JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Use of Two-Part Regression Calibration Model to Correct for Measurement Error in Episodically Consumed Foods in a Single-Replicate Study Design: EPIC Case Study.

In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model.

Predictive accuracy and usefulness of calibration of the ESC SCORE in Switzerland.

BACKGROUND: Prevention of cardiovascular disease (CVD) at the individual level should rely on the assessment of absolute risk using population-specific risk tables. OBJECTIVE: To compare the predictive accuracy of the original and the calibrated SCORE functions regarding 10-year cardiovascular risk in Switzerland. DESIGN: Cross-sectional, population-based study (5773 participants aged 35-74 years). METHODS: The SCORE equation for low-risk countries was calibrated based on the Swiss CVD mortality rates and on the CVD risk factor levels from the study sample. The predicted number of CVD deaths after a 10-year period was computed from the original and the calibrated equations and from the observed cardiovascular mortality for 2003. RESULTS: According to the original and calibrated functions, 16.3 and 15.8% of men and 8.2 and 8.9% of women, respectively, had a 10-year CVD risk > or =5%. Concordance correlation coefficient between the two functions was 0.951 for men and 0.948 for women, both P<0.001. Both risk functions adequately predicted the 10-year cumulative number of CVD deaths: in men, 71 (original) and 74 (calibrated) deaths for 73 deaths when using the CVD mortality rates; in women, 44 (original), 45 (calibrated) and 45 (CVD mortality rates), respectively. Compared to the original function, the calibrated function classified more women and fewer men at high-risk. Moreover, the calibrated function gave better risk estimates among participants aged over 65 years. CONCLUSION: The original SCORE function adequately predicts CVD death in Switzerland, particularly for individuals aged less than 65 years. The calibrated function provides more reliable estimates for older individuals.

Grain size analyses in tin-lead glazes based on 2d-sections

A problem in the archaeometric classification of Catalan Renaissance pottery is the fact, thatthe clay supply of the pottery workshops was centrally organized by guilds, and thereforeusually all potters of a single production centre produced chemically similar ceramics.However, analysing the glazes of the ware usually a large number of inclusions in the glaze isfound, which reveal technological differences between single workshops. These inclusionshave been used by the potters in order to opacify the transparent glaze and to achieve a whitebackground for further decoration.In order to distinguish different technological preparation procedures of the single workshops,at a Scanning Electron Microscope the chemical composition of those inclusions as well astheir size in the two-dimensional cut is recorded. Based on the latter, a frequency distributionof the apparent diameters is estimated for each sample and type of inclusion.Following an approach by S.D. Wicksell (1925), it is principally possible to transform thedistributions of the apparent 2D-diameters back to those of the true three-dimensional bodies.The applicability of this approach and its practical problems are examined using differentways of kernel density estimation and Monte-Carlo tests of the methodology. Finally, it istested in how far the obtained frequency distributions can be used to classify the pottery

SwissTargetPrediction: a web server for target prediction of bioactive small molecules.

Bioactive small molecules, such as drugs or metabolites, bind to proteins or other macro-molecular targets to modulate their activity, which in turn results in the observed phenotypic effects. For this reason, mapping the targets of bioactive small molecules is a key step toward unraveling the molecular mechanisms underlying their bioactivity and predicting potential side effects or cross-reactivity. Recently, large datasets of protein-small molecule interactions have become available, providing a unique source of information for the development of knowledge-based approaches to computationally identify new targets for uncharacterized molecules or secondary targets for known molecules. Here, we introduce SwissTargetPrediction, a web server to accurately predict the targets of bioactive molecules based on a combination of 2D and 3D similarity measures with known ligands. Predictions can be carried out in five different organisms, and mapping predictions by homology within and between different species is enabled for close paralogs and orthologs. SwissTargetPrediction is accessible free of charge and without login requirement at http://www.swisstargetprediction.ch.

Dense Deformation Field Estimation for Atlas Registration using the Active Contour Framework

In this paper, we propose a new paradigm to carry outthe registration task with a dense deformation fieldderived from the optical flow model and the activecontour method. The proposed framework merges differenttasks such as segmentation, regularization, incorporationof prior knowledge and registration into a singleframework. The active contour model is at the core of ourframework even if it is used in a different way than thestandard approaches. Indeed, active contours are awell-known technique for image segmentation. Thistechnique consists in finding the curve which minimizesan energy functional designed to be minimal when thecurve has reached the object contours. That way, we getaccurate and smooth segmentation results. So far, theactive contour model has been used to segment objectslying in images from boundary-based, region-based orshape-based information. Our registration technique willprofit of all these families of active contours todetermine a dense deformation field defined on the wholeimage. A well-suited application of our model is theatlas registration in medical imaging which consists inautomatically delineating anatomical structures. Wepresent results on 2D synthetic images to show theperformances of our non rigid deformation field based ona natural registration term. We also present registrationresults on real 3D medical data with a large spaceoccupying tumor substantially deforming surroundingstructures, which constitutes a high challenging problem.

New Early to Middle Triassic U-Pb ages from South China: Calibration with ammonoid biochronozones and implications for the timing of the Triassic biotic recovery

New zircon U-Pb ages are proposed for late Early and Middle Triassic volcanic ash layers from the Luolou and Baifeng formations (northwestern Guangxi, South China). These ages are based on analyses of single, thermally annealed and chemically abraded zircons. Calibration with ammonoid ages indicate a 250.6 +/- 0.5 Ma age for the early Spathian Tirolites/Columbites beds, a 248.1 +/- 0.4 Ma age for the late Spathian Neopopanoceras haugi Zone, a 246.9 +/- 0.4 Ma age for the early middle Anisian Acrochordiceras hyatti Zone, and a 244.6 +/- 0.5 Ma age for the late middle Anisian Balatonites shoshonensis Zone. The new dates and previously published U-Pb ages indicate a duration of ca. 3 my for the Spathian, and minimal durations of 4.5 +/- 0.6 my for the Early Triassic and of 6.6+0.7/-0.9 my for the Anisian. The new Spathian dates are in a better agreement with a 252.6 +/- 0.2 Ma age than with a 251.4 +/- 0.3 Ma age for the Permian-Triassic boundary. These dates also highlight the extremely uneven duration of the four Early Triassic substages (Griesbachian, Dienerian, Smithian, and Spathian), of which the Spathian exceeds half of the duration of the entire Early Triassic. The simplistic assumption of equal duration of the four Early Triassic subdivisions is no longer tenable for the reconstruction of recovery patterns following the end Permian mass extinction. (c) 2006 Elsevier B.V. All rights reserved.

Valoración de la disfunción del ventrículo derecho en pacientes con insuficiencia pulmonar mediante ecocardiografía-2D y resonancia cardíaca

En este trabajo valoramos la correlación de los parámetros de análisis de ventrículo derecho (VD) por ecocardiografía-2D frente a cardiorresonancia (CRMN) y su capacidad de discriminación frente a dilatación y disfunción de VD en 63 pacientes con insuficiencia pulmonar significativa. Se obtuvieron correlaciones significativas débiles entre los parámetros de valoración de VD de ambas técnicas. Los parámetros que mejor discriminaron dilatación de VD (VTDVDi≥150ml/m2) fueron diámetro basal y medio y los que mejor discriminaron disfunción (FEVD≤45%) fueron onda S´ lateral y septal e índice de Tei. En conclusión, los parámetros ecocardiográficos de VD habituales se correlacionan débilmente con los parámetros por CRMN aunque permiten discriminar dilatación y disfunción significativas.

Detailed 3D seismic imaging of a fault zone beneath Lake Geneva, Switzerland

An efficient high-resolution (HR) three-dimensional (3D) seismic reflection system for small-scale targets in lacustrine settings was developed. In Lake Geneva, near the city of Lausanne, Switzerland, the offshore extension of a complex fault zone well mapped on land was chosen for testing our system. A preliminary two-dimensional seismic survey indicated structures that include a thin (<40 m) layer of subhorizontal Quaternary sediments that unconformably overlie south-east-dipping Tertiary Molasse beds and a major fault zone (Paudeze Fault Zone) that separates Plateau and Subalpine Molasse (SM) units. A 3D survey was conducted over this test site using a newly developed three-streamer system. It provided high-quality data with a penetration to depths of 300 m below the water bottom of non-aliased signal for dips up to 30degrees and with a maximum vertical resolution of 1.1 m. The data were subjected to a conventional 3D processing sequence that included post-stack time migration. Tests with 3D pre-stack depth migration showed that such techniques can be applied to HR seismic surveys. Delineation of several horizons and fault surfaces reveals the potential for small-scale geologic and tectonic interpretation in three dimensions. Five major seismic facies and their detailed 3D geometries can be distinguished. Three fault surfaces and the top of a molasse surface were mapped in 3D. Analysis of the geometry of these surfaces and their relative orientation suggests that pre-existing structures within the Plateau Molasse (PM) unit influenced later faulting between the Plateau and SM. In particular, a change in strike of the PM bed dip may indicate a fold formed by a regional stress regime, the orientation of which was different from the one responsible for the creation of the Paudeze Fault Zone. This structure might have later influenced the local stress regime and caused the curved shape of the Paudeze Fault in our surveyed area.

Anàlisi de l'aplicació Geomedia 3D

Anàlisi de les diferents funcionalitats de l'aplicació Geomedia 3D i la seva utilitat dins del terreny dels sistemes d'informació geogràfica.

Evolution of a debris flow channel monitored using a 3D terrestrial laser scanner

Like numerous torrents in mountainous regions, the Illgraben creek (canton of Wallis, SW Switzerland) produces almost every year several debris flows. The total area of the active catchment is only 4.7 km², but large events ranging from 50'000 to 400'000 m³ are common (Zimmermann 2000). Consequently, the pathway of the main channel often changes suddenly. One single event can for instance fill the whole river bed and dig new several-meters-deep channels somewhere else (Bardou et al. 2003). The quantification of both, the rhythm and the magnitude of these changes, is very important to assess the variability of the bed's cross section and long profile. These parameters are indispensable for numerical modelling, as they should be considered as initial conditions. To monitor the channel evolution an Optech ILRIS 3D terrestrial laser scanner (LIDAR) was used. LIDAR permits to make a complete high precision 3D model of the channel and its surroundings by scanning it from different view points. The 3D data are treated and interpreted with the software Polyworks from Innovmetric Software Inc. Sequential 3D models allow for the determination of the variation in the bed's cross section and long profile. These data will afterwards be used to quantify the erosion and the deposition in the torrent reaches. To complete the chronological evolution of the landforms, precise digital terrain models, obtained by high resolution photogrammetry based on old aerial photographs, will be used. A 500 m long section of the Illgraben channel was scanned on 18th of August 2005 and on 7th of April 2006. These two data sets permit identifying the changes of the channel that occurred during the winter season. An upcoming scanning campaign in September 2006 will allow for the determination of the changes during this summer. Preliminary results show huge variations in the pathway of the Illgraben channel, as well as important vertical and lateral erosion of the river bed. Here we present the results of a river bank on the left (north-western) flank of the channel (Figure 1). For the August 2005 model the scans from 3 viewpoints were superposed, whereas the April 2006 3D image was obtained by combining 5 separate scans. The bank was eroded. The bank got eroded essentially on its left part (up to 6.3 m), where it is hit by the river and the debris flows (Figures 2 and 3). A debris cone has also formed (Figure 3), which suggests that a part of the bank erosion is due to shallow landslides. They probably occur when the river erosion creates an undercut slope. These geometrical data allow for the monitoring of the alluvial dynamics (i.e. aggradation and degradation) on different time scales and the influence of debris flows occurrence on these changes. Finally, the resistance against erosion of the bed's cross section and long profile will be analysed to assess the variability of these two key parameters. This information may then be used in debris flow simulation.

Interaction of cationic ultrasmall superparamagnetic iron oxide nanoparticles with human melanoma cells.

Ultrasmall superparamagnetic iron oxide nanoparticles (USPIONs) are currently under development for the intracellular delivery of therapeutics. However, the mechanisms of cellular uptake and the cellular reaction to this uptake, independent of therapeutics, are not well defined. The interactions of biocompatible cationic aminoUSPIONs with human cells was studied in 2D and 3D cultures using biochemical and electron microscopy techniques. AminoUSPIONs were internalized by human melanoma cells in 2D and 3D cultures. Uptake was clathrin mediated and the particles localized in lysosomes, inducing activation of the lysosomal cathepsin D and decreasing the expression of the transferrin receptor in human melanoma cells and/or skin fibroblasts. AminoUSPIONs deeply invaded 3D spheroids of human melanoma cells. Thus, aminoUSPIONs can invade tumors and their uptake by human cells induces cell reaction.

Disseny i modelació en 3D d'un habitacle en le jaciment ibèric d'Els Vilars

L'objectiu del projecte és reconstruir un habitacle del jaciment ibèric dels Vilars amb els objectes de l'època pertinents. Tot això servirà per obtenir una visió de la vida i les costums dels pobladors ibèrics.

Diseño e implementación de una interfície de lectura de un láser 2D

Con la realización del proyecto se pretende conocer y comprender el funcionamiento de un sistema de distancias basado en un láser que efectua medidas en un plano 2D y diseñar e implementar un software que permita la utilización de los recursos del mismo.