Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Addressing data quality issues in information systems remains a challenging task. Many approaches only tackle this issue at the extract, transform and load steps. Here we define a comprehensive method to gain greater insight into data quality characteristics within data warehouse. Our novel architecture was implemented for an hydroecological case study where massive French watercourse sampling data are collected. The method models and makes effective use of spatial, thematic and temporal accuracy, consistency and completeness for multidimensional data in order to offer analysts a “data quality” oriented framework. The results obtained in experiments carried out on the Saône River dataset demonstrated the relevance of our approach
ISSN: 0098-3004

hal-01223918
https://hal.archives-ouvertes.fr/hal-01223918
https://hal.archives-ouvertes.fr/hal-01223918/document
https://hal.archives-ouvertes.fr/hal-01223918/file/final-cogeo.pdf
DOI : 10.1016/j.cageo.2015.09.012

Éditeur(s) : HAL CCSD BMJ Publishing Group
Résumé : International audience
OBJECTIVE:To identify local meteorological drivers of dengue fever in French Guiana, we applied an original data mining method to the available epidemiological and climatic data. Through this work, we also assessed the contribution of the data mining method to the understanding of factors associated with the dissemination of infectious diseases and their spatiotemporal spread.METHODS:We applied contextual sequential pattern extraction techniques to epidemiological and meteorological data to identify the most significant climatic factors for dengue fever, and we investigated the relevance of the extracted patterns for the early warning of dengue outbreaks in French Guiana.RESULTS:The maximum temperature, minimum relative humidity, global brilliance, and cumulative rainfall were identified as determinants of dengue outbreaks, and the precise intervals of their values and variations were quantified according to the epidemiologic context. The strongest significant correlations were observed between dengue incidence and meteorological drivers after a 4-6-week lag.DISCUSSION:We demonstrated the use of contextual sequential patterns to better understand the determinants of the spatiotemporal spread of dengue fever in French Guiana. Future work should integrate additional variables and explore the notion of neighborhood for extracting sequential patterns.CONCLUSIONS:Dengue fever remains a major public health issue in French Guiana. The development of new methods to identify such specific characteristics becomes crucial in order to better understand and control spatiotemporal transmission.Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
ISSN: 1067-5027

lirmm-01379072
https://hal-lirmm.ccsd.cnrs.fr/lirmm-01379072
DOI : 10.1136/amiajnl-2013-002348
PUBMED : 24549761

Éditeur(s) : HAL CCSD Wiley-VCH Verlag
Résumé : International audience
Deciphering the assembly history of the Milky Way is a formidable task, which becomes possible only if one can produce high-resolution chrono-chemo-kinematical maps of the Galaxy. Data from large-scale astrometric and spectroscopic surveys will soon provide us with a well-defined view of the current chemo-kinematical structure of the Milky Way, but will only enable a blurred view on the temporal sequence that led to the present-day Galaxy. As demonstrated by the (ongoing) exploitation of data from the pioneering photometric missions CoRoT, Kepler, and K2, asteroseismology provides the way forward: solar-like oscillating giants are excellent evolutionary clocks thanks to the availability of seismic constraints on their mass and to the tight age-initial-mass relation they adhere to. In this paper we identify five key outstanding questions relating to the formation and evolution of the Milky Way that will need precise and accurate ages for large samples of stars to be addressed, and we identify the requirements in terms of number of targets and the precision on the stellar properties that are needed to tackle such questions. By quantifying the asteroseismic yields expected from PLATO for red-giant stars, we demonstrate that these requirements are within the capabilities of the current instrument design, provided that observations are sufficiently long to identify the evolutionary state and allow robust and precise determination of acoustic-mode frequencies. This will allow us to harvest data of sufficient quality to reach a 10% precision in age. This is a fundamental pre-requisite to then reach the more ambitious goal of a similar level of accuracy, which will only be possible if we have to hand a careful appraisal of systematic uncertainties on age deriving from our limited understanding of stellar physics, a goal which conveniently falls within the main aims of PLATO's core science.
ISSN: 0004-6337

hal-01541393
https://hal.archives-ouvertes.fr/hal-01541393
ARXIV : 1706.3778
BIBCODE : 2017AN....338..644M
DOI : 10.1002/asna.201713385

Éditeur(s) : HAL CCSD
Résumé : LPSC14037
Scientific data collected with modern sensors or dedicated detectors exceed very often the perimeter of the initial scientific design. These data are obtained more and more frequently with large material and human efforts. A large class of scientific experiments are in fact unique because of their large scale, with very small chances to be repeated and to superseded by new experiments in the same domain: for instance high energy physics and astrophysics experiments involve multi-annual developments and a simple duplication of efforts in order to reproduce old data is simply not affordable. Other scientific experiments are in fact unique by nature: earth science, medical sciences etc. since the collected data is "time-stamped" and thereby non-reproducible by new experiments or observations. In addition, scientific data collection increased dramatically in the recent years, participating to the so-called "data deluge" and inviting for common reflection in the context of "big data" investigations. The new knowledge obtained using these data should be preserved long term such that the access and the re-use are made possible and lead to an enhancement of the initial investment. Data observatories, based on open access policies and coupled with multi-disciplinary techniques for indexing and mining may lead to truly new paradigms in science. It is therefore of outmost importance to pursue a coherent and vigorous approach to preserve the scientific data at long term. The preservation remains nevertheless a challenge due to the complexity of the data structure, the fragility of the custom-made software environments as well as the lack of rigorous approaches in workflows and algorithms. To address this challenge, the PREDON project has been initiated in France in 2012 within the MASTODONS program: a Big Data scientific challenge, initiated and supported by the Interdisciplinary Mission of the National Centre for Scientific Research (CNRS). PREDON is a study group formed by researchers from different disciplines and institutes. Several meetings and workshops lead to a rich exchange in ideas, paradigms and methods. The present document includes contributions of the participants to the PREDON Study Group, as well as invited papers, related to the scientific case, methodology and technology. This document should be read as a "facts finding" resource pointing to a concrete and significant scientific interest for long term research data preservation, as well as to cutting edge methods and technologies to achieve this goal. A sustained, coherent and long term action in the area of scientific data preservation would be highly beneficial.
http://hal.in2p3.fr/in2p3-00959072

in2p3-00959072
http://hal.in2p3.fr/in2p3-00959072
http://hal.in2p3.fr/in2p3-00959072/document
http://hal.in2p3.fr/in2p3-00959072/file/PREDON_Scientific_Data_Preservation_2014.pdf

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The etiology of congenital heart defect (CHD) combines environmental and genetic factors. So far, there were studies reporting on the screening of a single gene on unselected CHD or on familial cases selected for specific CHD types. Our goal was to systematically screen a proband of familial cases of CHD on a set of genetic tests to evaluate the prevalence of disease-causing variant identification. A systematic screening of GATA4, NKX2-5, ZIC3 and Multiplex ligation-dependent probe amplification (MLPA) P311 Kit was setup on the proband of 154 families with at least two cases of non-syndromic CHD. Additionally, ELN screening was performed on families with supravalvular arterial stenosis. Twenty-two variants were found, but segregation analysis confirmed unambiguously the causality of 16 variants: GATA4 (1 x), NKX2-5 (6 x), ZIC3 (3 x), MLPA (2 x) and ELN (4 x). Therefore, this approach was able to identify the causal variant in 10.4% of familial CHD cases. This study demonstrated the existence of a de novo variant even in familial CHD cases and the impact of CHD variants on adult cardiac condition even in the absence of CHD. This study showed that the systematic screening of genetic factors is useful in familial CHD cases with up to 10.4% elucidated cases. When successful, it drastically improved genetic counseling by discovering unaffected variant carriers who are at risk of transmitting their variant and are also exposed to develop cardiac complications during adulthood thus prompting long-term cardiac follow-up. This study provides an important baseline at dawning of the next-generation sequencing era.
ISSN: 1018-4813

hal-01404211
https://hal-univ-bourgogne.archives-ouvertes.fr/hal-01404211
DOI : 10.1038/ejhg.2015.105
PUBMED : 26014430

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 : URL de l'article : http://www.sciencedirect.com/science/article/B6WPN-4XY3KDK-2/2/fd8508af63d82e29b4f9829c65194e26
The impact of climatic changes that occurred during the last glacial maximum and the Holocene on vegetation changes in the Amazon Basin and the Guiana Shield are still widely debated. The aim of our study was to investigate whether major changes in vegetation (i.e. transitions between rainforests and C4 savannas) occurred in northern French Guiana during the Holocene. We measured variations in the δ13C of soil organic matter at eight sites now occupied by forest or savannah. The forest sites were selected to cover two regions (forest refugia and peneplains) which are thought to have experienced different intensities of disturbance during the latest Pleistocene and the Holocene. We found that none of the forest sites underwent major disturbances during the Holocene, i.e. they were not replaced by C4 savannahs or C4 forest savannahs for long periods. Our results thus suggest that tropical rainforests in northern French Guiana were resilient to drier climatic conditions during the Holocene. Nevertheless, geographical and vertical variations in the 13C of SOM were compatible with minor changes in vegetation, variations in soil processes or in soil physical properties.
ISSN: 0033-5894

halshs-00551758
https://halshs.archives-ouvertes.fr/halshs-00551758
DOI : 10.1016/j.yqres.2009.11.007