Parallel Position Weight Matrices Algorithms

International audiencePosition Weight Matrices (PWMs) are broadly used in computational biology. The basic problems, Scan and MultipleScan, aim to find all the occurrences of a given PWM or a set of PWMs in long sequences. Some other PWM tasks share a common NP-hard subproblem, ScoreDistribution. The existing algorithms rely on the enumeration on a large set of scores or words, and they are mostly not suitable for parallelization. We propose a new algorithm, BucketScoreDistribution, that is both very efficient and suitable for parallelization. We bound the error induced by this algorithm. We realized a GPU prototype for Scan, MultipleScan and BucketScoreDistribution with the CUDA libraries, and report for the different problems speedups larger than 10× on several Nvidia cards

Manycore high-performance computing in bioinformatics

Mining the increasing amount of genomic data requires having very efficient tools. Increasing the efficiency can be obtained with better algorithms, but one could also take advantage of the hardware itself to reduce the application runtimes. Since a few years, issues with heat dissipation prevent the processors from having higher frequencies. One of the answers to maintain Moore's Law is parallel processing. Grid environments provide tools for effective implementation of coarse grain parallelization. Recently, another kind of hardware has attracted interest: multicore processors. Graphic processing units (GPUs) are a first step towards massively multicore processors. They allow everyone to have some teraflops of cheap computing power in its personal computer. The CUDA library (released in 2007) and the new standard OpenCL (specified in 2008) make programming of such devices very convenient. OpenCL is likely to gain a wide industrial support and to become a standard of choice for parallel programming. In all cases, the best speedups are obtained when combining precise algorithmic studies with a knowledge of the computing architectures. This is especially true with the memory hierarchy: the algorithms have to find a good balance between using large (and slow) global memories and some fast (but small) local memories. In this chapter, we will show how those manycore devices enable more efficient bioinformatics applications. We will first give some insights into architectures and parallelism. Then we will describe recent implementations specifically designed for manycore architectures, including algorithms on sequence alignment and RNA structure prediction. We will conclude with some thoughts about the dissemination of those algorithms and implementations: are they today available on the bookshelf for everyone

Identification of first active compounds in drug discovery. how to proceed?

In the quest for the discovery of new therapies, the identification of the initial active molecules is a major challenge. Although significant progress in chemistry and biology has been made in recent years, the process remains difficult. In this mini-review, we will explain the major approaches and experimental methods that can be used to identify these molecules. Two main approaches are described, target-based and phenotypic-based and a focus is made on some high throughput technologies and biophysical methods

Saint-Denis – La Plaine Saint-Denis (Zac Montjoie)

Cette opération archéologique concernait les îlots 1 et 2 de la Zac Montjoie, soit une surface d’environ 13 500 m2. Les deux îlots sondés ont été largement excavés depuis le xixe s. Les niveaux de sédiments du quaternaire sont probablement absents sur les deux tiers du terrain. Des remblais industriels et de démolition, recouvrant toute la parcelle, ont été observés, parfois jusqu’à 4 m de profondeur. Une importante dépression naturelle, située dans la partie centrale de la Zac, fut sans dout..

Chitosan-Based Sustainable Textile Technology: Process, Mechanism, Innovation, and Safety

This chapter reviews relevant findings regarding the activities and contributions of chitosan in different textile processing following the varieties of process, mechanism, and applications. Chitosan is a better candidate in both aspects of biodegradability and efficiency instead of synthetic polymers. The technical and scientific discussions behind the role of chitosan in all the processes and treatments have been explored in the chapter. Over the last few years, enormous efforts and challenges are being practiced in research and industry to design and development of eco-friendly and sustainable technologies. Therefore, the chapter emphasizes on chitosan-based formulations of fibers, fabrics, coatings, and functional textiles

P75 neurotrophin receptor is sequestered in the Golgi apparatus of the U-87 MG human glioblastoma cell line.

International audienceThe P75 neurotrophin receptor (p75NTR) is a cell surface receptor that can induce apoptosis in many cell types. This receptor plays a major role in the development of the central nervous system and is expressed in some adult brain cells. Its implication in cell apoptosis or survival is probably of major importance in cellular homeostasis and thus p75NTR could be implicated in tumor resistance to death. In this study, we investigated the intracellular expression of p75NTR in a human glioblastoma cell line. Detection of p75NTR receptor in Golgi apparatus by immunofluorescence microscopy, or after Golgi apparatus extraction, could be correlated with a decrease of cell apoptosis leading cells to become tumorous. This hypothesis is supported by a loss of ligand-induced apoptosis in this cell line. Our observations show that p75NTR can be sequestered in the Golgi complex and could then be, in part, responsible for the cell resistance to apoptosis and for brain tumor formation

High-Resolution Ultrasound Imaging System for the Evaluation of the Vascular Response to Stent or Balloon Injuries in the Rabbit Iliac Arteries

For novel therapeutic approaches of cardiovascular diseases, the preclinical investigation is of paramount and required appropriate technologies. We investigated the use of high-resolution ultrasound imaging system to evaluate the progression of vascular lesions in a rabbit model. Animals underwent vascular injury using two standard procedures. A bare-metal stent was placed within the left iliac artery, and a balloon injury was induced in the contralateral artery. The animals were kept on a regular diet for 8 weeks. A Vevo3100© VisualSonic high-resolution ultrasound imaging system and the associated software VevoVasc were used for the longitudinal evaluation of the injured arteries and the distal abdominal aorta. The lumen size increased rapidly after the intervention in both iliac arteries. In the balloon-injured artery, the augmentation was transient and significantly reversed, inducing an alteration of the blow flow. In contrast, in the stented segment, the lumen size was maintained enlarged overtime. We demonstrated a significant correlation for the wall thickness and the lumen size between ultrasonic and histological quantification. High-resolution ultrasound imaging in rabbit iliac arteries and the distal abdominal aorta is feasible, reliable and of relevance to investigate novel strategies for the inhibition of hyperplasia induced with standard injury models

Chitosan–Carboxymethylcellulose-Based Polyelectrolyte Complexation and Microcapsule Shell Formulation

Chitosan (CH)–carboxymethyl cellulose sodium salt (NaCMC) microcapsules containing paraffin oil were synthesized by complex formation, and crosslinked with glutaraldehyde (GTA). The electrostatic deposition of NaCMC onto the CH-coated paraffin oil emulsion droplets was demonstrated by zeta potential and optical microscopy. The optimal process conditions were identified in terms of pH of the aqueous solution (5.5) and CH/NaCMC mass ratio (1:1). Encapsulation of paraffin oil and microcapsule morphology were analyzed by ATR-FTIR and SEM, respectively. The effect of GTA crosslinking on paraffin oil latent heat was investigated by DSC and combined with the values of encapsulation efficiency and core content, supporting the compact shell formation

Biomanycores, open-source parallel code for many-core bioinformatics

International audienceBiomanycores is a collection of bioinformatics tools, designed to bridge the gap between researches in OpenCL/CUDA high-performance computing on GPU and other "manycore processors" and usual bioinformaticians and biologists