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.

Over-expression of PHO1 in Arabidopsis leaves reveals its role in mediating phosphate efflux.

Inorganic phosphate (Pi) homeostasis in multi-cellular eukaryotes depends not only on Pi influx into cells, but also on Pi efflux. Examples in plants for which Pi efflux is crucial are transfer of Pi into the xylem of roots and release of Pi at the peri-arbuscular interface of mycorrhizal roots. Despite its importance, no protein has been identified that specifically mediates phosphate efflux either in animals or plants. The Arabidopsis thaliana PHO1 gene is expressed in roots, and was previously shown to be involved in long-distance transfer of Pi from the root to the shoot. Here we show that PHO1 over-expression in the shoot of A. thaliana led to a two- to threefold increase in shoot Pi content and a severe reduction in shoot growth. (31) P-NMR in vivo showed a normal initial distribution of intracellular Pi between the cytoplasm and the vacuole in leaves over-expressing PHO1, followed by a large efflux of Pi into the infiltration medium, leading to a rapid reduction of the vacuolar Pi pool. Furthermore, the Pi concentration in leaf xylem exudates from intact plants was more than 100-fold higher in PHO1 over-expressing plants compared to wild-type. Together, these results show that PHO1 over-expression in leaves leads to a dramatic efflux of Pi out of cells and into the xylem vessel, revealing a crucial role for PHO1 in Pi efflux.

Skin permeation and metabolism of di(2-ethylhexyl) phthalate (DEHP).

Phthalates are suspected to be endocrine disruptors. Di(2-ethylhexyl) phthalate (DEHP) is assumed to have low dermal absorption; however, previous in vitro skin permeation studies have shown large permeation differences. Our aims were to determine DEHP permeation parameters and assess extent of skin DEHP metabolism among workers highly exposed to these lipophilic, low volatile substances. Surgically removed skin from patients undergoing abdominoplasty was immediately dermatomed (800 μm) and mounted on flow-through diffusion cells (1.77 cm(2)) operating at 32°C with cell culture media (aqueous solution) as the reservoir liquid. The cells were dosed either with neat DEHP or emulsified in aqueous solution (166 μg/ml). Samples were analysed by HPLC-MS/MS. DEHP permeated human viable skin only as the metabolite MEHP (100%) after 8h of exposure. Human skin was able to further oxidize MEHP to 5-oxo-MEHP. Neat DEHP applied to the skin hardly permeated skin while the aqueous solution readily permeated skin measured in both cases as concentration of MEHP in the receptor liquid. DEHP pass through human skin, detected as MEHP only when emulsified in aqueous solution, and to a far lesser degree when applied neat to the skin. Using results from older in vitro skin permeation studies with non-viable skin may underestimate skin exposures. Our results are in overall agreement with newer phthalate skin permeation studies.

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

Retroelements are important evolutionary forces but can be deleterious if left uncontrolled. Members of the human APOBEC3 family of cytidine deaminases can inhibit a wide range of endogenous, as well as exogenous, retroelements. These enzymes are structurally organized in one or two domains comprising a zinc-coordinating motif. APOBEC3G contains two such domains, only the C terminal of which is endowed with editing activity, while its N-terminal counterpart binds RNA, promotes homo-oligomerization, and is necessary for packaging into human immunodeficiency virus type 1 (HIV-1) virions. Here, we performed a large-scale mutagenesis-based analysis of the APOBEC3G N terminus, testing mutants for (i) inhibition of vif-defective HIV-1 infection and Alu retrotransposition, (ii) RNA binding, and (iii) oligomerization. Furthermore, in the absence of structural information on this domain, we used homology modeling to examine the positions of functionally important residues and of residues found to be under positive selection by phylogenetic analyses of primate APOBEC3G genes. Our results reveal the importance of a predicted RNA binding dimerization interface both for packaging into HIV-1 virions and inhibition of both HIV-1 infection and Alu transposition. We further found that the HIV-1-blocking activity of APOBEC3G N-terminal mutants defective for packaging can be almost entirely rescued if their virion incorporation is forced by fusion with Vpr, indicating that the corresponding region of APOBEC3G plays little role in other aspects of its action against this pathogen. Interestingly, residues forming the APOBEC3G dimer interface are highly conserved, contrasting with the rapid evolution of two neighboring surface-exposed amino acid patches, one targeted by the Vif protein of primate lentiviruses and the other of yet-undefined function.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Hybrid Multiscale Finite Volume method for two-phase flow in porous media

We present a novel hybrid (or multiphysics) algorithm, which couples pore-scale and Darcy descriptions of two-phase flow in porous media. The flow at the pore-scale is described by the Navier?Stokes equations, and the Volume of Fluid (VOF) method is used to model the evolution of the fluid?fluid interface. An extension of the Multiscale Finite Volume (MsFV) method is employed to construct the Darcy-scale problem. First, a set of local interpolators for pressure and velocity is constructed by solving the Navier?Stokes equations; then, a coarse mass-conservation problem is constructed by averaging the pore-scale velocity over the cells of a coarse grid, which act as control volumes; finally, a conservative pore-scale velocity field is reconstructed and used to advect the fluid?fluid interface. The method relies on the localization assumptions used to compute the interpolators (which are quite straightforward extensions of the standard MsFV) and on the postulate that the coarse-scale fluxes are proportional to the coarse-pressure differences. By numerical simulations of two-phase problems, we demonstrate that these assumptions provide hybrid solutions that are in good agreement with reference pore-scale solutions and are able to model the transition from stable to unstable flow regimes. Our hybrid method can naturally take advantage of several adaptive strategies and allows considering pore-scale fluxes only in some regions, while Darcy fluxes are used in the rest of the domain. Moreover, since the method relies on the assumption that the relationship between coarse-scale fluxes and pressure differences is local, it can be used as a numerical tool to investigate the limits of validity of Darcy's law and to understand the link between pore-scale quantities and their corresponding Darcy-scale variables.

Preretinal partial pressure of oxygen gradients before and after experimental pars plana vitrectomy.

PURPOSE: To evaluate preretinal partial pressure of oxygen (PO2) gradients before and after experimental pars plana vitrectomy. METHODS: Arteriolar, venous, and intervascular preretinal PO2 gradients were recorded in 7 minipigs during slow withdrawal of oxygen-sensitive microelectrodes (10-μm tip diameter) from the vitreoretinal interface to 2 mm into the vitreous cavity. Recordings were repeated after pars plana vitrectomy and balanced salt solution (BSS) intraocular perfusion. RESULTS: Arteriolar, venous, and intervascular preretinal PO2 at the vitreoretinal interface were 62.3 ± 13.8, 22.5 ± 3.3, and 17.0 ± 7.5 mmHg, respectively, before vitrectomy; 97.7 ± 19.9, 40.0 ± 21.9, and 56.3 ± 28.4 mmHg, respectively, immediately after vitrectomy; and 59.0 ± 27.4, 25.2 ± 3.0, and 21.5 ± 4.5 mmHg, respectively, 2½ hours after interruption of BSS perfusion. PO2 2 mm from the vitreoretinal interface was 28.4 ± 3.6 mmHg before vitrectomy; 151.8 ± 4.5 mmHg immediately after vitrectomy; and 34.8 ± 4.1 mmHg 2½ hours after interruption of BSS perfusion. PO2 gradients were still present after vitrectomy, with the same patterns as before vitrectomy. CONCLUSION: Preretinal PO2 gradients are not eliminated after pars plana vitrectomy. During BSS perfusion, vitreous cavity PO2 is very high. Interruption of BSS perfusion evokes progressive equilibration of vitreous cavity PO2 with concomitant progressive return of preretinal PO2 gradients to their previtrectomy patterns. This indicates that preretinal diffusion of oxygen is not altered after vitrectomy. The beneficial effect of vitrectomy in ischemic retinal diseases or macular edema may be related to other mechanisms, such as increased oxygen convection currents or removal of growth factors and cytokines secreted in the vitreous.

Generación de interfaces para aplicaciones por línea de comandos

Generación dinámica de interfaces web basadas en ficheros descriptivos XML para el control de la parametrización compleja y ejecución de programas por línea de comandos. La necesidad surge con la aplicación mlcoalsim, utilizada por investigadores de la UAB, cuya parametrización requiere la edición manual de un fichero de texto la sintaxis del cual es complicada y pesada. Con la generación de interfaces web se pretende ayudar a los usuarios en la correcta parametrización y ejecución de aplicaciones como mlcoalsim.

MyHits: a new interactive resource for protein annotation and domain identification.

The MyHits web server (http://myhits.isb-sib.ch) is a new integrated service dedicated to the annotation of protein sequences and to the analysis of their domains and signatures. Guest users can use the system anonymously, with full access to (i) standard bioinformatics programs (e.g. PSI-BLAST, ClustalW, T-Coffee, Jalview); (ii) a large number of protein sequence databases, including standard (Swiss-Prot, TrEMBL) and locally developed databases (splice variants); (iii) databases of protein motifs (Prosite, Interpro); (iv) a precomputed list of matches ('hits') between the sequence and motif databases. All databases are updated on a weekly basis and the hit list is kept up to date incrementally. The MyHits server also includes a new collection of tools to generate graphical representations of pairwise and multiple sequence alignments including their annotated features. Free registration enables users to upload their own sequences and motifs to private databases. These are then made available through the same web interface and the same set of analytical tools. Registered users can manage their own sequences and annotations using only web tools and freeze their data in their private database for publication purposes.

Generación de visitas virtuales a museos 3D para la inclusión en páginas web

Las páginas web junto a la animación 3D son dos grandes atractivos hoy en día en el mundo de Internet. Una interfaz web agradable e interactiva por la que navegar cómodamente; junto a una herramienta en dos dimensiones fácil de manejar, para diseñar y obtener un resultado en tres dimensiones. Esas han sido las bases de mi aplicación, la cual consiste en una página web dedicada al arte, donde cualquier persona podrá registrarse y dibujar mediante una paleta cómo sería un museo a su gusto. Visitando el museo virtual resultante, donde admirar las obras junto a su autor y título.

Desarrollo de una plataforma bioinformática para la gestión de datos fenotípicos y moleculares

Este proyecto está orientado a ayudar a un grupo de investigadores del Departamento de Ciencia Animal y de los Alimentos (UAB), que se dedican a recopilar datos genómicos obtenidos en experimentos. La aplicación constará de dos partes. La primera es la parte de los usuarios, donde se podrá crear proyectos, insertar, modificar o eliminar datos y consultar la información ya existente en la aplicación. La segunda parte es la del administrador, que como tal podrá dar de alta a nuevos usuarios, restaurar versiones anteriores de la base de datos, eliminar usuarios y consultar las acciones realizadas por los usuarios.

"Echoing approval": a new speech disorder.

We report the cases of two patients presenting a peculiar speech disorder, which we have named "echoing approval", in which the patients echo, in replying to questions in a dialogue with short phrases, the positive or negative syntactical construction of a question, or its positive or negative intonation, but without any repetition of whole or part of sentences. When asked about their symptoms, the patients replied 80% of the time with "yes, yes", "that's right", or "exactly" to positive questions and "no, no" or "absolutely not" to negative questions, regardless of their actual symptoms and oblivious to self-contradiction. In addition, when the examining doctor was speaking to a medical colleague in the patient's presence and using medical terminology that the patient did not understand, he/she agreed or disagreed with any sentence and technical word uttered in a way entirely dependent on the syntax or intonation used. To distinguish this speech disorder from echolalia or verbal perseverations, with which it may be superficially confused, we suggest that it be called "echoing approval", as it may be part one of the manifestations of the environment-dependency syndrome. This clinical picture was found to be associated with features of transcortical motor aphasia and frontal lobe signs. One patient had a bilateral callosofrontal malignant glioma and the other a probable multiple system atrophy with global deterioration, pre-eminent frontal release signs, diffuse leukoencephalopathy and multiple lacunes. On the basis of these clinical deficits and neuroimaging features, we are unable to delineate the common, or minimal, lesioned network required for this symptomatology to occur, especially in the absence of a series of patients, and with such a difference in both the location and causes of the lesions. However, bilateral frontosubcortical dysfunction was pre-eminent in the clinical picture in both patients, even though more diffuse brain pathology was seen in one, and it might be speculated that dysfunction of the bilateral orbitofrontal and frontomesial motor frontosubcortical circuits might be involved in the aetiology of this peculiar speech disorder.

The InterPro Database, 2003 brings increased coverage and new features.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Recrystallisation rims in zircon (Valle d'Arbedo, Switzerland): an integrated cathodoluminescence, LA-ICP-MS, SHRIMP, and TEM study

Recrystallization rims are a common feature of zircon crystals that underwent metamorphism. We present a microstructural and microchemical study of partially recrystallized zircon grains collected in polymetamorphic migmatites (Valle d'Arbedo, Ticino, Switzerland). The rims are bright in cathodo-luminescence (CL), with sharp and convex contacts characterized by inward-penetrating embayments transgressing igneous zircon cores. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) data and transmission electron microscopy (TEM) imaging indicate that the rims are chemically and microstructurally different from the cores. The rims are strongly depleted in REE, with concentrations up to two orders of magnitude lower than in the cores, indicating a significant loss of REE during zircon recrystallization. Enrichment in non-formula elements, such as Ca, has not been observed in the rims. The microstructure of zircon cores shows a dappled intensity at and below the 100 nm scale, possibly due to radiation damage. Other defects such as pores and dislocations are absent in the core except at healed cracks. Zircon rims are mostly dapple-free, but contain nanoscale pores and strain centers, interpreted as fluid inclusions and chemical residues, respectively. Sensitive high-resolution ion microprobe (SHRIMP) U-Pb ages show that the recrystallization of the rims took place >200 Ma ago when the parent igneous zircon was not metamict. The chemical composition and the low-Ti content of the rims indicate that they form at sub-solidus temperatures (550-650 degrees C). Recrystallization rims in Valle d'Arbedo zircon are interpreted as the result of the migration of chemical reaction fronts in which fluid triggered in situ and contemporaneous interface-coupled dissolution-reprecipitation mechanisms. This study indicates that strong lattice strain resulting from the incorporation of a large amount of impurities and structural defects is not a necessary condition for zircon to recrystallize. Our observations suggest that the early formation of recrystallization rims played a major role in preserving zircon from the more recent Alpine metamorphic overprint.

OnTheBus

El projecte OnTheBus pretén ser un sistema de guiatge gratuït, destinat per a la plataforma mòbil Android, útil com a eina d’ajuda pel desplaçament d’un punt d’origen a un punt de destí dins de la ciutat, utilitzant la xarxa de transport metropolità. Aquesta memòria s’enllaça amb 6 memòries més, dels meus companys amb els qui he realitzat el projecte OnTheBus. Per poder elaborar amb èxit l’aplicació OntheBus, cal donar importància al disseny i a la implementació de la interfície d’usuari. L’objectiu d’aquesta memòria és explicar com s’ha realitzat i dissenyat l’aplicació perquè sigui accessible per a tothom. Ja que pot tenir un rang molt ampli d’edats d’usuaris, la implementació de la interfície està basada en les directrius del Disseny Universal.