La cohorte OstéoLaus: évaluation des outils de routine clinique pour la prédiction de la fracture ostéoporotique [OsteoLaus: prediction of osteoporotic fractures by clinical risk factors and DXA, IVA and TBS].

OsteoLaus is a cohort of 1400 women 50 to 80 years living in Lausanne, Switzerland. Clinical risk factors for osteoporosis, bone ultrasound of the heel, lumbar spine and hip bone mineral density (BMD), assessment of vertebral fracture by DXA, and microarchitecture evaluation by TBS (Trabecular Bone Score) will be recorded. TBS is a new parameter obtained after a re-analysis of a DXA exam. TBS is correlated with parameters of microarchitecture. His reproducibility is good. TBS give an added diagnostic value to BMD, and predict osteoporotic fracture (partially) independently to BMD. The position of TBS in clinical routine in complement to BMD and clinical risk factors will be evaluated in the OsteoLaus cohort.

Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e. g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

Editor interactivo de policubos

Hoy en día existen numerosas técnicas para aplicar texturas sobre objetos 3D genéricos, pero los mecanismos para su creación son, en general, o bien complejos y poco intuitivos para el artista, o bien poco eficientes en aspectos como obtener un texturado global sin costuras. Recientemente, la invención de los policubos ha abierto un nuevo espectro de posibilidades a la hora de realizar estas tareas, e incluso otras como animación y subdivisión, de crucial importancia para industrias como el cine o los videojuegos. Desafortunadamente, no existen herramientas automáticas y editables que permitan generar el modelo de policubos base. Un policubo es una agregación de cubos idénticos de forma que cada cubo tiene como mínimo en común una cara con otro cubo. Con la agrupación de estos cubos se pueden generar diferentes figuras espaciales. El objetivo es desarrollar una herramienta para la creación y edición interactiva de un modelo de policubos a partir de un objeto tridimensional, la cual proporcionara una libertad y control al usuario no existente en las herramientas actualmente disponibles

Generació semi-automàtica de façanes procedurals

L’objectiu d’aquest PFC és desenvolupar una eina d’edició de façanes procedural apartir d’una imatge d’una façana real. L’aplicació generarà les regles procedurals de lafaçana a partir de dades adquirides del model que es vol representar, com unafotografia. L’usuari de l’aplicació generarà de forma semi-automàtica i interactiva lesregles de subdivisió i repetició, especificant també la inserció de elementsarquitectònics (portes, finestres), que podran ser instanciats a partir d’una llibreria. Uncop generades, les regles s’escriuran en el format del sistema BuildingEngine perintegrar-se completament dins el procés de modelatge urbà.Aquest projecte es desenvoluparà en Matlab

Modelat d'edificis basats en extrusions procedurals per a skylineEngine

Actualment ens trobem en un món on tot gira al voltant de les noves tecnologies, i un pilar fonamental és l'oci i l'entreteniment. Això engloba principalment les indústries del cinema, videojocs i realitat virtual. Un dels problemes que tenen aquestes indústries és com crear l'escenari on es produeix la història. L'objectiu d'aquest projecte de final de carrera és crear una eina integrada al skylineEngine, que serveixi per crear edificis de manera procedural, on l'usuari pugui definir l'estètica d'aquest edifici, introduint la seva planta i els perfils adequats. El que s'implementarà serà una eina de modelatge per a dissenyadors, que a partir d'una planta i perfils pugui crear l'edifici.Aquest projecte es desenvoluparà a sobre del mòdul de generació d'edificis del skylineEngine, una eina pel modelatge de ciutats que s'executa sobre el Houdini 3D, que és una plataforma genèrica pel modelatge procedural d'objectes.El desenvolupament d'aquest projecte implica:• Estudi de la plataforma de desenvolupament Houdini 3D i de les llibreries necessàries per la incorporació de scripts Python. Estudi de les EEDD internes de Houdini.• Aprendre i manejar el llenguatge de programació Python.• Estudi del codi de l'article Interactive Architectural Modeling with Procedural Extrusions, per en Tom Kelly i en Peter Wonka, publicat a la revista ACM Transactions on Graphics (2011).• Desenvolupament d'algorismes de conversió de geometria d'una estructura tipus face-vertex a una de tipus half-edge, i viceversa.• Modificació del codi Java per acceptar crides sense interfície d'usuari i amb estructures de dades generades des de Python.• Aprendre el funcionament de la llibreria JPype per permetre enllaçar el Java dins el Python.• Estudi del skylineEngine i de les llibreries per la creació d'edificis.• Integració del resultat dintre del skylineEngine.• Verificació i ajust de les regles i paràmetres de la simulació per a diferents edificis

Desenvolupament d’una biblioteca per a la generació de diagrames vectorials basat en l’entorn gràfic de JAVA2D i aplicació d’aquesta biblioteca per a la implementació d’una eina per al desenvolupament de diagrames d’E/R

En aquest projecte es vol implementar una llibreria en Java, que proporcioni leseines necessàries per a crear diagrames i esquemes. Es vol proporcionar a la llibreria unconjunt d’objectes bàsics, també mètodes i funcionalitats suficients per a gestionaraquests objectes. Per altra part, es vol implementar una aplicació per a dissenyar diagrames Entitat-Relació que utilitzi aquesta llibreria

MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

The effects of physiologically plausible connectivity structure on local and global dynamics in large scale brain models.

Functionally relevant large scale brain dynamics operates within the framework imposed by anatomical connectivity and time delays due to finite transmission speeds. To gain insight on the reliability and comparability of large scale brain network simulations, we investigate the effects of variations in the anatomical connectivity. Two different sets of detailed global connectivity structures are explored, the first extracted from the CoCoMac database and rescaled to the spatial extent of the human brain, the second derived from white-matter tractography applied to diffusion spectrum imaging (DSI) for a human subject. We use the combination of graph theoretical measures of the connection matrices and numerical simulations to explicate the importance of both connectivity strength and delays in shaping dynamic behaviour. Our results demonstrate that the brain dynamics derived from the CoCoMac database are more complex and biologically more realistic than the one based on the DSI database. We propose that the reason for this difference is the absence of directed weights in the DSI connectivity matrix.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

A post-processing pipeline to reconstruct the developing fetal brain using low-resolution MRI

Introduction. Development of the fetal brain surfacewith concomitant gyrification is one of the majormaturational processes of the human brain. Firstdelineated by postmortem studies or by ultrasound, MRIhas recently become a powerful tool for studying in vivothe structural correlates of brain maturation. However,the quantitative measurement of fetal brain developmentis a major challenge because of the movement of the fetusinside the amniotic cavity, the poor spatial resolution,the partial volume effect and the changing appearance ofthe developing brain. Today extensive efforts are made todeal with the âeurooepost-acquisitionâeuro reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution (Rousseau, F., 2006;Jiang, S., 2007). We here propose a framework devoted tothe segmentation of the basal ganglia, the gray-whitetissue segmentation, and in turn the 3D corticalreconstruction of the fetal brain. Method. Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences in fetuses aged from 29 to 32gestational weeks (slice thickness 5.4mm, in planespatial resolution 1.09mm). For each fetus, 6 axialvolumes shifted by 1 mm were acquired (about 1 min pervolume). First, each volume is manually segmented toextract fetal brain from surrounding fetal and maternaltissues. Inhomogeneity intensity correction and linearintensity normalization are then performed. A highspatial resolution image of isotropic voxel size of 1.09mm is created for each fetus as previously published byothers (Rousseau, F., 2006). B-splines are used for thescattered data interpolation (Lee, 1997). Then, basalganglia segmentation is performed on this superreconstructed volume using active contour framework witha Level Set implementation (Bach Cuadra, M., 2010). Oncebasal ganglia are removed from the image, brain tissuesegmentation is performed (Bach Cuadra, M., 2009). Theresulting white matter image is then binarized andfurther given as an input in the Freesurfer software(http://surfer.nmr.mgh.harvard.edu/) to provide accuratethree-dimensional reconstructions of the fetal brain.Results. High-resolution images of the cerebral fetalbrain, as obtained from the low-resolution acquired MRI,are presented for 4 subjects of age ranging from 29 to 32GA. An example is depicted in Figure 1. Accuracy in theautomated basal ganglia segmentation is compared withmanual segmentation using measurement of Dice similarity(DSI), with values above 0.7 considering to be a verygood agreement. In our sample we observed DSI valuesbetween 0.785 and 0.856. We further show the results ofgray-white matter segmentation overlaid on thehigh-resolution gray-scale images. The results arevisually checked for accuracy using the same principlesas commonly accepted in adult neuroimaging. Preliminary3D cortical reconstructions of the fetal brain are shownin Figure 2. Conclusion. We hereby present a completepipeline for the automated extraction of accuratethree-dimensional cortical surface of the fetal brain.These results are preliminary but promising, with theultimate goal to provide âeurooemovieâeuro of the normal gyraldevelopment. In turn, a precise knowledge of the normalfetal brain development will allow the quantification ofsubtle and early but clinically relevant deviations.Moreover, a precise understanding of the gyraldevelopment process may help to build hypotheses tounderstand the pathogenesis of several neurodevelopmentalconditions in which gyrification have been shown to bealtered (e.g. schizophrenia, autismâeuro¦). References.Rousseau, F. (2006), 'Registration-Based Approach forReconstruction of High-Resolution In Utero Fetal MR Brainimages', IEEE Transactions on Medical Imaging, vol. 13,no. 9, pp. 1072-1081. Jiang, S. (2007), 'MRI of MovingSubjects Using Multislice Snapshot Images With VolumeReconstruction (SVR): Application to Fetal, Neonatal, andAdult Brain Studies', IEEE Transactions on MedicalImaging, vol. 26, no. 7, pp. 967-980. Lee, S. (1997),'Scattered data interpolation with multilevel B-splines',IEEE Transactions on Visualization and Computer Graphics,vol. 3, no. 3, pp. 228-244. Bach Cuadra, M. (2010),'Central and Cortical Gray Mater Segmentation of MagneticResonance Images of the Fetal Brain', ISMRM Conference.Bach Cuadra, M. (2009), 'Brain tissue segmentation offetal MR images', MICCAI.

Recommendations for raloxifene use in daily clinical practice in the Swiss setting.

BACKGROUND/AIM: Raloxifene is the first selective estrogen receptor modulator that has been approved for the treatment and prevention of osteoporosis in postmenopausal women in Europe and in the US. Although raloxifene reduces the risk of invasive breast cancer in postmenopausal women with osteoporosis and in postmenopausal women at high risk for invasive breast cancer, it is approved in that indication in the US but not in the EU. The aim was to characterize the clinical profiles of postmenopausal women expected to benefit most from therapy with raloxifene based on published scientific evidence to date. METHODS: Key individual patient characteristics relevant to the prescription of raloxifene in daily practice were defined by a board of Swiss experts in the fields of menopause and metabolic bone diseases and linked to published scientific evidence. Consensus was reached about translating these insights into daily practice. RESULTS: Through estrogen agonistic effects on bone, raloxifene reduces biochemical markers of bone turnover to premenopausal levels, increases bone mineral density (BMD) at the lumbar spine, proximal femur, and total body, and reduces vertebral fracture risk in women with osteopenia or osteoporosis with and without prevalent vertebral fracture. Through estrogen antagonistic effects on breast tissue, raloxifene reduces the risk of invasive estrogen-receptor positive breast cancer in postmenopausal women with osteoporosis and in postmenopausal women at high risk for invasive breast cancer. Finally, raloxifene increases the incidence of hot flushes, the risk of venous thromboembolic events, and the risk of fatal stroke in postmenopausal women at increased risk for coronary heart disease. Postmenopausal women in whom the use of raloxifene is considered can be categorized in a 2 × 2 matrix reflecting their bone status (osteopenic or osteoporotic based on their BMD T-score by dual energy X-ray absorptiometry) and their breast cancer risk (low or high based on the modified Gail model). Women at high risk of breast cancer should be considered for treatment with raloxifene. CONCLUSION: Postmenopausal women between 50 and 70 years of age without climacteric symptoms with either osteopenia or osteoporosis should be evaluated with regard to their breast cancer risk and considered for treatment with raloxifene within the framework of its contraindications and precautions.

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any combination, data on the following features: predicted protein properties such as mass, pI, cellular location and transmembrane domains; SWISS-PROT annotations; Interpro domains; Gene Ontology records; verified transcription; BLAST matches to the proteomes of A.thaliana, Oryza sativa (rice), Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. The tool lends itself particularly well to the rapid analysis of contigs or of tens or hundreds of genes identified by high-throughput gene expression experiments. In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode. AVAILABILITY: http://centrifuge.unil.ch/ CONTACT: edward.farmer@unil.ch.

A numeric model to simulate solar individual ultraviolet exposure.

Exposure to solar ultraviolet (UV) light is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors. Individual exposure data remain scarce and development of alternative assessment methods is greatly needed. We developed a model simulating human exposure to solar UV. The model predicts the dose and distribution of UV exposure received on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a rendering engine that estimates the solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by each triangle was calculated, taking into account reflected, direct and diffuse radiation, and shading from other body parts. Dosimetric measurements (n = 54) were conducted in field conditions using a foam manikin as surrogate for an exposed individual. Dosimetric results were compared to the model predictions. The model predicted exposure to solar UV adequately. The symmetric mean absolute percentage error was 13%. Half of the predictions were within 17% range of the measurements. This model provides a tool to assess outdoor occupational and recreational UV exposures, without necessitating time-consuming individual dosimetry, with numerous potential uses in skin cancer prevention and research.

Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. UV irradiance is monitored via different techniques including ground measurements and satellite observations. However it is difficult to translate such observations into human UV exposure or dose because of confounding factors (shape of the exposed surface, shading, behavior, etc.) A collaboration between public health institutions, a meteorological office and an institute specialized in computing techniques developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop this tool, which estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. The radiation components are deduced from corresponding measurements of UV irradiance, and the related UV dose received by each triangle of the virtual manikin is computed accounting for shading by other body parts and eventual protection measures. The model was verified with dosimetric measurements (n=54) in field conditions using a foam manikin as surrogate for an exposed individual. Dosimetric results were compared to the model predictions. The model predicted exposure to solar UV adequately. The symmetric mean absolute percentage error was 13%. Half of the predictions were within 17% range of the measurements. This model allows assessing outdoor occupational and recreational UV exposures, without necessitating time-consuming individual dosimetry, with numerous potential uses in skin cancer prevention and research. Using this tool, we investigated solar UV exposure patterns with respect to the relative contribution of the direct, diffuse and reflected radiation. We assessed exposure doses for various body parts and exposure scenarios of a standing individual (static and dynamic postures). As input, the model used erythemally-weighted ground irradiance data measured in 2009 at Payerne, Switzerland. A year-round daily exposure (8 am to 5 pm) without protection was assumed. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e.g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose. Acute diffuse exposures were also obtained for cloudy summer days. The importance of diffuse UV radiation should not be underestimated when advocating preventive measures. Messages focused on avoiding acute direct exposures may be of limited efficiency to prevent skin cancers associated with chronic exposure (e.g., squamous cell carcinomas).