CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature and linked to an improved annotation system

Résumé: L'automatisation du séquençage et de l'annotation des génomes, ainsi que l'application à large échelle de méthodes de mesure de l'expression génique, génèrent une quantité phénoménale de données pour des organismes modèles tels que l'homme ou la souris. Dans ce déluge de données, il devient très difficile d'obtenir des informations spécifiques à un organisme ou à un gène, et une telle recherche aboutit fréquemment à des réponses fragmentées, voir incomplètes. La création d'une base de données capable de gérer et d'intégrer aussi bien les données génomiques que les données transcriptomiques peut grandement améliorer la vitesse de recherche ainsi que la qualité des résultats obtenus, en permettant une comparaison directe de mesures d'expression des gènes provenant d'expériences réalisées grâce à des techniques différentes. L'objectif principal de ce projet, appelé CleanEx, est de fournir un accès direct aux données d'expression publiques par le biais de noms de gènes officiels, et de représenter des données d'expression produites selon des protocoles différents de manière à faciliter une analyse générale et une comparaison entre plusieurs jeux de données. Une mise à jour cohérente et régulière de la nomenclature des gènes est assurée en associant chaque expérience d'expression de gène à un identificateur permanent de la séquence-cible, donnant une description physique de la population d'ARN visée par l'expérience. Ces identificateurs sont ensuite associés à intervalles réguliers aux catalogues, en constante évolution, des gènes d'organismes modèles. Cette procédure automatique de traçage se fonde en partie sur des ressources externes d'information génomique, telles que UniGene et RefSeq. La partie centrale de CleanEx consiste en un index de gènes établi de manière hebdomadaire et qui contient les liens à toutes les données publiques d'expression déjà incorporées au système. En outre, la base de données des séquences-cible fournit un lien sur le gène correspondant ainsi qu'un contrôle de qualité de ce lien pour différents types de ressources expérimentales, telles que des clones ou des sondes Affymetrix. Le système de recherche en ligne de CleanEx offre un accès aux entrées individuelles ainsi qu'à des outils d'analyse croisée de jeux de donnnées. Ces outils se sont avérés très efficaces dans le cadre de la comparaison de l'expression de gènes, ainsi que, dans une certaine mesure, dans la détection d'une variation de cette expression liée au phénomène d'épissage alternatif. Les fichiers et les outils de CleanEx sont accessibles en ligne (http://www.cleanex.isb-sib.ch/). Abstract: The automatic genome sequencing and annotation, as well as the large-scale gene expression measurements methods, generate a massive amount of data for model organisms. Searching for genespecific or organism-specific information througout all the different databases has become a very difficult task, and often results in fragmented and unrelated answers. The generation of a database which will federate and integrate genomic and transcriptomic data together will greatly improve the search speed as well as the quality of the results by allowing a direct comparison of expression results obtained by different techniques. The main goal of this project, called the CleanEx database, is thus to provide access to public gene expression data via unique gene names and to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and crossdataset comparisons. A consistent and uptodate gene nomenclature is achieved by associating each single gene expression experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of genes from model organisms, such as human and mouse. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing crossreferences to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resources, such as cDNA clones or Affymetrix probe sets. The Affymetrix mapping files are accessible as text files, for further use in external applications, and as individual entries, via the webbased interfaces . The CleanEx webbased query interfaces offer access to individual entries via text string searches or quantitative expression criteria, as well as crossdataset analysis tools, and crosschip gene comparison. These tools have proven to be very efficient in expression data comparison and even, to a certain extent, in detection of differentially expressed splice variants. The CleanEx flat files and tools are available online at: http://www.cleanex.isbsib. ch/.

Biblio-MetReS: A bibliometric network reconstruction application and server

Background: Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow expert users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no user friendly tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available. Results: This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document. Conclusions: Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio- MetReS is an application that can be downloaded from http://metres.udl.cat/. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.

Supergravity models of (3+1)-dimensional QCD

The most general black M5-brane solution of eleven-dimensional supergravity (with a flat R4 spacetime in the brane and a regular horizon) is characterized by charge, mass and two angular momenta. We use this metric to construct general dual models of large-N QCD (at strong coupling) that depend on two free parameters. The mass spectrum of scalar particles is determined analytically (in the WKB approximation) and numerically in the whole two-dimensional parameter space. We compare the mass spectrum with analogous results from lattice calculations, and find that the supergravity predictions are close to the lattice results everywhere on the two dimensional parameter space except along a special line. We also examine the mass spectrum of the supergravity Kaluza-Klein (KK) modes and find that the KK modes along the compact D-brane coordinate decouple from the spectrum for large angular momenta. There are however KK modes charged under a U(1)×U(1) global symmetry which do not decouple anywhere on the parameter space. General formulas for the string tension and action are also given.

V0 production in p+A collisions at √s = 41.6 GeV

Inclusive doubly differential cross sections d 2 σ pA /dx F   dp T 2 as a function of Feynman-x (x F ) and transverse momentum (p T ) for the production of K S 0 , Λ and Λ¯ in proton-nucleus interactions at 920 GeV are presented. The measurements were performed by HERA-B in the negative x F range (−0.12

N=1 SQCD-like theories with N_f massive flavors from AdS/CFT and beta functions

We study new supergravity solutions related to large-N c N=1 supersymmetric gauge field theories with a large number N f of massive flavors. We use a recently proposed framework based on configurations with N c color D5 branes and a distribution of N f flavor D5 branes, governed by a function N f S(r). Although the system admits many solutions, under plausible physical assumptions the relevant solution is uniquely determined for each value of x ≡ N f /N c . In the IR region, the solution smoothly approaches the deformed Maldacena-Núñez solution. In the UV region it approaches a linear dilaton solution. For x < 2 the gauge coupling β g function computed holographically is negative definite, in the UV approaching the NSVZ β function with anomalous dimension γ 0 = −1/2 (approaching − 3/(32π 2)(2N c  − N f )g 3)), and with β g  → −∞ in the IR. For x = 2, β g has a UV fixed point at strong coupling, suggesting the existence of an IR fixed point at a lower value of the coupling. We argue that the solutions with x > 2 describe a"Seiberg dual" picture where N f  − 2N c flips sign.

STACK OVERWRITING ATTACKS AND DEFENCES IN UNIX ENVIRONMENT

Työn tarkoituksena on tutkia pinon ylikirjoitukseen perustuvien hyökkäysten toimintaa ja osoittaa kokeellisesti nykyisten suojaustekniikoiden olevan riittämättömiä. Tutkimus suoritetaan testaamalla miten valitut tietoturvatuotteet toimivat eri testitilanteissa. Testatut tuotteet ovat Openwall, PaX, Libsafe 2.0 ja Immunix 6.2. Testaus suoritetaan pääasiassa RedHat 7.0 ympäristössä testiohjelman avulla. Testeissä mitataan sekä tuotteiden kyky havaita hyökkäyksiä että niiden nopeusvaikutukset. Myös erityyppisten hyökkäysten ja niitä vastaan kehitettyjen metodien toimintaperiaatteet esitellään seikkaperäisesti ja havainnollistetaan yksinkertaistetuilla esimerkeillä. Esitellyt tekniikat sisältävät puskurin ylivuodot, laittomat muotoiluparametrit, loppumerkittömät merkkijonot ja taulukoiden ylivuodot. Testit osoittavat, etteivät valitut tuotteet estä kaikkia hyökkäyksiä, joten lopuksi perehdytään myös vahinkojen minimointiin onnistuneiden hyökkäysten varalta.

Laparoscopic technique to perform a true Stamm gastrostomy in children.

PURPOSE: A surgical gastrostomy is mandatory in cases where a PEG is not feasible. Various minimally invasive techniques have been described, but many involve unusable materials in small children and/or have risk of disunion. We describe a technique for true Stamm gastrostomy performed by laparoscopy (LSG) with a purse string suture and four points of attachment onto the wall. METHOD: We reviewed 20 children who underwent an LSG from 2010 to 2013. After incision of the skin at the location planned for the gastrostomy, using three 3-5mm ports the stomach is fixed to the wall by three suspension stitches, which are entered and then emerged subcutaneously. A fourth stitch of attachment is used to make an award on the stomach and tie around the gastrostomy tube. RESULTS: Mean age was 4.2years, with 70% aged <2years. All children were malnourished, most often severely. All but two underwent a concomitant fundoplication. Feeding through the gastrostomy started on D0 or D1. Total feeding by gastrostomy was achieved in a mean duration of 2.9day. Mean hospital stay was 4.5days. There was no perioperative complication. Mean follow-up was 14months. Once, the balloon was accidently deflated and reinflated in the wall leading to its necrosis. Five peristomial granulomas were noticed. It was always possible to replace the tube by a gastrostomy device at least 6weeks after surgery. CONCLUSION: This new technique for true Stamm gastrostomy by laparoscopy reproduces exactly the one done by laparotomy, without special equipment. It can be made since the neonatal period, in all the circumstances when a laparoscopy is possible.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Efeito do campo magnético na precipitação de parafinas

In the oil industry, the paraffination phenomenon is a major problem during oil production, displacement and treatment. Paraffin deposition in subsea flowlines, surface equipment, production string or even in the reservoir, can cause significant and increasing oil losses. To minimize paraffin precipitation, the application of magnetic field in the petroleum path has been suggested based on empiric studies. In this study, we assembled a labscale magnetic conditioner to determine the influence of magnetic field on the physical-chemical properties of two fluids : oil and a paraffin mixture. We observed that magnetic field reduce sample aparent viscosity due to crystal morphology alteration.

Quartet No. 2 in D Major

Soitinnus: Viulut (2), alttoviulu, sello.

Quintet in F minor, op. 34

The Hollywood String Quartet: Slatkin, Felix, viulu ; Shure, Paul, viulu ; Robyn, Paul, alttoviulu ; Aller, Eleanor, sello.

Quartet no. 1 in D, op. 11

Soitinnus: Viulut (2), alttoviulu, sello.

Excitation modes of vortices in submicron magnetic disks

Classical and quantum theory of spin waves in the vortex state of a mesoscopic submicron magnetic disk have been developed with account of the finite mass density of the vortex. Oscillations of the vortex core resemble oscillations of a charged string in a potential well in the presence of the magnetic field. A conventional gyrotropic frequency appears as a gap in the spectrum of spin waves of the vortex. The mass of the vortex has been computed, and the result agrees with experimental findings. The finite vortex mass generates a high-frequency branch of spin waves. The effects of an external magnetic field and dissipation have been addressed.

Bowing the violin : a case study for auditory-motor pattern modelling in the context of music performance

This project addresses methodological and technological challenges in the development of multi-modal data acquisition and analysis methods for the representation of instrumental playing technique in music performance through auditory-motor patterning models. The case study is violin playing: a multi-modal database of violin performances has been constructed by recording different musicians while playing short exercises on different violins. The exercise set and recording protocol have been designed to sample the space defined by dynamics (from piano to forte) and tone (from sul tasto to sul ponticello), for each bow stroke type being played on each of the four strings (three different pitches per string) at two different tempi. The data, containing audio, video, and motion capture streams, has been processed and segmented to facilitate upcoming analyses. From the acquired motion data, the positions of the instrument string ends and the bow hair ribbon ends are tracked and processed to obtain a number of bowing descriptors suited for a detailed description and analysis of the bow motion patterns taking place during performance. Likewise, a number of sound perceptual attributes are computed from the audio streams. Besides the methodology and the implementation of a number of data acquisition tools, this project introduces preliminary results from analyzing bowing technique on a multi-modal violin performance database that is unique in its class. A further contribution of this project is the data itself, which will be made available to the scientific community through the repovizz platform.