hacia el este del frente volcanico. Ademas, la mezcla entre remanentes de este magmatismo calcoalcalino almacenados en la corteza y fundidos alcalinos posteriores, provenientes de la astenosfera, se presenta como el proceso responsable de la generacion de la signatura transicional (i.e., intermedia entre calcoalcalina y alcalina, La/Nb>1; TiO2 2 wt%) reconocida en algunos basaltos que ocurren contemporaneamente con otros puramente alcalinos en la provincia de las Lavas Neogenas de Plateau de la Patagonia.
ANDEAN GEOLOGY

insu-00561888
https://hal-insu.archives-ouvertes.fr/insu-00561888
DOI : 10.5027/andgeo2010-678

Éditeur(s) : HAL CCSD Springer-Verlag
Résumé : The Chile-Argentina Patagonian Cordillera is a natural laboratory to study the interactions between oceanic and continental lithosphere during the subduction of an active spreading ridge beneath a continent. Subduction of the South Chile spreading ridge, which separates the Nazca plate from the Antarctic plate, started around 15–14 Ma at the southern tip of Patagonia. Presently, the southernmost segment of the Chile Ridge enters the Peru-Chile trench at 46°S, at the site of the Chile Triple Junction (CTJ). We review the main events which occurred on land in the CTJ region (46–47°S), related with processes of ridge subduction. We summarize tectonic, sedimentary, and magmatic features in a 30 Ma-to Present chronological table. A preridge subduction stage, from 30 to 15 Ma, is characterized by the onset and growth of Patagonian relief and by a shift from marine to continental detrital sedimentation in the foreland at 20–22 Ma. The change from pre-ridge subduction to ridge subduction is marked on land by a transition from calc-alkaline to alkaline volcanism, at 14–12 Ma, and by the onset of eruption of very large fl ood basalt provinces (future volcanic plateaus) following rapid erosion of the eastern foreland belt. Post-plateau basaltic volcanism (<4 Ma) is coeval with a period of tectonic and morphological rejuvenation during which the eastern foreland of the Cordillera has been affected by extensional/transtensional tectonics. We place these events in the framework of a tectonomagmatic model involving the opening of slab windows due to both slab tear and ridge axis subduction.
Subduction Zone Geodynamics

hal-00421053
https://hal.archives-ouvertes.fr/hal-00421053
DOI : 10.1007/978-3-540-87974-9_12

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The levels and duration of physical activity that can be considered as completely safe in patients with sickle cell anemia (SCA) is unknown. The present study compared the hemorheological and hematological profile, cell density distribution and basic biochemistry between a group of 17 patients with SCA and 21 healthy subjects before and after a 20 min duration submaximal cycling exercise at the same absolute workload. Blood was sampled at rest and 3 min after the end of exercise for measurement of biological parameters. Exercise did not affect the hematocrit and blood viscosity in the two groups. Plasma viscosity was not different between the two groups at rest and similarly increased with exercise. The proportion of intermediary dense cells (with density between 1.11 and 1.12 g/ml) decreased with exercise in the SCA group resulting in an increase in the proportion of red blood cells with a density > 1.12 g/ml. No change was observed in the control group. The present study suggests that mild-moderate exercise is not very harmful for SCA patients. The hemorheological and hematological changes very mild, except for the formation of dense cells but no clinically significant signs of medical complication were present in any of the patients.
ISSN: 0007-1048

hal-00640629
https://hal.archives-ouvertes.fr/hal-00640629
https://hal.archives-ouvertes.fr/hal-00640629/document
https://hal.archives-ouvertes.fr/hal-00640629/file/PEER_stage2_10.1111%252Fj.1365-2141.2011.08728.x.pdf
DOI : 10.1111/j.1365-2141.2011.08728.x

Éditeur(s) : HAL CCSD
Résumé : 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.
ISSN: 2222-1751

Droits : http://creativecommons.org/licenses/by/
hal-01528488
http://hal.upmc.fr/hal-01528488
http://hal.upmc.fr/hal-01528488/document
http://hal.upmc.fr/hal-01528488/file/emi20177a.pdf
DOI : 10.1038/emi.2017.7