GeneSigDB—a curated database of gene expression signatures

The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats

Concurrent OH imager and sodiumtemperature/wind lidar observation of a mesopause region undular bore event over Fort Collins/Platteville, CO

We reported the observation of a mesospheric front with the properties of an undular bore by an OH imager, over the Fort Collins/Platteville area on 6/7 October 2002. Unlike the earlier bore observations, a Na lidar capable of measuring mesopause region temperature, zonal, and meridional winds was in operation concurrently. The lidar data confirm, for the first time, the existence of a collocated temperature inversion layer to serve as the ducting region for bore propagation, as required by the simple theory proposed by Dewan and Picard 6 years ago. In addition, the lidar data in principle provide sufficient information for the determination of all parameters of the bore as suggested by the simple theory. The parameters so determined are compared to two bores previously studied. Like the earlier cases, the horizontal wavelength estimated from the theory is in good agreement with the observation. The lifetime of this undular bore, ∼120 min, was considerably shorter than the other two. Continued lidar observation after the bore event reveals that the ducting region may be controlled by a long-period wave, most likely related to a semidiurnal tide, and that atmospheric dynamic instability occurs simultaneously with the destruction of the wave train associated with the bore. It is possible that this constitutes, for the first time, the observation of the transition from an undular to a turbulent, or foaming, internal bore predicted by the theory

Isolement et identification sur culture cellulaire du virus de la gastro-entérite transmissible du porc

Un virus à effet cytolytique inhibé par l’action des sérums de référence T.G.E., sensible à l'éther et résistant à pH 3, a été isolé, pour la première fois en France, à partir de porcelets IOPS ayant manifesté un épisode gastro-entéritique consécutivement à l'inoculation d'un matériel cliniquement suspect de T.G.E

Global embedding of the Kerr black hole event horizon into hyperbolic 3-space

An explicit global and unique isometric embedding into hyperbolic 3-space, H^3, of an axi-symmetric 2-surface with Gaussian curvature bounded below is given. In particular, this allows the embedding into H^3 of surfaces of revolution having negative, but finite, Gaussian curvature at smooth fixed points of the U(1) isometry. As an example, we exhibit the global embedding of the Kerr-Newman event horizon into H^3, for arbitrary values of the angular momentum. For this example, considering a quotient of H^3 by the Picard group, we show that the hyperbolic embedding fits in a fundamental domain of the group up to a slightly larger value of the angular momentum than the limit for which a global embedding into Euclidean 3-space is possible. An embedding of the double-Kerr event horizon is also presented, as an example of an embedding which cannot be made global.Comment: 16 pages, 13 figure

Deep Radio Imaging of Globular Clusters and the Cluster Pulsar Population

We have obtained deep multifrequency radio observations of seven globular clusters using the Very Large Array and the Australia Telescope Compact Array. Five of these, NGC 6440, NGC 6539, NGC 6544, NGC 6624 and Terzan 5 had previously been detected in a shallower survey for steep spectrum radio sources in globular clusters (Fruchter and Goss 1990). The sixth, the rich globular cluster, Liller 1, had heretofore been undetected in the radio, and the seventh, 47 Tucanae, was not included in our original survey. High resolution 6 and 20 cm images of three of the clusters, NGC 6440, NGC 6539, NGC 6624 reveal only point sources coincident with pulsars which have been discovered subsequent to our first imaging survey. 21 and 18 cm images reveal several point sources within a few core-radii of the center of 47 Tuc. Two of these are identified pulsars, and a third, which is both variable and has a steep spectrum, is also most likely a pulsar previously identified by a pulsed survey. However, the 6, 20 and 90 cm images of NGC 6544, Liller 1 and Terzan 5 display strong steep-spectrum emission which cannot be associated with known pulsars. The image of the rich cluster Terzan 5 displays numerous point sources within $30''$, or 4 core radii of the cluster center. The density of these objects rises rapidly toward the core, where an elongated region of emission is found. The brightest individual sources, as well as the extended emission, possess the steep spectra expected of pulsars. Furthermore, the flux distribution of the sources agrees well with the standard pulsar luminosity function. The total luminosity and number of objects observed suggest that Terzan 5 contains more pulsars than any other Galactic globular cluster.Comment: 33 pages, 6 Postscript figures; Accepted for publication in the Astrophysical Journal; abstract abridged. PDF version also available at http://nemesis.stsci.edu/~fruchter/fg99/fg99.pd

Linking benthic biodiversity to the functioning of coastal ecosystems subjected to river runoff (NW Mediterranean)

Continental particulate organic matter (POM) plays a major role in the functioning of coastal marine ecosystems as a disturbance as well as an input of nutrients. Relationships linking continental inputs from the Rhone River to biodiversity of the coastal benthic ecosystem and fishery production were investigated in the Golfe du Lion (NW Mediterranean Sea). Macrobenthic community diversity decreased when continen¬tal inputs of organic matter increased, whereas ecosystem production, measured by common sole (Solea solea) fishery yields in the area, increased. Decreases in macrobenthic diversity were mainly related to an increasing abundance of species with specific functional traits, particularly deposit-feeding polychaetes. The decrease in macrobenthic diversity did not result in a decrease, but an increase in ecosystem production, as it enhanced the transfer of continental POM into marine food webs. The present study showed that it is necessary to consider functional traits of species, direct and indirect links between species, and feedback loops to understand the effects of biodiversity on ecosystem functioning and productivity

Pest management and biodiversity in organic fruit production: the case of apple orchards

Numerous pesticide applications are required for orchard protection, regardless of the guidelines. Organic fruit production (OFP) mainly relies on the use of mineral fungicides and microbiological or naturally-occurring insecticides. The environmental impact of this type of production does not significantly differ from that of conventional production when assessed in terms of synthetic indicators. However, the abundance of earthworms, as well as the abundance and specific richness of arthropod pests and beneficials in the orchards and surrounding hedges, is greater in OFP than in conventional orchards. Generalist predators are usually less affected by OFP compounds than by the chemical pesticides applied in conventional orchards. OFP also benefits avian communities, and above all, insectivorous birds, for which organic orchards offer a suitable habitat similar to that of undisturbed natural areas. In addition to this general trend, discrepancies may be observed in the protection responses of different insect groups. The abundance of hymenopteran parasitoids is the lowest in organic orchards in which outbreaks of phytophagous mites are also recorded in relation to the intensive use of sulphur for scab protection. Biological insecticides often act in ways that are similar to those of chemical ones, and the restricted choice of available compounds is likely to induce resistance selection in insect pests. Although maintaining biodiversity is not a direct result of the implementation of OFP guidelines, it seems to be widely considered as an option by organic growers, both alone and as a complementary tool for pest regulation

Interactivity Improves Usability of Geographic Maps for Visually Impaired People

International audienceTactile relief maps are used by visually impaired people to acquire mental representation of space, but they retain important limitations (limited amount of information, braille text, etc.). Interactive maps may overcome these limitations. However, usability of these two types of maps had never been compared. It is then unknown whether interactive maps are equivalent or even better solutions than traditional raised-line maps. This study presents a comparison of usability of a classical raised-line map vs. an interactive map composed by a multi-touch screen, a raised-line overlay and audio output. Both maps were tested by 24 blind participants. We measured usability as efficiency, effectiveness and satisfaction. Our results show that replacing braille with simple audio-tactile interaction significantly improved efficiency and user satisfaction. Effectiveness was not related to the map type but depended on users' characteristics as well as the category of assessed spatial knowledge. Long-term evaluation of acquired spatial information revealed that maps, whether interactive or not, are useful to build robust survey-type mental representations in blind users. Altogether, these results are encouraging as they show that interactive maps are a good solution for improving map exploration and cognitive mapping in visually impaired people