An atlas of human gene expression from massively parallel signature sequencing (MPSS).

We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences in gene expression between cell and tissue types are largely determined by transcripts derived from a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little more than half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance. The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com.

Detector de contorns basat en el domini transformat

RESUM En aquest document es presenta un detector de contorns d’imatges basat en el domini transformat. A partir de la interpretació de la transformada de Fourier de la imatge i la seva formulació matricial en termes dels diferents modes, es realitza una selecció de les components passa baixes a partir de les quals es reconstrueix la component de baixa freqüència que es resta de la imatge original per tal d’obtenir el detector. Aquest detector de contorns no és esbiaixat. L’algorisme pot ser aplicat utilitzant diferents mides del bloc de processament, que pot anar de la imatge sencera a blocs de reduïdes dimensions: 36X36, 16x16 o 8x8, per fer un seguiment de les propietats locals de la imatge quan aquesta és presenta característiques espacials poc uniformes.

Fusion of Multi-Atlas Segmentations with Spatial Distribution Modeling

In recent years, multi-atlas fusion methods have gainedsignificant attention in medical image segmentation. Inthis paper, we propose a general Markov Random Field(MRF) based framework that can perform edge-preservingsmoothing of the labels at the time of fusing the labelsitself. More specifically, we formulate the label fusionproblem with MRF-based neighborhood priors, as an energyminimization problem containing a unary data term and apairwise smoothness term. We present how the existingfusion methods like majority voting, global weightedvoting and local weighted voting methods can be reframedto profit from the proposed framework, for generatingmore accurate segmentations as well as more contiguoussegmentations by getting rid of holes and islands. Theproposed framework is evaluated for segmenting lymphnodes in 3D head and neck CT images. A comparison ofvarious fusion algorithms is also presented.

Proyecto Atlas: servidor de datos geoespaciales, descarga de información cartográfica

La present memòria descriu el projecte final: Atlas, servidor de dades geoespaciales, descàrrega d'informació cartogràfica, en l'es desenvolupa la metodologia necessària i s'expliquen els passos per a la creació d'un geoportal, un objectiu especifico del projecte és inserir i assolir el funcionament de l'eina que permet realitzar les descàrregues de la informació cartogràfica, que un usuari final desitgi obtenir des d'un ordinador personal, entre les solucions tecnologies emprades per a assolir la descàrrega de cartografia digital es pot esmentar les solucions del Grup Esri: ArcIMS i Data Delivery Extension (DDE) i per a visualitzar la informació cartogràfica es va utilitzar Openlayers.

Monitorització d'alt nivell per a el computing de l'experiment ATLAS (LHC)

Aquest projecte descriu la fusió de les necessitats diaries de monitorització del experiment ATLAS des del punt de vista del cloud. La idea principal es desenvolupar un conjunt de col·lectors que recullin informació de la distribució i processat de les dades i dels test de wlcg (Service Availability Monitoring), emmagatzemant-la en BBDD específiques per tal de mostrar els resultats en una sola pàgina HLM (High Level Monitoring). Un cop aconseguit, l’aplicació ha de permetre investigar més enllà via interacció amb el front-end, el qual estarà alimentat per les estadístiques emmagatzemades a la BBDD.

Stratigraphy and palaeoenvironment of Early Jurassic dinosaur-bearing volcaniclastic deposits from Toundoute (Province of Ouarzazate, Haut-Atlas, Morocco)

The Early Jurassic dinosaur site of Toundoute which yielded the basal sauropod Tazoudasaurus naimi is examined in the light of its stratigraphic, sedimentological and palaeoenvironmental context. A thin succession of Early Liassic marine carbonates (probably Hettangian-Sinemurian in age) is continuously overlain by continental beds with dinosaurs. These latter are assumed to be of Middle to Late Liassic age. The continental deposits include a large part of volcanoclastics, different from the Triassic basalts. The Jurassic volcanoclastics originated from an unknown but obviously close eruption centre. The continental sediments (channels and flood plain) were deposited under tropical climate conditions with alternating humid and dry episodes. The bones occur as isolated or partly articulated elements (parts of carcasses). The two bone-beds are related to typical mud-flows. This type of transport protected the bones from erosion, and favoured their burying and fossilization.

Atlas iconographique tomodensitométrique des pathologies bénignes de l'amiante [Computed tomographic atlas of benign asbestos related pathology].

The demonstration by computed tomography of abnormalities related to asbestos is essential for the recognition of industrial disease, the compensation of which has considerable economic consequences. The use of compute tomography, the most reliable technique for the detection of pleuro-parenchymatous abnormalities related to asbestos exposure, has increased considerably in France since the publication of the results of a consensus conference in Paris in 1999. Since that time, developments in technology have noticeably modified the protocols of investigation and increased the sensitivity of the detection of pleural and interstitial parenchymatous abnormalities and of nodules. The technical recommendations and those for the interpretation of pleural and parenchymatous abnormalities need to be well known. They are presented in the form of an atlas that gives detailed criteria for asbestosis, pleural plaques and pleural fibrosis. The diagnosis of pleural plaques depends on the combination of clear limits at the pleural and pulmonary interface, typical topography and multiple, bilateral localization. In the context of asbestos exposure the plaques are characteristic of this exposure, unlike diffuse pleural thickening, crow's feet images, parenchymatous bands and entrapped atalectasis. The writing of the radiological report would be most appropriate on this basis.

Segmentació d'imatge de ressonància magnètica de pit utilitzant atlas probabilístic

La localització d'òrgans és un tòpic important en l'àmbit de la imatge mèdica per l'ajuda del tractament i diagnosi del càncer. Un exemple es pot trobar en la cal•libració de models farmacoquinètics. Aquesta pot ésser realitzada utilitzant un teixit de referència, on, per exemple en imatges de ressonància magnètica de pit, una correcta segmentació del múscul pectoral és necessària per a la detecció de signes de malignitat. Els mètodes de segmentació basat en atlas han estat altament avaluats en imatge de ressonància magnètica de cervell, obtenint resultats satisfactoris. En aquest projecte, en col•laboració amb el el Diagnostic Image Analysis Group de la Radboud University Nijmegen Medical Centre i la supervisió del Dr. N.Karssemeijer, es presenta la primera aproximació d'un mètode de segmentació basat en atlas per segmentar els diferents teixits visibles en imatges de ressonància magnètica (T1) del pit femení. L'atlas consisteix en 5 estructures (teixit greixòs, teixit dens, cor, pulmons i múscul pectoral) i ha estat utilitzat en un algorisme de segmentació Bayesià per tal de delinear les esmentades estructures. A més a més, s'ha dut a terme una comparació entre un mètode de registre global i un de local, utilitzats tant en la construcció de l'atlas com en la fase de segmentació, essent el primer el que ha presentat millors resultats en termes d'eficiència i precisió. Per a l'avaluació, s'ha dut a terme una comparació visual i numèrica entre les segmentacions obtingudes i les realitzades manualment pels experts col•laboradors. Pel que fa a la numèrica, s'ha emprat el coeficient de similitud de Dice ( mesura que dóna valors entre 0 i 1, on 0 significa no similitud i 1 similitud màxima) i s'ha obtingut una mitjana general de 0.8. Aquest resultat confirma la validesa del mètode presentat per a la segmentació d'imatges de ressonància magnètica del pit.

From central Atlantic continental rift to Neogene uplift - western Anti-Atlas (Morocco)

P>To put constraints on the Mesozoic to recent growth of the Anti-Atlas system, we investigated the temperature-time history of rocks by applying extensive low-temperature thermochronological analysis to three Precambrian inliers along the coast and 250 km into the interior. Bedrocks yield old U-Th/He ages on zircon (248-193 Ma) and apatite (150-50 Ma) and also fission-track ages of 173-121 Ma on apatite. These datasets are interpreted as recording passive margin upward movements from central Atlantic rifting until the Early Cretaceous. A phase of sedimentary burial was evidenced for the Cretaceous-Eocene. The extension of this thin (1.5 km) basin is loosely constrained but can be extended to the western regions of northern Africa. Effects of the existing thermal perturbation of lithospheric origin 100 km below the Atlas show that the 120-60 degrees C isotherms are not much deflected. Large-scale uplift has possibly occurred in the western Anti-Atlas since c. 30 Ma and is associated with a mean denudation rate of 0.08 km Ma-1.

Criteria for establishing shielding of multi-detector computed tomography (MDCT) rooms.

The aim of this work is to compare two methods used for determining the proper shielding of computed tomography (CT) rooms while considering recent technological advances in CT scanners. The approaches of the German Institute for Standardisation and the US National Council on Radiation Protection and Measurements were compared and a series of radiation measurements were performed in several CT rooms at the Lausanne University Hospital. The following three-step procedure is proposed for assuring sufficient shielding of rooms hosting new CT units with spiral mode acquisition and various X-ray beam collimation widths: (1) calculate the ambient equivalent dose for a representative average weekly dose length product at the position where shielding is required; (2) from the maximum permissible weekly dose at the location of interest, calculate the transmission factor F that must be taken to ensure proper shielding and (3) convert the transmission factor into a thickness of lead shielding. A similar approach could be adopted to use when designing shielding for fluoroscopy rooms, where the basic quantity would be the dose area product instead of the load of current (milliampere-minute).

Ascending aorta measurements as assessed by ECG-gated multi-detector computed tomography : a pilot study to etablish normative values for transcatheters therapies

Rapport de synthèse : Mesures de l'aorte ascendante par scanner synchronisé au rythme cardiaque: une étude pilote pour établir des valeurs normatives dans le cadre des futures thérapies par transcathéter. Objectif : L'objectif de cette étude est d'établir les valeurs morphométriques normatives de l'aorte ascendante à l'aide de l'angiographie par scanner synchronisé au rythme cardiaque, afin d'aider au développement des futurs traitements par transcathéter. Matériels et méthodes : Chez soixante-dix-sept patients (âgé de 22 à 83 ans, âge moyen: 54,7 ans), une angiographie par scanner synchronisé au rythme cardiaque a été réalisée pour évaluation des vaisseaux coronaires. Les examens ont été revus afin d'étudier l'anatomie de la chambre de chasse du ventricule gauche jusqu'au tronc brachio-céphalique droit. A l'aide de programmes de reconstructions multiplanaires et de segmentation automatique, différents diamètres et longueurs considérés comme importants pour les futurs traitements par transcathéter ont été mesurés. Les valeurs sont exprimées en moyennes, médianes, maximums, minimums, écart-types et en coefficients de variation. Les variations de diamètre de l'aorte ascendante durant le cycle cardiaque ont été aussi considérées. Résultats : Le diamètre moyen de la chambre de chasse du ventricule gauche était de 20.3+/-3.4 mm. Au niveau du sinus coronaire de l'aorte, il était de 34.2+/-4.1 mm et au niveau de la jonction sinotubulaire il était de 29.7+/-3.4 mm. Le diamètre moyen de l'aorte ascendante était de 32.7+/-3.8 mm. Le coefficient de variation de ces mesures variait de 12 à 17%. La distance moyenne entre l'insertion proximale des valvules aortiques et le départ du tronc brachio-céphalique droit était de 92.6+/-11.8 mm. La distance moyenne entre l'insertion proximale des valvules aortiques et l'origine de l'artère coronaire proximale était de 12.1+/-3.7 mm avec un coefficient de variation de 31%. La distance moyenne entre les deux ostia coronaires était de 7.2+/-3.1 mm avec un coefficient de variation de 43%. La longueur moyenne du petit arc de l'aorte ascendante entre l'artère coronaire gauche et le tronc brachio-céphalique droit était de 52.9+/-9.5 mm. La longueur moyenne de la continuité fibreuse entre la valve aortique et la valvule mitrale antérieure était de 14.6+/-3.3 mm avec un coefficient de variation de 23%. L'aire moyenne de la valve aortique était de 582.0+/-131.9 mm2. La variation du diamètre antéro-postérieur et transverse de l'aorte ascendante était respectivement de 8.4% et de 7.3%. Conclusion Il existe d'importantes variations inter-individuelles dans les mesures de l'aorte ascendante avec cependant des variations intra-individuelles faibles durant le cycle cardiaque. De ce fait, une approche personnalisée pour chaque patient est recommandée dans la confection des futures endoprothèses de l'aorte ascendante. Le scanner synchronisé au rythme cardiaque jouera un rôle prépondérant dans le bilan préthérapeutique. Abstract : The aim of this study was to provide an insight into normative values of the ascending aorta in regards to novel endovascular procedures using ECG-gated multi-detector CT angiography. Seventy-seven adult patients without ascending aortic abnormalities were evaluated. Measurements at relevant levels of the aortic root and ascending aorta were obtained. Diameter variations of the ascending aorta during cardiac cycle were also considered. Mean diameters (mm) were as follows: LV outflow tract 20.3+/-3.4, coronary sinus 34.2+/-4.1, sinotubular junction 29.7+-3.4 and mid ascending aorta 32.7+/-3.8 with coefficients of variation (CV) ranging from 12 to 17%. Mean distances (mm) were: from the plane passing through the proximal insertions of the aortic valve cusps to the right brachio-cephalic artery (BCA) 92.6111.8, from the plane passing through the proximal insertions of the aortic valve cusps to the proximal coronary ostium 12.1+/-3.7, and between both coronary ostia 7.2+/-3.1, minimal arc of the ascending aorta from left coronary ostium to right BCA 52.9 X9.5, and the fibrous continuity between the aortic valve and the anterior leaflet of the mitral valve 14.óf3.3, CV 13-43%. Mean aortic valve area was 582+-131.9 mm2. The variations of the antero-posterior and transverse diameters of the ascending aorta during the cardiac cycle were 8.4% and 7.3%, respectively. Results showed large inter-individual variations in diameters and distances but with limited intra-individual variations during the cardiac cycle. A personalized approach for planning endovascular devices must be considered.

Atlas interactivo de mortalidad de Andalucía (AIMA)

Until now, mortality atlases have been static. Most of them describe the geographical distribution of mortality using count data aggregated over time and standardized mortality rates. However, this methodology has several limitations. Count data aggregated over time produce a bias in the estimation of death rates. Moreover, this practice difficult the study of temporal changes in geographical distribution of mortality. On the other hand, using standardized mortality hamper to check differences in mortality among groups. The Interactive Mortality Atlas in Andalusia (AIMA) is an alternative to conventional static atlases. It is a dynamic Geographical Information System that allows visualizing in web-site more than 12.000 maps and 338.00 graphics related to the spatio-temporal distribution of the main death causes in Andalusia by age and sex groups from 1981. The objective of this paper is to describe the methods used for AIMA development, to show technical specifications and to present their interactivity. The system is available from the link products in www.demap.es. AIMA is the first interactive GIS that have been developed in Spain with these characteristics. Spatio-temporal Hierarchical Bayesian Models were used for statistical data analysis. The results were integrated into web-site using a PHP environment and a dynamic cartography in Flash. Thematic maps in AIMA demonstrate that the geographical distribution of mortality is dynamic, with differences among year, age and sex groups. The information nowadays provided by AIMA and the future updating will contribute to reflect on the past, the present and the future of population health in Andalusia.