Controlled access under review : improving the governance of genomic data access

In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention

Les paysages de Chapelle-des-Bois hier, aujourd'hui et demain

Plus qu'ailleurs, en raison de la fragilité des équilibres économiques dont ils dépendent, les terroirs de moyenne montagne se contractent au profit de la forêt et la de friche. Cette évolution modifie le contenu et l'ampleur visuelle des paysages qui tendent à se fermer : là où, naguère, le regard portait de crête en crête, la vue, aujourd'hui, se casse sur de jeunes friches qui, demain, retourneront à la forêt

Rheological properties and structure of a semi-solid tin-lead alloy.

Massachusetts Institute of Technology. Dept. of Metallurgy and Materials Science. Thesis. 1974. Ph.D.MICROFICHE COPY ALSO AVAILABLE IN SCIENCE LIBRARY.Leaf number 102 omitted in paging. Vita.Includes bibliographical references.Ph.D

The Activation-Relaxation Technique : ART nouveau and kinetic ART

The evolution of many systems is dominated by rare activated events that occur on timescale ranging from nanoseconds to the hour or more. For such systems, simulations must leave aside the full thermal description to focus specifically on mechanisms that generate a configurational change. We present here the activation relaxation technique (ART), an open-ended saddle point search algorithm, and a series of recent improvements to ART nouveau and kinetic ART, an ART-based on-the-fly off-lattice self-learning kinetic Monte Carlo method

African monsoon teleconnections with tropical SSTs: validation and evolution in a set of IPCC4 simulations

A set of 12 state-of-the-art coupled oceanatmosphere general circulation models (OAGCMs) is explored to assess their ability to simulate the main teleconnections between the West African monsoon (WAM) and the tropical sea surface temperatures (SSTs) at the interannual to multi-decadal time scales. Such teleconnections are indeed responsible for the main modes of precipitation variability observed over West Africa and represent an interesting benchmark for the models that have contributed to the fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC4). The evaluation is based on a maximum covariance analysis (MCA) applied on tropical SSTs and WAM rainfall. To distinguish between interannual and multi-decadal variability, all datasets are partitioned into low-frequency (LF) and high-frequency (HF) components prior to analysis. First applied to HF observations, the MCA reveals two major teleconnections. The first mode highlights the strong influence of the El Niño Southern Oscillation (ENSO). The second mode reveals a relationship between the SST in the Gulf of Guinea and the northward migration of the monsoon rainbelt over the West African continent. When applied to HF outputs of the twentieth century IPCC4 simulations, the MCA provides heterogeneous results. Most simulations show a single dominant Pacific teleconnection, which is, however, of the wrong sign for half of the models. Only one model shows a significant second mode, emphasizing the OAGCMs’ difficulty in simulating the response of the African rainbelt to Atlantic SST anomalies that are not synchronous with Pacific anomalies. The LF modulation of these HF teleconnections is then explored through running correlations between expansion coefficients (ECs) for SSTs and precipitation. The observed time series indicate that both Pacific and Atlantic teleconnections get stronger during the twentieth century. The IPCC4 simulations of the twentieth and twenty-first centuries do not show any significant change in the pattern of the teleconnections, but the dominant ENSO teleconnection also exhibits a significant strengthening, thereby suggesting that the observed trend could be partly a response to the anthropogenic forcing. Finally, the MCA is also applied to the LF data. The first observed mode reveals a well-known inter-hemispheric SST pattern that is strongly related to the multi-decadal variability of the WAM rainfall dominated by the severe drying trend from the 1950s to the 1980s. Whereas recent studies suggest that this drying could be partly caused by anthropogenic forcings, only 5 among the 12 IPCC4 models capture some features of this LF coupled mode. This result suggests the need for a more detailed validation of the WAM variability, including a dynamical interpretation of the SST–rainfall relationships

Influence of Gauss and Gauss-Lobatto quadrature rules on the accuracy of a quadrilateral finite element method in the time domain.

International audienceIn this paper, we examine the infl uence of numerical integration on finite element methods using quadrilateral or hexahedral meshes in the time domain. We pay special attention to the use of Gauss-Lobatto points to perform mass lumping for any element order. We provide some theoretical results through several error estimates that are completed by various numerical experiments

Modélisation de vibrations de barres aux moyennes fréquences par des quantités énergétiques

Cet article présente une méthode basée sur des grandeurs quadratiques moyennées temporellement et spatialement, afin de décrire les tranferts énergétiques dans les barres quand l'augmentation de la fréquence rend prohibitive l'utilisation d'une formulation classique en déplacemment. Dans le cas particulier d'un amortissement faible, cette méthode est similaire à l'approche VCA (Vibrational Conductivity Approach). L'aspect novateur réside dans l'écriture de conditions limites pour les parties actives et réactives de l'intensité de structure, à partir d'une description des différentes jonctions par des impédances

X-ray magnetic circular dichroism in (Ge,Mn) compounds: experiments and modeling

X-ray absorption (XAS) and x-ray magnetic circular dichroism (XMCD) spectra at the L$_{2,3}$ edges of Mn in (Ge,Mn) compounds have been measured and are compared to the results of first principles calculation. Early \textit{ab initio} studies show that the Density Functional Theory (DFT) can very well describe the valence band electronic properties but fails to reproduce a characteristic change of sign in the L$_{3}$ XMCD spectrum of Mn in Ge$_3$Mn$_5$, which is observed in experiments. In this work we demonstrate that this disagreement is partially related to an underestimation of the exchange splitting of Mn 2$p$ core states within the local density approximation. It is shown that the change in sign experimentally observed is reproduced if the exchange splitting is accurately calculated within the Hartree-Fock approximation, while the final states can be still described by the DFT. This approach is further used to calculate the XMCD in different (Ge,Mn) compounds. It demonstrates that the agreement between experimental and theoretical spectra can be improved by combining state of the art calculations for the core and valence states respectively.Comment: 8 page

Differential regulation of abundance and deadenylation of maternal transcripts during bovine oocyte maturation in vitro and in vivo

<p>Abstract</p> <p>Background</p> <p>In bovine maturing oocytes and cleavage stage embryos, gene expression is mostly controlled at the post-transcriptional level, through degradation and deadenylation/polyadenylation. We have investigated how post transcriptional control of maternal transcripts was affected during in vitro and in vivo maturation, as a model of differential developmental competence.</p> <p>Results</p> <p>Using real time PCR, we have analyzed variation of maternal transcripts, in terms of abundance and polyadenylation, during in vitro or in vivo oocyte maturation and in vitro embryo development. Four genes are characterized here for the first time in bovine: ring finger protein 18 (<it>RNF18</it>) and breast cancer anti-estrogen resistance 4 (<it>BCAR4</it>), whose oocyte preferential expression was not previously reported in any species, as well as Maternal embryonic leucine zipper kinase (<it>MELK</it>) and <it>STELLA</it>. We included three known oocyte marker genes (Maternal antigen that embryos require (<it>MATER</it>), Zygote arrest 1 (<it>ZAR1</it>), NACHT, leucine rich repeat and PYD containing 9 (<it>NALP9</it>)). In addition, we selected transcripts previously identified as differentially regulated during maturation, peroxiredoxin 1 and 2 (<it>PRDX1, PRDX2</it>), inhibitor of DNA binding 2 and 3 (<it>ID2</it>, <it>ID3</it>), cyclin B1 (<it>CCNB1</it>), cell division cycle 2 (<it>CDC2</it>), as well as Aurora A (<it>AURKA</it>). Most transcripts underwent a moderate degradation during maturation. But they displayed sharply contrasted deadenylation patterns that account for variations observed previously by DNA array and correlated with the presence of a putative cytoplasmic polyadenylation element in their 3' untranslated region. Similar variations in abundance and polyadenylation status were observed during in vitro maturation or in vivo maturation, except for <it>PRDX1</it>, that appears as a marker of in vivo maturation. Throughout in vitro development, oocyte restricted transcripts were progressively degraded until the morula stage, except for <it>MELK </it>; and the corresponding genes remained silent after major embryonic genome activation.</p> <p>Conclusion</p> <p>Altogether, our data emphasize the extent of post-transcriptional regulation during oocyte maturation. They do not evidence a general alteration of this phenomenon after in vitro maturation as compared to in vivo maturation, but indicate that some individual messenger RNA can be affected.</p