Automatic annotation of musical audio for interactive applications

PhDAs machines become more and more portable, and part of our everyday life, it becomes apparent that developing interactive and ubiquitous systems is an important aspect of new music applications created by the research community. We are interested in developing a robust layer for the automatic annotation of audio signals, to be used in various applications, from music search engines to interactive installations, and in various contexts, from embedded devices to audio content servers. We propose adaptations of existing signal processing techniques to a real time context. Amongst these annotation techniques, we concentrate on low and mid-level tasks such as onset detection, pitch tracking, tempo extraction and note modelling. We present a framework to extract these annotations and evaluate the performances of different algorithms. The first task is to detect onsets and offsets in audio streams within short latencies. The segmentation of audio streams into temporal objects enables various manipulation and analysis of metrical structure. Evaluation of different algorithms and their adaptation to real time are described. We then tackle the problem of fundamental frequency estimation, again trying to reduce both the delay and the computational cost. Different algorithms are implemented for real time and experimented on monophonic recordings and complex signals. Spectral analysis can be used to label the temporal segments; the estimation of higher level descriptions is approached. Techniques for modelling of note objects and localisation of beats are implemented and discussed. Applications of our framework include live and interactive music installations, and more generally tools for the composers and sound engineers. Speed optimisations may bring a significant improvement to various automated tasks, such as automatic classification and recommendation systems. We describe the design of our software solution, for our research purposes and in view of its integration within other systems.EU-FP6-IST-507142 project SIMAC (Semantic Interaction with Music Audio Contents); EPSRC grants GR/R54620; GR/S75802/01

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis

Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%–61%median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize ?-glucans rather than ?-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease

Use of a photoactivatable lipid to probe the topology of PA63 of Bacillus anthracis in lipid membranes.

The protective antigen of Bacillus anthracis is a key protein that promotes the translocation of the enzymatic moieties of the two toxins of B. anthracis into the cell cytoplasm. The membrane topology of the active form of the protective antigen (PA63) was investigated by proteolysis of PA63 inserted into liposomes containing a photoactivatable, radioactive lipid, and characterization of the N-terminal moiety of the deeply-inserted (and therefore radiolabeled) peptides. A single sequence starting at residue Ala258 was identified. Fourier-transform infrared spectroscopy showed that the protected peptide was mainly adopting a beta-sheet structure whose orientation was compatible with a transmembrane organization.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe

Le risque en agriculture

Le risque en agriculture... un titre ambitieux pour un sujet complexe, mais un thème de réflexion à coup sûr essentiel. Agriculteurs, responsables du développement, chercheurs,... ne peuvent que se sentir concernés dans la mesure où les choix et les décisions en agriculture s’expriment dans un environnement où l’aléa et l’incertitude se manifestent de façon permanente et sous les formes les plus variées. Une cinquantaine d’auteurs relevant des sciences de la terre, des sciences biologiques et des sciences humaines, livrent leurs réflexions sur le risque en agriculture. Le lecteur est invité à parcourir un vaste champ thématique que la notion de diversité marque profondément : multiplicité des sources du risque, diversité des réponses et réponses par la diversité, pluralité des points de vue et des exemples retenus empruntés pour la plupart au monde tropical. Quatre thèmes principaux structurent l’ouvrage : — Caractérisation des risques : principes méthodologiques pour l’analyse du risque et la prise de décision, spécificité des risques liés à la manifestation de phénomènes particuliers. — Risque et pratiques paysannes : perception du risque par les acteurs, réponses tactiques et stratégiques, poids de l’environnement dans la modulation des effets du risque, incidence sur le fonctionnement et l’évolution des systèmes agraires. — Risque et changements techniques : transformations induites dans les systèmes agricoles et les conditions de milieu. Le changement technique considéré comme réponse au risque ou comme source de nouveaux risques. Contribution à la problématique de l’intensification et du transfert de technologie en agriculture. — Contexte macro-économique et politique du risque : manifestations du risque à des niveaux qui échappent en général au pouvoir des agriculteurs mais qui conditionnent largement l’activité; agricole