SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages

SAGE (Serial Analysis of Gene Expression) experiments generate short nucleotide sequences called ‘tags’ which are assumed to map unambiguously to their original transcripts (1 tag to 1 transcript mapping). Nevertheless, many tags are generated that do not map to any transcript or map to multiple transcripts. Current bioinformatics resources, such as SAGEmap and TAGmapper, have focused on reducing the number of unmapped tags. Here, we describe SAGETTARIUS, a new high-throughput program that performs successive precise Nla3 and Sau3A tag to transcript mapping, based on specifically designed Virtual Tag (VT) libraries. First, SAGETTARIUS decreases the number of tags mapped to multiple transcripts. Among the various mapping resources compared, SAGETTARIUS performed the best in this respect by decreasing up to 11% the number of multiply mapped tags. Second, SAGETTARIUS allows the establishment of a guideline for SAGE experiment sequencing efforts through efficient mapping of the CRT (Cytoplasmic Ribosomal protein Transcripts)-specific tags. Using all publicly available human and mouse Nla3 SAGE experiments, we show that sequencing 100 000 tags is sufficient to map almost all CRT-specific tags and that four sequencing stages can be identified when carrying out a human or mouse SAGE project. SAGETTARIUS is web interfaced and freely accessible to academic users

Synthesis and polymerization of cyclobutenyl-functionalized polylactide and polycaprolactone: a consecutive ROP/ROMP route towards poly(1,4-butadiene)-g-polyesters

International audienceEfficient preparation of cyclobutenyl end-functionalized polyester macromonomers bearing polylactide (PLA) or poly(ε-caprolactone) (PCL) arms was achieved by organocatalyzed ring-opening polymerization (ROP) of L-lactide or ε-caprolactone in the presence of cis-3,4-bis(hydroxymethyl)cyclobutene or cis-4-benzyloxymethyl-3-hydroxymethylcyclobutene acting as an initiator. Cyclobutenyl end-functionalized PLA and PCL macromonomers having one or two arms were obtained in high yields with excellent control over molecular weights (up to 11 000 g mol−1) and dispersity (PDI < 1.25) by organocatalyzed ROP using 4-(N,N-dimethylamino)pyridine (DMAP) and 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), respectively. Ring-opening metathesis polymerization (ROMP) of the macromonomers using ruthenium-based Grubbs' second generation catalyst afforded well-defined polybutadiene-g-polyester copolymers having an exclusively linear polybutadiene backbone with a strictly 1,4-type microstructure, with molecular weights ranging from 20 000 to 170 000 g mol−1 and low dispersities (PDI ≤ 1.30). The products resulting from this consecutive ROP/ROMP route represent the first examples of poly(1,4-butadiene)-g-polyesters through the macromonomer route

Stratégie d'étude de la baisse des températures de forgeage appliquée à un alliage de cuivre Cu-Ni-Si

La baisse des températures de forgeage représenterait une source d'économie d'énergie importante pour les industries. Cependant, une telle modi?cation ne peut être sans conséquence sur la faisabilité d'un procédé. Cette communication présente la stratégie scienti?que développée pour répondre à cette problématique appliquée à une pièce forgée en alliage Cu-Ni-Si. La première phase de cette stratégie a consisté à caractériser le matériau et le procédé de forgeage effectifs. L'analyse ?ne de l'ensemble de ces résultats a démontré l'existence d'un fort couplage matériau-procédé. Pour aller vers l'optimisation du procédé, la connaissance des limites de formabilité du ma tériau sollicité dans les conditions de forgeage de la pièce est essentielle. Une boucle d'optimisation couplant un modèle numérique du procédé et une étude de formabilité permettrait d'identi?er les températures minimales admissibles par le procédé

Report of the JRC’s Descriptor 2 workshop in support to the review of the Commission Decision 2010/477/EU concerning MSFD criteria for assessing Good Environmental Status for NIS

The MSFD workshop on non-indigenous species (NIS, MSFD D2), held in Ispra JRC (10th-11th of September 2015) aimed to provide clear proposals and conclusions on some of the outstanding issues identified in the D2 review manual (May 2015 consultation version: D2 review manual: https://circabc.europa.eu/sd/a/cd4bbd6a-454a-40db-b805-52fb195d4e56/COMDEC_Review_D2_V6.pdf) in the broader context of support to the review of Commission Decision 2010/477/EU. This report is complementing the Commission Decision 2010/477/EU review manual (JRC96884) and presents the result of the scientific and technical review concluding phase 1 of the review of the Commission Decision 2010/477/EU in relation to Descriptor 2. The review has been carried out by the EC JRC together with experts nominated by EU Member States, and has considered contributions from the GES Working Group in accordance with the roadmap set out in the MSFD implementation strategy (agreed on at the 11th CIS MSCG meeting). The main issues addressed and tackled in this workshop’s report are: - Proposed changes in D2 assessment criteria; - Indicators and methodological standards; - GES threshold values and reference points; - Way forward.JRC.H.1-Water Resource

Prevalence, risk factors, and impact on outcome of cytomegalovirus replication in serum of Cambodian HIV-infected patients (2004-2007)

BACKGROUND: In developing countries, the study of cytomegalovirus (CMV) coinfection in HIV-infected patients remains neglected. Quantitative CMV polymerase chain reaction (PCR) is the gold standard diagnostic tool for analyzing serum CMV replication and for predicting CMV disease. We estimated the prevalence of replicating CMV in sera of newly diagnosed HIV-infected Cambodian patients and examined its impact on mortality. METHODS: This cohort study was based on 2 highly active antiretroviral therapy treatment programs in Cambodia between 2004 and 2007. Quantitative CMV PCR was performed on baseline serum samples of 377 HIV-infected patients. RESULTS: The prevalence of serum CMV DNA was 55.2% (150 of 272) in patients with CD4 count <100/mm. In multivariate analysis, hemoglobin <9 g/dL, CD4 count <100/mm, and Karnofsky index <50 were independently associated with positive serum CMV DNA at baseline. During a 3-year follow-up period, CMV viral load >or=3.1 log10 copies per milliliter was significantly associated with death independently of CD4 count, other opportunistic infections, and highly active antiretroviral therapy. CONCLUSIONS: As in industrialized countries, serum CMV replication is highly prevalent among HIV-infected Cambodian patients and is associated with increased mortality. This underscores the importance of diagnostic CMV infection by PCR in sera of HIV-infected patients with CD4 count <100/mm and treating this opportunistic infection to reduce its associated mortality

Dynamic recrystallization behaviour of spheroidal graphite iron. Application to cutting operations

To increase the competitiveness of manufacturing processes, numerical approaches are unavoidable. Nevertheless, a precise knowledge of the thermo-mechanical behaviour of the materials is necessary to simulate accurately these processes. Previous experimental studies have provided a limited information concerning dynamic recrystallization of spheroidal graphite iron under hot cutting operations. The purpose of this paper is to develop a constitutive model able to describe accurately the occurrence of this phenomenon. Compression tests are carried out using a Gleeble 3500 thermo-mechanical simulator to determine the hot deformation behaviour of spheroidal graphite iron at high strains. Once the activation range of the dynamic recrystallization process is assessed, a constitutive model taking into account this phenomenon is developed and implemented in the Abaqus/Explicit software. Finally, a specific cutting test and its finite element model are introduced. The ability of the numerical model to predict the occurrence of dynamic recrystallization is then compared to experimental observations

Tailoring Anderson localization by disorder correlations in 1D speckle potentials

We study Anderson localization of single particles in continuous, correlated, one-dimensional disordered potentials. We show that tailored correlations can completely change the energy-dependence of the localization length. By considering two suitable models of disorder, we explicitly show that disorder correlations can lead to a nonmonotonic behavior of the localization length versus energy. Numerical calculations performed within the transfer-matrix approach and analytical calculations performed within the phase formalism up to order three show excellent agreement and demonstrate the effect. We finally show how the nonmonotonic behavior of the localization length with energy can be observed using expanding ultracold-atom gases

Effect of a reduction in glomerular filtration rate after nephrectomy on arterial stiffness and central hemodynamics: rationale and design of the EARNEST study

Background: There is strong evidence of an association between chronic kidney disease (CKD) and cardiovascular disease. To date, however, proof that a reduction in glomerular filtration rate (GFR) is a causative factor in cardiovascular disease is lacking. Kidney donors comprise a highly screened population without risk factors such as diabetes and inflammation, which invariably confound the association between CKD and cardiovascular disease. There is strong evidence that increased arterial stiffness and left ventricular hypertrophy and fibrosis, rather than atherosclerotic disease, mediate the adverse cardiovascular effects of CKD. The expanding practice of live kidney donation provides a unique opportunity to study the cardiovascular effects of an isolated reduction in GFR in a prospective fashion. At the same time, the proposed study will address ongoing safety concerns that persist because most longitudinal outcome studies have been undertaken at single centers and compared donor cohorts with an inappropriately selected control group.&lt;p&gt;&lt;/p&gt; Hypotheses: The reduction in GFR accompanying uninephrectomy causes (1) a pressure-independent increase in aortic stiffness (aortic pulse wave velocity) and (2) an increase in peripheral and central blood pressure.&lt;p&gt;&lt;/p&gt; Methods: This is a prospective, multicenter, longitudinal, parallel group study of 440 living kidney donors and 440 healthy controls. All controls will be eligible for living kidney donation using current UK transplant criteria. Investigations will be performed at baseline and repeated at 12 months in the first instance. These include measurement of arterial stiffness using applanation tonometry to determine pulse wave velocity and pulse wave analysis, office blood pressure, 24-hour ambulatory blood pressure monitoring, and a series of biomarkers for cardiovascular and bone mineral disease.&lt;p&gt;&lt;/p&gt; Conclusions: These data will prove valuable by characterizing the direction of causality between cardiovascular and renal disease. This should help inform whether targeting reduced GFR alongside more traditional cardiovascular risk factors is warranted. In addition, this study will contribute important safety data on living kidney donors by providing a longitudinal assessment of well-validated surrogate markers of cardiovascular disease, namely, blood pressure and arterial stiffness. If any adverse effects are detected, these may be potentially reversed with the early introduction of targeted therapy. This should ensure that kidney donors do not come to long-term harm and thereby preserve the ongoing expansion of the living donor transplant program.&lt;p&gt;&lt;/p&gt

Report of the JRC’s Descriptor 1 workshop to support the review of the Commission Decision 2010/477/EU concerning MSFD criteria for assessing Good Environmental Status

The MSFD workshop on biodiversity (MSFD D1), held in Ispra JRC (7th-9th of September 2015) aimed to provide clear proposals and conclusions on some of the outstanding issues identified in the D1 review manual (May 2015 consultation version: https://circabc.europa.eu/w/browse/46d2b7ba-d2fd-4b3c-9eaf-18c7cb702b53) in the broader context of support to the review of Commission Decision 2010/477/EU. This report is complementing the Commission Decision 2010/477/EU review manual (JRC96521) and presents the result of the scientific and technical review concluding phase 1 of the review of the Commission Decision 2010/477/EU in relation to Descriptor 1. The review has been carried out by the EC JRC together with experts nominated by EU Member States, and has considered contributions from the GES Working Group in accordance with the roadmap set out in the MSFD implementation strategy (agreed on at the 11th CIS MSCG meeting). The main issues addressed and tackled in this workshop’s report are: - Common lists of elements for the biodiversity assessments (species & habitats) o Review of the “Biological Features” in Table 1 in the MSFD Annex III in relation to D1 requirements o Review of the “Habitat Types” entries in Table 1 in the MSFD Annex III in relation to D1 requirements - Selection/deselection criteria for the inclusion of species and habitats in a group - Updated criteria and indicators for D1 - Habitat/Bird Directives, WFD, Common Fisheries Policy and D1 o Use of species and habitats for the MSFD needs that are already included in other legislation and agreements o Links between status classification approaches (FCS vs GES, GEcS vs GES) - Streamlining of assessments, including scales of assessments - Cross-cutting issues related to D1 implementation o Aggregation rules within D1 criteria/indicators o Final GES integration across descriptors assessments Steps forward and technical needs for D1.JRC.H.1-Water Resource