Linearizing torsion classes in the Picard group of algebraic curves over finite fields

We address the problem of computing in the group of $\ell^k$-torsion rational points of the jacobian variety of algebraic curves over finite fields, with a view toward computing modular representations.Comment: To appear in Journal of Algebr

Random perfect lattices and the sphere packing problem

Motivated by the search for best lattice sphere packings in Euclidean spaces of large dimensions we study randomly generated perfect lattices in moderately large dimensions (up to d=19 included). Perfect lattices are relevant in the solution of the problem of lattice sphere packing, because the best lattice packing is a perfect lattice and because they can be generated easily by an algorithm. Their number however grows super-exponentially with the dimension so to get an idea of their properties we propose to study a randomized version of the algorithm and to define a random ensemble with an effective temperature in a way reminiscent of a Monte-Carlo simulation. We therefore study the distribution of packing fractions and kissing numbers of these ensembles and show how as the temperature is decreased the best know packers are easily recovered. We find that, even at infinite temperature, the typical perfect lattices are considerably denser than known families (like A_d and D_d) and we propose two hypotheses between which we cannot distinguish in this paper: one in which they improve Minkowsky's bound phi\sim 2^{-(0.84+-0.06) d}, and a competitor, in which their packing fraction decreases super-exponentially, namely phi\sim d^{-a d} but with a very small coefficient a=0.06+-0.04. We also find properties of the random walk which are suggestive of a glassy system already for moderately small dimensions. We also analyze local structure of network of perfect lattices conjecturing that this is a scale-free network in all dimensions with constant scaling exponent 2.6+-0.1.Comment: 19 pages, 22 figure

ROOOH: A missing piece of the puzzle for OH measurements in low-NO environments?

Abstract. Field campaigns have been carried out with the FAGE (fluorescence assay by gas expansion) technique in remote biogenic environments in the last decade to quantify the in situ concentrations of OH, the main oxidant in the atmosphere. These data have revealed concentrations of OH radicals up to a factor of 10 higher than predicted by models, whereby the disagreement increases with decreasing NO concentration. This was interpreted as a major lack in our understanding of the chemistry of biogenic VOCs (volatile organic compounds), particularly isoprene, which are dominant in remote pristine conditions. But interferences in these measurements of unknown origin have also been discovered for some FAGE instruments: using a pre-injector, all ambient OH is removed by fast reaction before entering the FAGE cell, and any remaining OH signal can be attributed to an interference. This technique is now systematically used for FAGE measurements, allowing the reliable quantification of ambient OH concentrations along with the signal due to interference OH. However, the disagreement between modelled and measured high OH concentrations of earlier field campaigns as well as the origin of the now-quantifiable background OH is still not understood. We present in this paper the compelling idea that this interference, and thus the disagreement between model and measurement in earlier field campaigns, might be at least partially due to the unexpected decomposition of a new class of molecule, ROOOH, within the FAGE instruments. This idea is based on experiments, obtained with the FAGE set-up of the University of Lille, and supported by a modelling study. Even though the occurrence of this interference will be highly dependent on the design and measurement conditions of different FAGE instruments, including ROOOH in atmospheric chemistry models might reflect a missing piece of the puzzle in our understanding of OH in clean atmospheres. </jats:p

The BMV experiment : a novel apparatus to study the propagation of light in a transverse magnetic field

In this paper, we describe in detail the BMV (Bir\'efringence Magn\'etique du Vide) experiment, a novel apparatus to study the propagation of light in a transverse magnetic field. It is based on a very high finesse Fabry-Perot cavity and on pulsed magnets specially designed for this purpose. We justify our technical choices and we present the current status and perspectives.Comment: To be published in the European Physical Journal

Bis(monoacylglycero)phosphate regulates oxysterol binding protein-related protein 11 dependent sterol trafficking

Bis(Monoacylglycero) Phosphate (BMP) is a unique phospholipid localized in late endosomes, a critical cellular compartment in low density lipoprotein (LDL)-cholesterol metabolism. In previous work, we demonstrated the important role of BMP in the regulation of macrophage cholesterol homeostasis. BMP exerts a protective role against the pro-apoptotic effect of oxidized LDL (oxLDL) by reducing the production of deleterious oxysterols. As the intracellular sterol traffic in macrophages is in part regulated by oxysterol binding protein (OSBP) and OSBP-related proteins (ORPs), we investigated the role of ORP11, localized at the Golgi-late endosomes interface, in the BMP-mediated protection from oxLDL/oxysterol cytotoxicity. Stably silencing of ORP11 in mouse RAW264.7 macrophages via a shRNA lentiviruses system had no effect on BMP production. However, ORP11 knockdown abrogated the protective action of BMP against oxLDL induced apoptosis. In oxLDL treated control cells, BMP enrichment was associated with reduced generation of 7-oxysterols, while these oxysterol species were abundant in the ORP11 knock-down cells. Of note, BMP enrichment in ORP11 knock-down cells was associated with a drastic increase in free cholesterol and linked to a decrease of cholesterol efflux. The expression of ATP-binding cassette-transporter G1 (ABCG1) was also reduced in the ORP11 knock-down cells. These observations demonstrate a cooperative function of OPR11 and BMP, in intracellular cholesterol trafficking in cultured macrophages. We suggest that BMP favors the egress of cholesterol from late endosomes via an ORP11-dependent mechanism, resulting in a reduced production of cytotoxic 7-oxysterols.Peer reviewe

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench