Towards a Better Knowledge of Natural Methane Releases in the French Alps: A Field Approach

International audienceWe report investigations performed at some hydrocarbon gas seeps located in the French Subalpine Chains in zones of outcropping Jurassic black shales, increasing the reported number of such occurrences in this part of the Alps. We present the characteristics of each of the seeps, based on soil flux measurements and soil gas measurements. Gases emitted are CH4-rich (87-94%) with the exception of one site (78.5% CH4 + 8.2% CO2) where an active landslide may induce dilution by atmospheric air. CO2 is generally measured at low levels (<1.6%). Concentrations in C2H6 are more variable, from less than 1% to more than 2.3%. Gas is emitted over areas of various sizes. The smallest gas emission area measures only 60x20cm, characterized by a strong hydrocarbon flux (release of about 100kg of CH4 per year). At a second site, hydrocarbon emissions are measured over a surface of 12m(2). For this site, methane emission is evaluated at 235kg per year and CO2 emission is 600kg per year, 210kg being related to gas seepage. At the third site, hydrocarbons are released over a 60m(2) area but strong gas venting is restricted to localized seeps. Methane emission is evaluated at 5.1 tons per year and CO2 emission at 1.58 tons per year, out of which 0.53 tons are attributed to gas seepage. Several historical locations remain uninvestigated at present, and numerous others may still be unknown. We outline strategies to search for such unrecorded sites. Considering the topography of the potential alpine and perialpine emission areas, the possibilities to detect gas emissions appear of the size recorded so far seem to be restricted to ground-based methods or to methods offering the possibility to point orthogonally to the soil towards the seep maximum. If such sites are to be investigated in the future in the frame of Environmental Baseline Assessment (EBA), even establishing appropriate monitoring protocols will be challenging

Incised-valley morphologies and sedimentary-fills within the inner shelf of the northern Bay of Biscay

This study is a first synthesis focused on incised-valleys located within the inner shelf of the Bay of Biscay. It is based on previously published results obtained during recent seismic surveys and coring campaigns. The morphology of the valleys appears to be strongly controlled by tectonics and lithology. The Pleistocene sedimentary cover of the shelf is very thin and discontinuous with a maximum thickness ranging between 30 and 40 m in incised-valley fills. Thus the incised bedrock morphology plays a key-role by controlling hydrodynamics and related sediment transport and deposition that explains some variations of those incised-valley fills with respect to the previously published general models

Structure and dynamics of the Shapley Supercluster

We present results of our wide-field redshift survey of galaxies in a 285 square degree region of the Shapley Supercluster (SSC), based on a set of 10529 velocity measurements (including 1201 new ones) on 8632 galaxies obtained from various telescopes and from the literature. Our data reveal that the main plane of the SSC (v~ 14500 km/s) extends further than previous estimates, filling the whole extent of our survey region of 12~degrees by 30~degrees on the sky (30 x 75~h-1 Mpc). There is also a connecting structure associated with the slightly nearer Abell~3571 cluster complex (v~ 12000km/s. These galaxies seem to link two previously identified sheets of galaxies and establish a connection with a third one at V= 15000 km/s near R.A.= 13h. They also tend to fill the gap of galaxies between the foreground Hydra-Centaurus region and the more distant SSC. In the velocity range of the Shapley Supercluster (9000 km/s < cz < 18000 km/s), we found redshift-space overdensities with b\_j < 17.5 of ~5.4 over the 225 square degree central region and ~3.8 in a 192 square degree region excluding rich clusters. Over the large region of our survey, we find that the intercluster galaxies make up 48 per cent of the observed galaxies in the SSC region and, accounting for the different completeness, may contribute nearly twice as much mass as the cluster galaxies. In this paper, we discuss the completeness of the velocity catalogue, the morphology of the supercluster, the global overdensity, and some properties of the individual galaxy clusters in the Supercluster.Comment: Accepted for publication in Astronomy and Astrophysic

Correction: Exome-wide association study reveals novel susceptibility genes to sporadic dilated cardiomyopathy

This corrects the article DOI: 10.1371/journal.pone.017299

Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology

<p>Abstract</p> <p>Background</p> <p>The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, mosquito control programs are now threatened by the emergence of insecticide resistance. Hitherto, most research efforts have been focused on elucidating the molecular basis of inherited resistance. Less attention has been paid to the short-term response of mosquitoes to insecticides and pollutants which could have a significant impact on insecticide efficacy. Here, a combination of LongSAGE and Solexa sequencing was used to perform a deep transcriptome analysis of larvae of the dengue vector <it>Aedes aegypti </it>exposed for 48 h to sub-lethal doses of three chemical insecticides and three anthropogenic pollutants.</p> <p>Results</p> <p>Thirty millions 20 bp cDNA tags were sequenced, mapped to the mosquito genome and clustered, representing 6850 known genes and 4868 additional clusters not located within predicted genes. Mosquitoes exposed to insecticides or anthropogenic pollutants showed considerable modifications of their transcriptome. Genes encoding cuticular proteins, transporters, and enzymes involved in the mitochondrial respiratory chain and detoxification processes were particularly affected. Genes and molecular mechanisms potentially involved in xenobiotic response and insecticide tolerance were identified.</p> <p>Conclusions</p> <p>The method used in the present study appears as a powerful approach for investigating fine transcriptome variations in genome-sequenced organisms and can provide useful informations for the detection of novel transcripts. At the biological level, despite low concentrations and no apparent phenotypic effects, the significant impact of these xenobiotics on mosquito transcriptomes raise important questions about the 'hidden impact' of anthropogenic pollutants on ecosystems and consequences on vector control.</p

No evidence for an association between the -871 T/C promoter polymorphism in the B-cell-activating factor gene and primary Sjögren's syndrome

Polyclonal B cell activation might be related to pathogenic over-expression of B-cell-activating factor (BAFF) in primary Sjögren's syndrome (pSS) and other autoimmune diseases. We therefore investigated whether BAFF over-expression in pSS could be a primary, genetically determined event that leads to the disease. The complete BAFF gene was sequenced in Caucasian pSS patients and control individuals. The only single nucleotide polymorphism frequently observed, namely -871 T/C in the promoter region, was then genotyped in 162 French patients with pSS and 90 French control individuals. No significant differences in allele (T allele frequency: 49.7% in patients with pSS versus 50% in controls; P = 0.94) and genotype frequencies of BAFF polymorphism were detected between pSS patients and control individuals. BAFF gene polymorphism was not associated with a specific pattern of antibody secretion either. T allele carriers had significantly increased BAFF protein serum levels (mean values of 8.6 and 5.7 ng/ml in patients with TT and TC genotypes, respectively, versus 3.3 ng/ml in patients with CC genotype; P = 0.01), although no correlation was observed between BAFF polymorphism and mRNA level. In conclusion, BAFF gene polymorphism is neither involved in genetic predisposition to pSS nor associated with a specific pattern of antibody production

Analysis of the 24-Hour Activity Cycle: An illustration examining the association with cognitive function in the Adult Changes in Thought (ACT) Study

The 24-hour activity cycle (24HAC) is a new paradigm for studying activity behaviors in relation to health outcomes. This approach captures the interrelatedness of the daily time spent in physical activity (PA), sedentary behavior (SB), and sleep. We illustrate and compare the use of three popular approaches, namely isotemporal substitution model (ISM), compositional data analysis (CoDA), and latent profile analysis (LPA) for modeling outcome associations with the 24HAC. We apply these approaches to assess an association with a cognitive outcome, measured by CASI item response theory (IRT) score, in a cohort of 1034 older adults (mean [range] age = 77 [65-100]; 55.8% female; 90% White) who were part of the Adult Changes in Thought (ACT) Activity Monitoring (ACT-AM) sub-study. PA and SB were assessed with thigh-worn activPAL accelerometers for 7 days. We highlight differences in assumptions between the three approaches, discuss statistical challenges, and provide guidance on interpretation and selecting an appropriate approach. ISM is easiest to apply and interpret; however, the typical ISM model assumes a linear association. CoDA specifies a non-linear association through isometric logratio transformations that are more challenging to apply and interpret. LPA can classify individuals into groups with similar time-use patterns. Inference on associations of latent profiles with health outcomes need to account for the uncertainty of the LPA classifications which is often ignored. The selection of the most appropriate method should be guided by the scientific questions of interest and the applicability of each model's assumptions. The analytic results did not suggest that less time spent on SB and more in PA was associated with better cognitive function. Further research is needed into the health implications of the distinct 24HAC patterns identified in this cohort.Comment: 51 pages, 11 tables, 8 figure

Front Psychol

The 24-h activity cycle (24HAC) is a new paradigm for studying activity behaviors in relation to health outcomes. This approach inherently captures the interrelatedness of the daily time spent in physical activity (PA), sedentary behavior (SB), and sleep. We describe three popular approaches for modeling outcome associations with the 24HAC exposure. We apply these approaches to assess an association with a cognitive outcome in a cohort of older adults, discuss statistical challenges, and provide guidance on interpretation and selecting an appropriate approach. We compare the use of the isotemporal substitution model (ISM), compositional data analysis (CoDA), and latent profile analysis (LPA) to analyze 24HAC. We illustrate each method by exploring cross-sectional associations with cognition in 1,034 older adults (Mean age = 77; Age range = 65-100; 55.8% female; 90% White) who were part of the Adult Changes in Thought (ACT) Activity Monitoring (ACT-AM) sub-study. PA and SB were assessed with thigh-worn activPAL accelerometers for 7-days. For each method, we fit a multivariable regression model to examine the cross-sectional association between the 24HAC and Cognitive Abilities Screening Instrument item response theory (CASI-IRT) score, adjusting for baseline characteristics. We highlight differences in assumptions and the scientific questions addressable by each approach. ISM is easiest to apply and interpret; however, the typical ISM assumes a linear association. CoDA uses an isometric log-ratio transformation to directly model the compositional exposure but can be more challenging to apply and interpret. LPA can serve as an exploratory analysis tool to classify individuals into groups with similar time-use patterns. Inference on associations of latent profiles with health outcomes need to account for the uncertainty of the LPA classifications, which is often ignored. Analyses using the three methods did not suggest that less time spent on SB and more in PA was associated with better cognitive function. The three standard analytical approaches for 24HAC each have advantages and limitations, and selection of the most appropriate method should be guided by the scientific questions of interest and applicability of each model's assumptions. Further research is needed into the health implications of the distinct 24HAC patterns identified in this cohort

Collaboration for conservation: assessing countrywide carnivore occupancy dynamics from sparse data

Aim: Assessing the distribution and persistence of species across their range is a crucial component of wildlife conservation. It demands data at adequate spatial scales and over extended periods of time, which may only be obtained through collaborative efforts, and the development of methods that integrate heterogeneous datasets. We aimed to combine existing data on large carnivores to evaluate population dynamics and improve knowledge on their distribution nationwide. Location: Botswana. Methods: Between 2010 and 2016, we collated data on African wild dog, cheetah, leopard, brown and spotted hyaena and lion gathered with different survey methods by independent researchers across Botswana. We used a multi-species, multi-method dynamic occupancy model to analyse factors influencing occupancy, persistence and colonization, while accounting for imperfect detection. Lastly, we used the gained knowledge to predict the probability of occurrence of each species countrywide. Results: Wildlife areas and communal rangelands had similar occupancy probabilities for most species. Large carnivore occupancy was low in commercial farming areas and where livestock density was high, except for brown hyaena. Lion occupancy was negatively associated with human density; lion and spotted hyaena occupancy was high where rainfall was high, while the opposite applied to brown hyaena. Lion and leopard occupancy remained constant countrywide over the study period. African wild dog and cheetah occupancy declined over time in the south and north, respectively, whereas both hyaena species expanded their ranges. Countrywide predictions identified the highest occupancy for leopards and lowest for the two hyaena species. Main Conclusions: We highlight the necessity of data sharing and propose a generalizable analytical method that addresses the challenges of heterogeneous data common in ecology. Our approach, which enables a comprehensive multi-species assessment at large spatial and temporal scales, supports the development of data-driven conservation guidelines and the implementation of evidence-based management strategies nationally and internationally

CA-125 early dynamics to predict overall survival in women with newly diagnosed advanced ovarian cancer based on meta-analysis data

(1) Background: Cancer antigen 125 (CA-125) is a protein produced by ovarian cancer cells that is used for patients’ monitoring. However, the best ways to analyze its decline and prognostic role are poorly quantified. (2) Methods: We leveraged individual patient data from the Gynecologic Cancer Intergroup (GCIG) meta-analysis (N = 5573) to compare different approaches summarizing the early trajectory of CA-125 before the prediction time (called the landmark time) at 3 or 6 months after treatment initiation in order to predict overall survival. These summaries included observed and estimated measures obtained by a linear mixed model (LMM). Their performances were evaluated by 10-fold cross-validation with the Brier score and the area under the ROC (AUC). (3) Results: The estimated value and the last observed value at 3 months were the best measures used to predict overall survival, with an AUC of 0.75 CI 95% [0.70; 0.80] at 24 and 36 months and 0.74 [0.69; 0.80] and 0.75 [0.69; 0.80] at 48 months, respectively, considering that CA-125 over 6 months did not improve the AUC, with 0.74 [0.68; 0.78] at 24 months and 0.71 [0.65; 0.76] at 36 and 48 months. (4) Conclusions: A 3-month surveillance provided reliable individual information on overall survival until 48 months for patients receiving first-line chemotherapy