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/.

Mediació intercultural i institucions escolars: l'exemple del Quebec

L’increment de la multiplicitat cultural ha comportat que, en diversos països, s’elaborin diferents actuacions per aproximar posicions i millorar la comunicació entre progenitors i professionals de les institucions escolars, així com per facilitar l’adaptació del currículum a la diversitat cultural. Una de les opcions preses, amb cert èxit però no exempta d’errors,és la dels anomenats «mediadors interculturals». Una societat on aquesta figura, amb els noms d’agents de liaison i de milieu, s’ha desenvolupat és el Quebec. L’estudi dels seus encerts i limitacions, específicament a les institucions escolars, creiem que pot ser un referent a partir del qual cal reflexionar, atès el notable increment d’aquesta pràctica a Catalunya.

Els diccionaris de pronúncia del català: passat, present i futur

La llengua catalana disposa d’informació fonètica detallada multidialectal d’ençà que el Diccionari català-valencià-balear d’Alcover & Moll (1926/1930-1962/1968) fou enllestit quatre dècades enrere. Més endavant aparegué el primer diccionari de pronunciació del català (Bruguera, 1990, 20042), restringit al català central i amb una sola pronúncia per entrada -per tant, sense variants i amb informació reduïda en relació amb noms propis, manlleus i neologismes. Més endavant es publicà un vocabulari d’unes 2.000 paraules (Paloma & Rico, 2000) en els dos estàndards orals de Catalunya: central i nord-occidental, de caràcter normatiu i en transcripció ampla, suficient per als parlants catalans. Poc després veié la llum un diccionari de pronúncia de la varietat valenciana (Lacreu, ed., 2001), que conté un nombre elevat d’entrades, però sense informació onomàstica, morfològica ni relativa a la variació de la pronúncia d’aquest parlar. Finalment, es presenta un diccionari en procés d’elaboració d’unes 70.000 entrades i de més de 200.000 pronúncies. El Diccionari de pronúncia catalana (DPC) ha estat concebut per Julià-Muné & Creus com un diccionari de pronúncia descriptiva, en principi de les varietats nord-ocidental i central de la llengua catalana, que ofereix a més la pronunciació estàndard recomanada.

Las monedas con nombres de étnicos del s. II a.C. en el nordeste peninsular: ¿Reflejo de posibles circunscripciones? ¿Civitates con doble nombre?

En el s. II a.C. se emiten en el nordeste de Hispania monedas con el nombre de étnicos conocidos por las fuentes escritas. Se plantea el problema de si responden a una organización territorial en circunscripciones que, curiosamente, correponden con las regiones principales populi que cita Plinio. Por otro lado estas cecas podrían corresponder a localidades que pudieran tener otro nombre.

Zn and K influence in fruit sizes of Valencia orange

In orange commercial farms, Zn deficiencies symptoms and small fruits were observed in Corrientes, Argentine. During four years (1995 to 1998), Valencia orange (Citrus sinensis Osb.) on Rough lemon (C. jambhiri Lush.) rootstock, implanted in 1974 in sandy soil, where six treatments were tested. Treatments varied from 1 to 3 Kg KCl.tree-1.year-1 (applied in April and December) with and without Zineb 80, 0,35%. year-1, 20 L. tree-1 (13,3 g Zn.tree-1 applied in December). The experimental design was a randomized complete block with four replications, with a single tree and borders in the experimental plot. Foliar sample were taken every year in Autumn and Summer, foliar concentrations of Zn and K were determined by atomic spectrum absorption. Harvested fruits were classified into small, medium and big. Analysis of Variance, Tukey test and Pearson correlations between production and foliar concentrations were performed. Higher fertilization levels of K with Zn increased medium and big fruits production (Kg and percentage). Foliar concentrations of K and Zn were positively correlated with big and medium fruit production and negatively correlated with small one. Chemical names used: Ethilenbis-ditiocarbamate of Zn (Zineb).

Marooned plants : vernacular naming practices in the Mascarene Islands

This article explores possible histories of plant exchanges and plant naming tied to the slave trade between East Africa, Madagascar and the Mascarene Islands. The subsequent 'marronnage' of slaves on these islands - their escape from captivity, sometimes to live in mountain hideouts - continues to inspire cultural references. Inspired by the use of the adjective 'marron/marronne' for a number of plants on Reunion Island, we compile evidence of plant exchanges and plant naming from ecological records, historical accounts and the use of descriptive, emotive or symbolic vernacular names as clues for deepening our knowledge of historical societies and environments. The evidence from the Mascarenes opens a window into the role of the African diaspora in plant introduction, diffusion, domestication and cultivation. We document that maroons relied on a variety of wild, escaped and cultivated plants for their subsistence. We also highlight the role of marronnage in the popular and literary imaginary, with the result that many plants are named 'marron/marrone' in a metaphorical sense. Finally, we identify a few plants that may have been transported, cultivated, or encouraged in one way or another by maroons. Along the way, we reflect on the pitfalls and opportunities of such interdisciplinary work.

Fer mapes per conèixer la Història: aportacions de la cartografia a l'estudi de l'Alta Edat Mitjana

To make maps to know history: contributions from the cartography to the study of the early middle ages. The accomplishment of maps can allow us to know many aspects that documents written do not allow us to have knowledge. This paper focuses on the boundaries of the townships or the parishes, on the routes and ways, and on the place names or on the invocations of the churches, in order to get to know like it was the territory in the early medieval centuries. One reaches the conclusion that often the limits, the ways and the settlements were created at early middle ages. This study allows to raise the ruptures and the continuities that took place throughout these centuries in the settlement.

Espeleotoponímia de motivació paleontològica i antracotoponímia de les Illes Balears

En aquest treball es recopilen i estudien, des d’una perspectiva etnopaleontològica, les aportacions i influencies exercides pels fòssils en relació al patrimoni onomàstic toponímic relacionat amb cavitats càrstiques de l’àmbit geogràfic de les Illes Balears. Generalment es tracta de microtopònims moderns o recents, en vies de popularització i/o tradicionalització (neotopònims), establerts pels científics que estudien les coves i/o esportistes del món de l’espeleologia (topocultismes). Es poden distingir entre espeleotopònims de primer ordre (quan es refereixen a cavitats completes) i de segon ordre (quan es refereixen a un sector d’una cavitat). També es realitza una primera aproximació als topònims referits a mines d’extracció de carbó fòssil (antracotopònims).

Passiflora edulis Sims: the correct taxonomic way to cite the yellow passion fruit (and of others colors)

Passiflora edulis, the passion fruit native from Brazil, has several common names (such as sour passion fruit, yellow passion fruit, black passion fruit, and purple passion fruit), and presents a wide variability with the different rind colors of its fruits, which are very easy to notice. However, in 1932, Otto Degener suggested that the yellow passion fruit had its origin in Australia through breeding, calling it P. edulis forma flavicarpa, and that it could be distinguished by the color of the fruit, the deeper shade of purple of the corona, and the presence of glands on the sepals. These distinctions do not support themselves, for the glands are common to the species (although they may be absent), and the corona has a wide range of colors, regardless of the color of the fruit. A more critical ingredient is the fact that the external coloration of the fruit is a character of complex inheritance and is not dominant, thus displaying a number of intermediate colors, making it difficult to identify the extreme colors. For the correct scientific naming of agricultural plants, the International Code of Botanical Nomenclature must be used in conjunction with the International Code of Nomenclature for Cultivated Plants, with the selections with significant agronomic characteristics recognized and named cultivars. In accordance with the international convention promoted by the UPOV, of which Brazil is a signatory, several colors (light yellow, yellow, orange yellow, pink red, red, red purple, green purple, purple, and dark purple) can be recognized in order to adequately characterize passion fruit cultivars within the species P. edulis. At taxonomic level, Passiflora edulis Sims must be used for any plant and color of sour passion fruits, in combination with a cultivar name for the selected materials.

Antroponímia i toponímia en un capbreu de Conesa de mitjan segle XVIII

Estudi d’un capbreu del terme de Conesa del segle xviii dipositat en el fons notarial de Valls, des del punt de vista de l’onomàstica, els terratinents i el noms de les partides de terra que s ́hi conreaven. El treball detalla la presència dels cognoms anotats des del segle XVII fins al XIX i si els noms dels topònims relacionats en aquest document són vius actualment.

Short communication.Wood identification based on their common name and their transversal surface anatomy. Application to the batch from the expedition of Ruiz and Pavon

Aim of study: To identify species of wood samples based on common names and anatomical analyses of their transversal surfaces (without microscopic preparations). Area of study: Spain and South America Material and methods: The test was carried out on a batch of 15 lumber samples deposited in the Royal Botanical Garden in Madrid, from the expedition by Ruiz and Pavon (1777-1811). The first stage of the methodology is to search and to make a critical analysis of the databases which list common nomenclature along with scientific nomenclature. A geographic filter was then applied to the information resulting from the samples with a more restricted distribution. Finally an anatomical verification was carried out with a pocket microscope with a magnification of x40, equipped with a 50 micrometers resolution scale. Main results: The identification of the wood based exclusively on the common name is not useful due to the high number of alternative possibilities (14 for “naranjo”, 10 for “ébano”, etc.). The common name of one of the samples (“huachapelí mulato”) enabled the geographic origin of the samples to be accurately located to the shipyard area in Guayaquil (Ecuador). Given that Ruiz y Pavon did not travel to Ecuador, the specimens must have been obtained by Tafalla. It was possible to determine correctly 67% of the lumber samples from the batch. In 17% of the cases the methodology did not provide a reliable identification. Research highlights: It was possible to determine correctly 67% of the lumber samples from the batch and their geographic provenance. The identification of the wood based exclusively on the common name is not useful.

Léxico patrimonial y metacedeusis en los nombres de lugar

En este artículo vamos a ocuparnos de uno de los mecanismos de transformación del patrimonio lingüístico: la metacedeusis. Es un procedimiento que contribuye a la renovación del repertorio léxico y, en especial, del toponímico. Intentamos en primer lugar mostrar que no coincide con lo que se ha venido llamando etimología popular. En segundo lugar enumeramos y ejemplificamos algunos de los factores que favorecen la aparición de este fenómeno. A lo largo de toda la exposición, nos esforzamos en demostrar que solo el conocimiento del léxico patrimonial permite detectar los casos de metacedeusis y, en consecuencia, trazar adecuadamente la historia del topónimo.

Espigueo por la toponimia mayor del Valle Medio e Inferior del Ésera (Huesca)

El present treball pretén donar llum a una sèrie de topònims majors de la Ribagorça occidental, tot al llarg de la vall mitjana i inferior del riu Éssera. Aquests topònims es remunten a temps molt antics: preromans, romans i germànics bàsicament. Aquesta anàlisi permet apreciar l'estratigrafi a lingüística de la zona. La no-aparició de topònims d'origen àrab en el nostre treball no vol dir que no hi hagués penetració àrab a la zona, sinó que la seva arribada va ser posterior a la creació dels principals nuclis de població. Sí que hi ha topònims àrabs a la toponímia menor, que resta fora del present treball.

Verkkoliitteessä ilmestyvät lektiot

Antti Leino: Peruskartalta kielioppiin ; Eveliina Korpela: Oireista puhuminen lääkärin vastaanotolla

Authorship in scientific publications: analysis and recommendations.

In 2008, a Swiss Academies of Arts and Sciences working group chaired by Professor Emilio Bossi issued a "Memorandum on scientific integrity and the handling of misconduct in the scientific context", together with a paper setting out principles and procedures concerning integrity in scientific research. In the Memorandum, unjustified claims of authorship in scientific publications are referred to as a form of scientific misconduct - a view widely shared in other countries. In the Principles and Procedures, the main criteria for legitimate authorship are specified, as well as the associated responsibilities. It is in fact not uncommon for disputes about authorship to arise with regard to publications in fields where research is generally conducted by teams rather than individuals. Such disputes may concern not only the question who is or is not to be listed as an author but also, frequently, the precise sequence of names, if the list is to reflect the various authors' roles and contributions. Subjective assessments of the contributions made by the individual members of a research group may differ substantially. As scientific collaboration - often across national boundaries - is now increasingly common, ensuring appropriate recognition of all parties is a complex matter and, where disagreements arise, it may not be easy to reach a consensus. In addition, customs have changed over the past few decades; for example, the practice of granting "honorary" authorship to an eminent researcher - formerly not unusual - is no longer considered acceptable. It should be borne in mind that the publications list has become by far the most important indicator of a researcher's scientific performance; for this reason, appropriate authorship credit has become a decisive factor in the careers of young researchers, and it needs to be managed and protected accordingly. At the international and national level, certain practices have therefore developed concerning the listing of authors and the obligations of authorship. The Scientific Integrity Committee of the Swiss Academies of Arts and Sciences has collated the relevant principles and regulations and formulated recommendations for authorship in scientific publications. These should help to prevent authorship disputes and offer guidance in the event of conflicts.