p-BioSPRE-an information and communication technology framework for transnational biomaterial sharing and access

Biobanks represent key resources for clinico-genomic research and are needed to pave the way to personalised medicine. To achieve this goal, it is crucial that scientists can securely access and share high-quality biomaterial and related data. Therefore, there is a growing interest in integrating biobanks into larger biomedical information and communication technology (ICT) infrastructures. The European project p-medicine is currently building an innovative ICT infrastructure to meet this need. This platform provides tools and services for conducting research and clinical trials in personalised medicine. In this paper, we describe one of its main components, the biobank access framework p-BioSPRE (p-medicine Biospecimen Search and Project Request Engine). This generic framework enables and simplifies access to existing biobanks, but also to offer own biomaterial collections to research communities, and to manage biobank specimens and related clinical data over the ObTiMA Trial Biomaterial Manager. p-BioSPRE takes into consideration all relevant ethical and legal standards, e.g., safeguarding donors’ personal rights and enabling biobanks to keep control over the donated material and related data. The framework thus enables secure sharing of biomaterial within open and closed research communities, while flexibly integrating related clinical and omics data. Although the development of the framework is mainly driven by user scenarios from the cancer domain, in this case, acute lymphoblastic leukaemia and Wilms tumour, it can be extended to further disease entities.FP7/2007-2013/27008

MIPAS IMK/IAA Carbon Tetrachloride (CCl4) Retrieval and First Comparison With Other Instruments

MIPAS thermal limb emission measurements were used to derive vertically resolved profiles of carbon tetrachloride (CCl4). Level-1b data versions MIPAS/5.02 to MIPAS/5.06 were converted into volume mixing ratio profiles using the level-2 processor developed at Karlsruhe Institute of Technology (KIT) Institute of Meteorology and Climate Research (IMK) and Consejo Superior de Investigaciones Cientificas (CSIC), Instituto de Astrofisica de Andalucia (IAA). Consideration of peroxyacetyl nitrate (PAN) as an interfering species, which is jointly retrieved, and CO2 line mixing is crucial for reliable retrievals. Parts of the CO2 Q-branch region that overlap with the CCl4 signature were omitted, since large residuals were still found even though line mixing was considered in the forward model. However, the omitted spectral region could be narrowed noticeably when line mixing was accounted for. A new CCl4 spectro-scopic data set leads to slightly smaller CCl4 volume mixing ratios. In general, latitude-altitude cross sections show the expected CCl4 features with highest values of around 90 pptv at altitudes at and below the tropical tropopause and values decreasing with altitude and latitude due to stratospheric decomposition. Other patterns, such as subsidence in the polar vortex during winter and early spring, are also visible in the distributions. The decline in CCl4 abundance during the MI-PAS Envisat measurement period (July 2002 to April 2012) is clearly reflected in the altitude-latitude cross section of trends estimated from the entire retrieved data set

On the improved stability of the version 7 MIPAS ozone record

The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) was an infrared limb emission spectrometer on the Envisat platform. From 2002 to 2012, it performed pole-to-pole measurements during day and night, producing more than 1000 profiles per day. The European Space Agency (ESA) recently released the new version 7 of Level 1B MIPAS spectra, in which a new set of time-dependent correction coefficients for the nonlinearity in the detector response functions was implemented. This change is expected to reduce the long-term drift of the MIPAS Level 2 data. We evaluate the long-term stability of ozone Level 2 data retrieved from MIPAS v7 Level 1B spectra with the IMK/IAA scientific level 2 processor. For this, we compare MIPAS data with ozone measurements from the Microwave Limb Sounder (MLS) instrument on NASA\u27s Aura satellite, ozonesondes and ground-based lidar instruments. The ozonesondes and lidars alone do not allow us to conclude with enough significance that the new version is more stable than the previous one, but a clear improvement in long-term stability is observed in the satellite-data-based drift analysis. The results of ozonesondes, lidars and satellite drift analysis are consistent: all indicate that the drifts of the new version are less negative/more positive nearly everywhere above 15km. The 10-year MIPAS ozone trends calculated from the old and the new data versions are compared. The new trends are closer to old drift-corrected trends than the old uncorrected trends were. From this, we conclude that the nonlinearity correction performed on Level 1B data is an improvement. These results indicate that MIPAS data are now even more suited for trend studies, alone or as part of a merged data record

BDNF-Live-Exon-Visualization (BLEV) Allows Differential Detection of BDNF Transcripts in vitro and in vivo

Bdnf exon-IV and exon-VI transcripts are driven by neuronal activity and are involved in pathologies related to sleep, fear or memory disorders. However, how their differential transcription translates activity changes into long-lasting network changes is elusive. Aiming to trace specifically the network controlled by exon-IV and -VI derived BDNF during activity-dependent plasticity changes, we generated a transgenic reporter mouse for BDNF-live-exon-visualization (BLEV), in which expression of Bdnf exon-IV and -VI can be visualized by co-expression of CFP and YFP. CFP and YFP expression was differentially activated and targeted in cell lines, primary cultures and BLEV reporter mice without interfering with BDNF protein synthesis. CFP and YFP expression, moreover, overlapped with BDNF protein expression in defined hippocampal neuronal, glial and vascular locations in vivo. So far, activity-dependent BDNF cannot be explicitly monitored independent of basal BDNF levels. The BLEV reporter mouse therefore provides a new model, which can be used to test whether stimulus-induced activity-dependent changes in BDNF expression are instrumental for long-lasting plasticity modifications

Clusters of galaxies : observational properties of the diffuse radio emission

Clusters of galaxies, as the largest virialized systems in the Universe, are ideal laboratories to study the formation and evolution of cosmic structures...(abridged)... Most of the detailed knowledge of galaxy clusters has been obtained in recent years from the study of ICM through X-ray Astronomy. At the same time, radio observations have proved that the ICM is mixed with non-thermal components, i.e. highly relativistic particles and large-scale magnetic fields, detected through their synchrotron emission. The knowledge of the properties of these non-thermal ICM components has increased significantly, owing to sensitive radio images and to the development of theoretical models. Diffuse synchrotron radio emission in the central and peripheral cluster regions has been found in many clusters. Moreover large-scale magnetic fields appear to be present in all galaxy clusters, as derived from Rotation Measure (RM) studies. Non-thermal components are linked to the cluster X-ray properties, and to the cluster evolutionary stage, and are crucial for a comprehensive physical description of the intracluster medium. They play an important role in the cluster formation and evolution. We review here the observational properties of diffuse non-thermal sources detected in galaxy clusters: halos, relics and mini-halos. We discuss their classification and properties. We report published results up to date and obtain and discuss statistical properties. We present the properties of large-scale magnetic fields in clusters and in even larger structures: filaments connecting galaxy clusters. We summarize the current models of the origin of these cluster components, and outline the improvements that are expected in this area from future developments thanks to the new generation of radio telescopes.Comment: Accepted for the publication in The Astronomy and Astrophysics Review. 58 pages, 26 figure

Exposure assessment of process-related contaminants in food by biomarker monitoring

Exposure assessment is a fundamental part of the risk assessment paradigm, but can often present a number of challenges and uncertainties. This is especially the case for process contaminants formed during the processing, e.g. heating of food, since they are in part highly reactive and/or volatile, thus making exposure assessment by analysing contents in food unreliable. New approaches are therefore required to accurately assess consumer exposure and thus better inform the risk assessment. Such novel approaches may include the use of biomarkers, physiologically based kinetic (PBK) modelling-facilitated reverse dosimetry, and/or duplicate diet studies. This review focuses on the state of the art with respect to the use of biomarkers of exposure for the process contaminants acrylamide, 3-MCPD esters, glycidyl esters, furan and acrolein. From the overview presented, it becomes clear that the field of assessing human exposure to process-related contaminants in food by biomarker monitoring is promising and strongly developing. The current state of the art as well as the existing data gaps and challenges for the future were defined. They include (1) using PBK modelling and duplicate diet studies to establish, preferably in humans, correlations between external exposure and biomarkers; (2) elucidation of the possible endogenous formation of the process-related contaminants and the resulting biomarker levels; (3) the influence of inter-individual variations and how to include that in the biomarker-based exposure predictions; (4) the correction for confounding factors; (5) the value of the different biomarkers in relation to exposure scenario’s and risk assessment, and (6) the possibilities of novel methodologies. In spite of these challenges it can be concluded that biomarker-based exposure assessment provides a unique opportunity to more accurately assess consumer exposure to process-related contaminants in food and thus to better inform risk assessment