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

Pediatric T-ALL type-1 and type-2 relapses develop along distinct pathways of clonal evolution

The mechanisms underlying T-ALL relapse remain essentially unknown. Multilevel-omics in 38 matched pairs of initial and relapsed T-ALL revealed 18 (47%) type-1 (defined by being derived from the major ancestral clone) and 20 (53%) type-2 relapses (derived from a minor ancestral clone). In both types of relapse, we observed known and novel drivers of multidrug resistance including MDR1 and MVP, NT5C2 and JAK-STAT activators. Patients with type-1 relapses were specifically characterized by IL7R upregulation. In remarkable contrast, type-2 relapses demonstrated (1) enrichment of constitutional cancer predisposition gene mutations, (2) divergent genetic and epigenetic remodeling, and (3) enrichment of somatic hypermutator phenotypes, related to BLM, BUB1B/PMS2 and TP53 mutations. T-ALLs that later progressed to type-2 relapses exhibited a complex subclonal architecture, unexpectedly, already at the time of initial diagnosis. Deconvolution analysis of ATAC-Seq profiles showed that T-ALLs later developing into type-1 relapses resembled a predominant immature thymic T-cell population, whereas T-ALLs developing into type-2 relapses resembled a mixture of normal T-cell precursors. In sum, our analyses revealed fundamentally different mechanisms driving either type-1 or type-2 T-ALL relapse and indicate that differential capacities of disease evolution are already inherent to the molecular setup of the initial leukemia

Effect of ABCG2, OCT1, and ABCB1(MDR1) Gene Expression on Treatment-Free Remission in a EURO-SKI Subtrial

Introduction Tyrosine kinase inhibitors (TKIs) can safely be discontinued in chronic myeloid leukemia (CML) patients with sustained deep molecular response. ABCG2 (breast cancer resistance protein), OCT1 (organic cation transporter 1), and ABCB1 (multidrug resistance protein 1) gene products are known to play a crucial role in acquired pharmacogenetic TKI resistance. Their influence on treatment-free remission (TFR) has not yet been investigated. Materials and Methods RNA was isolated on the last day of TKI intake from peripheral blood leukocytes of 132 chronic phase CML patients who discontinued TKI treatment within the European Stop Tyrosine Kinase Inhibitor Study trial. Plasmid standards were designed including subgenic inserts of OCT1, ABCG2, and ABCB1 together with GUSB as reference gene. For expression analyses, quantitative real-time polymerase chain reaction was used. Multiple Cox regression analysis was performed. In addition, gene expression cutoffs for patient risk stratification were investigated. Results The TFR rate of 132 patients, 12 months after TKI discontinuation, was 54% (95% confidence interval [CI], 46%-62%). ABCG2 expression (‰) was retained as the only significant variable (P = .02; hazard ratio, 1.04; 95% CI, 1.01-1.07) in multiple Cox regression analysis. Only for the ABCG2 efflux transporter, a significant cutoff was found (P = .04). Patients with an ABCG2/GUSB transcript level >4.5‰ (n = 93) showed a 12-month TFR rate of 47% (95% CI, 37%-57%), whereas patients with low ABCG2 expression (≤4.5‰; n = 39) had a 12-month TFR rate of 72% (95% CI, 55%-82%). Conclusion In this study, we investigated the effect of pharmacogenetics in the context of a CML treatment discontinuation trial. The transcript levels of the efflux transporter ABCG2 predicted TFR after TKI discontinuation

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