L'usage des systèmes d'informations électroniques en recherche scientifique : le cas de la neurophysiologie.

Nous présentons les premiers résultats d'une enquête destinée à mieux connaître les pratiques de recherche d'information bibliographique et documentaire chez les chercheurs scientifiques. 64 chercheurs et étudiants doctorants en neurophysiologie ont répondu à un questionnaire portant sur les méthodes, les outils, et les objectifs des recherches d'information typiques dans leur activité. De plus, 11 personnes parmi les répondants ont participé à un entretien individuel semi structuré. Il en ressort que l'usage d'outils informatisés de recherche d'information bibliographique (RIB) est désormais pratique courante, au détriment des index et autres sources imprimées. Les principaux outils utilisés sont la base de données bibliographiques PubMed et le moteur de recherche Google, avec toutefois de nombreux autres outils plus spécifiques utilisés à titre complémentaire. Les répondants mentionnent des objectifs très variés, comme l'acquisition de connaissances nouvelles, mais aussi la recherche de techniques expérimentales, la veille documentaire, l'alimentation du débat scientifique, ou l'aide à l'enseignement. Les difficultés que rencontrent les experts en neurosciences intégratives dans l'exploitation des outils informatiques de RIB spécialisés semblent surtout liées à l'absence de formation des experts à ces outils. Les chercheurs définissent l'outil informatique de RIB « idéal » comme fiable et exhaustif, mais aussi rapide et facile à utiliser et apprendre . De fait, le facteur temps apparaît déterminant dans leur choix d'utilisation ou non d'un outil particulier. Cette étude ouvre la voie à des expériences plus spécifiques, qui porteront sur les stratégies cognitives des experts dans ce type de tâches

An Iterative Genetic and Dynamical Modelling Approach Identifies Novel Features of the Gene Regulatory Network Underlying Melanocyte Development

The mechanisms generating stably differentiated cell-types from multipotent precursors are key to understanding normal development and have implications for treatment of cancer and the therapeutic use of stem cells. Pigment cells are a major derivative of neural crest stem cells and a key model cell-type for our understanding of the genetics of cell differentiation. Several factors driving melanocyte fate specification have been identified, including the transcription factor and master regulator of melanocyte development, Mitf, and Wnt signalling and the multipotency and fate specification factor, Sox10, which drive mitf expression. While these factors together drive multipotent neural crest cells to become specified melanoblasts, the mechanisms stabilising melanocyte differentiation remain unclear. Furthermore, there is controversy over whether Sox10 has an ongoing role in melanocyte differentiation. Here we use zebrafish to explore in vivo the gene regulatory network (GRN) underlying melanocyte specification and differentiation. We use an iterative process of mathematical modelling and experimental observation to explore methodically the core melanocyte GRN we have defined. We show that Sox10 is not required for ongoing differentiation and expression is downregulated in differentiating cells, in response to Mitfa and Hdac1. Unexpectedly, we find that Sox10 represses Mitf-dependent expression of melanocyte differentiation genes. Our systems biology approach allowed us to predict two novel features of the melanocyte GRN, which we then validate experimentally. Specifically, we show that maintenance of mitfa expression is Mitfa-dependent, and identify Sox9b as providing an Mitfa-independent input to melanocyte differentiation. Our data supports our previous suggestion that Sox10 only functions transiently in regulation of mitfa and cannot be responsible for long-term maintenance of mitfa expression; indeed, Sox10 is likely to slow melanocyte differentiation in the zebrafish embryo. More generally, this novel approach to understanding melanocyte differentiation provides a basis for systematic modelling of differentiation in this and other cell-types

An Ishihara-style test of animal colour vision

ABSTRACT Colour vision mediates ecologically relevant tasks for many animals, such as mate choice, foraging and predator avoidance. However, our understanding of animal colour perception is largely derived from human psychophysics, and behavioural tests of non-human animals are required to understand how colour signals are perceived. Here, we introduce a novel test of colour vision in animals inspired by the Ishihara colour charts, which are widely used to identify human colour deficiencies. In our method, distractor dots have a fixed chromaticity (hue and saturation) but vary in luminance. Animals can be trained to find single target dots that differ from distractor dots in chromaticity. We provide MATLAB code for creating these stimuli, which can be modified for use with different animals. We demonstrate the success of this method with triggerfish, Rhinecanthus aculeatus, which quickly learnt to select target dots that differed from distractor dots, and highlight behavioural parameters that can be measured, including success of finding the target dot, time to detection and error rate. We calculated discrimination thresholds by testing whether target colours that were of increasing colour distances (ΔS) from distractor dots could be detected, and calculated discrimination thresholds in different directions of colour space. At least for some colours, thresholds indicated better discrimination than expected from the receptor noise limited (RNL) model assuming 5% Weber fraction for the long-wavelength cone. This methodology could be used with other animals to address questions such as luminance thresholds, sensory bias, effects of sensory noise, colour categorization and saliency

First Detection of Polarization of the Submillimetre Diffuse Galactic Dust Emission by Archeops

We present the first determination of the Galactic polarized emission at 353 GHz by Archeops. The data were taken during the Arctic night of February 7, 2002 after the balloon--borne instrument was launched by CNES from the Swedish Esrange base near Kiruna. In addition to the 143 GHz and 217 GHz frequency bands dedicated to CMB studies, Archeops had one 545 GHz and six 353 GHz bolometers mounted in three polarization sensitive pairs that were used for Galactic foreground studies. We present maps of the I, Q, U Stokes parameters over 17% of the sky and with a 13 arcmin resolution at 353 GHz (850 microns). They show a significant Galactic large scale polarized emission coherent on the longitude ranges [100, 120] and [180, 200] deg. with a degree of polarization at the level of 4-5%, in agreement with expectations from starlight polarization measurements. Some regions in the Galactic plane (Gem OB1, Cassiopeia) show an even stronger degree of polarization in the range 10-20%. Those findings provide strong evidence for a powerful grain alignment mechanism throughout the interstellar medium and a coherent magnetic field coplanar to the Galactic plane. This magnetic field pervades even some dense clouds. Extrapolated to high Galactic latitude, these results indicate that interstellar dust polarized emission is the major foreground for PLANCK-HFI CMB polarization measurement.Comment: Submitted to Astron. & Astrophys., 14 pages, 12 Fig., 2 Table

Prime Focus Spectrograph (PFS) for the Subaru Telescope: Overview, recent progress, and future perspectives

PFS (Prime Focus Spectrograph), a next generation facility instrument on the 8.2-meter Subaru Telescope, is a very wide-field, massively multiplexed, optical and near-infrared spectrograph. Exploiting the Subaru prime focus, 2394 reconfigurable fibers will be distributed over the 1.3 deg field of view. The spectrograph has been designed with 3 arms of blue, red, and near-infrared cameras to simultaneously observe spectra from 380nm to 1260nm in one exposure at a resolution of ~1.6-2.7A. An international collaboration is developing this instrument under the initiative of Kavli IPMU. The project is now going into the construction phase aiming at undertaking system integration in 2017-2018 and subsequently carrying out engineering operations in 2018-2019. This article gives an overview of the instrument, current project status and future paths forward.Comment: 17 pages, 10 figures. Proceeding of SPIE Astronomical Telescopes and Instrumentation 201

A bioimage informatics platform for high-throughput embryo phenotyping

High-throughput phenotyping is a cornerstone of numerous functional genomics projects. In recent years, imaging screens have become increasingly important in understanding gene–phenotype relationships in studies of cells, tissues and whole organisms. Three-dimensional (3D) imaging has risen to prominence in the field of developmental biology for its ability to capture whole embryo morphology and gene expression, as exemplified by the International Mouse Phenotyping Consortium (IMPC). Large volumes of image data are being acquired by multiple institutions around the world that encompass a range of modalities, proprietary software and metadata. To facilitate robust downstream analysis, images and metadata must be standardized to account for these differences. As an open scientific enterprise, making the data readily accessible is essential so that members of biomedical and clinical research communities can study the images for themselves without the need for highly specialized software or technical expertise. In this article, we present a platform of software tools that facilitate the upload, analysis and dissemination of 3D images for the IMPC. Over 750 reconstructions from 80 embryonic lethal and subviable lines have been captured to date, all of which are openly accessible at mousephenotype.org. Although designed for the IMPC, all software is available under an open-source licence for others to use and develop further. Ongoing developments aim to increase throughput and improve the analysis and dissemination of image data. Furthermore, we aim to ensure that images are searchable so that users can locate relevant images associated with genes, phenotypes or human diseases of interest

Evolution of laparoscopic left lateral sectionectomy without the Pringle maneuver: through resection of benign and malignant tumors to living liver donation

BACKGROUND: Laparoscopic left lateral sectionectomy (LLS) has gained popularity in its use for benign and malignant tumors. This report describes the evolution of the authors' experience using laparoscopic LLS for different indications including living liver donation. METHODS: Between January 2004 and January 2009, 37 consecutive patients underwent laparoscopic LLS for benign, primary, and metastatic liver diseases, and for one case of living liver donation. Resection of malignant tumors was indicated for 19 (51%) of the 37 patients. RESULTS: All but three patients (deceased due to metastatic cancer disease) are alive and well after a median follow-up period of 20 months (range, 8-46 months). Liver cell adenomas (72%) were the main indication among benign tumors, and colorectal liver metastases (84%) were the first indication of malignancy. One case of live liver donation was performed. Whereas 16 patients (43%) had undergone a previous abdominal surgery, 3 patients (8%) had LLS combined with bowel resection. The median operation time was of 195 min (range, 115-300 min), and the median blood loss was of 50 ml (range, 0-500 ml). Mild to severe steatosis was noted in 7 patients (19%) and aspecific portal inflammation in 11 patients (30%). A median free margin of 5 mm (range, 5-27 mm) was achieved for all cancer patients. The overall recurrence rate for colorectal liver metastases was of 44% (7 patients), but none recurred at the surgical margin. No conversion to laparotomy was recorded, and the overall morbidity rate was 8.1% (1 grade 1 and 2 grade 2 complications). The median hospital stay was 6 days (range, 2-10 days). CONCLUSIONS: Laparoscopic LLS without portal clamping can be performed safely for cases of benign and malignant liver disease with minimal blood loss and overall morbidity, free resection margins, and a favorable outcome. As the ultimate step of the learning curve, laparoscopic LLS could be routinely proposed, potentially increasing the donor pool for living-related liver transplantation