A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer

[Abstract] Introduction. The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. Methods. This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials. To ensure interoperability across different institutions, we have developed a Semantic Interoperability Layer (SIL) to facilitate homogeneous access to clinical and genetic information, based on different well-established biomedical standards and following International Health (IHE) recommendations. Results. The SIL has shown suitability for integrating biomedical knowledge and technologies to match the latest clinical advances in healthcare and the use of genomic information. This genomic data integration in the SIL has been tested with a diagnostic classifier tool that takes advantage of harmonized multi-center clinico-genomic data for training statistical predictive models. Conclusions. The SIL has been adopted in national and international research initiatives, such as the EURECA-EU research project and the CIMED collaborative Spanish project, where the proposed solution has been applied and evaluated by clinical experts focused on clinico-genomic studies.Instituto de Salud Carlos III, PI13/02020Instituto de Salud Carlos III, PI13/0028

Soil and water bioengineering: practice and research needs for reconciling natural hazard control and ecological restoration

Soil and water bioengineering is a technology that encourages scientists and practitioners to combine their knowledge and skills in the management of ecosystems with a common goal to maximize benefits to both man and the natural environment. It involves techniques that use plants as living building materials, for: (i) natural hazard control (e.g., soil erosion, torrential floods and landslides) and (ii) ecological restoration or nature-based re-introduction of species on degraded lands, river embankments, and disturbed environments. For a bioengineering project to be successful, engineers are required to highlight all the potential benefits and ecosystem services by documenting the technical, ecological, economic and social values. The novel approaches used by bioengineers raise questions for researchers and necessitate innovation from practitioners to design bioengineering concepts and techniques. Our objective in this paper, therefore, is to highlight the practice and research needs in soil and water bioengineering for reconciling natural hazard control and ecological restoration. Firstly, we review the definition and development of bioengineering technology, while stressing issues concerning the design, implementation, and monitoring of bioengineering actions. Secondly, we highlight the need to reconcile natural hazard control and ecological restoration by posing novel practice and research questions

GATE : a simulation toolkit for PET and SPECT

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols, and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at the address http://www-lphe.epfl.ch/GATE/

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Correspondence: Strongly-driven Re + CO2 redox reaction at high-pressure and high-temperature

Santamaría-Perez, D.; Mcguire, C.; Makhluf, A.; Kavner, A.; Chulia-Jordan, R.; Jorda Moret, JL.; Rey Garcia, F.... (2016). Correspondence: Strongly-driven Re + CO2 redox reaction at high-pressure and high-temperature. Nature Communications. 7:1-3. doi:10.1038/ncomms13647S137Yoo, C. S. et al. Crystal structure of carbon dioxide at high pressure: “superhard” polymeric carbon dioxide. Phys. Rev. Lett. 83, 5527–5530 (1999).Santoro, M. et al. Partially collapsed cristobalite structure in the non molecular phase V in CO2 . Proc. Natl Acad. Sci. 109, 5176–5179 (2012).Datchi, F., Mallick, B., Salamat, A. & Ninet, S. Structure of polymeric carbon dioxide CO2-V. Phys. Rev. Lett. 108, 125701 (2012).Santoro, M. et al. Silicon carbonate phase formed from carbon dioxide and silica under pressure. Proc. Natl Acad. Sci. 108, 7689–7692 (2011).Santoro, M. et al. Carbon enters silica forming a cristobalite-type CO2.SiO2 solid solution. Nat. Commun. 5, 3761 (2014).Corma, A., Rey, F., Rius, J., Sabater, M. J. & Valencia, S. Supramolecular self-assembled molecules as organic directing agent for synthesis of zeolites. Nature 431, 287–290 (2004).Guth, J.-L., Kessler, H. & Wey, R. in Studies in Surface Science and Catalysis Vol. 28 (eds Murakami, Y., Iijima, A. & Ward, J. W.) 121 (Kodansha-Elsevier, 1986).Santamaria-Perez, D. et al. Exploring the chemical reactivity between carbon dioxide and three transition metals (Au, Pt, and Re) at high-pressure high-temperature conditions. Inorg. Chem. 55, 10793–10799 (2016).Magneli, A. Studies on rhenium oxides. Acta Chem. Scand. 11, 28–33 (1957)

The ANTARES Optical Beacon System

ANTARES is a neutrino telescope being deployed in the Mediterranean Sea. It consists of a three dimensional array of photomultiplier tubes that can detect the Cherenkov light induced by charged particles produced in the interactions of neutrinos with the surrounding medium. High angular resolution can be achieved, in particular when a muon is produced, provided that the Cherenkov photons are detected with sufficient timing precision. Considerations of the intrinsic time uncertainties stemming from the transit time spread in the photomultiplier tubes and the mechanism of transmission of light in sea water lead to the conclusion that a relative time accuracy of the order of 0.5 ns is desirable. Accordingly, different time calibration systems have been developed for the ANTARES telescope. In this article, a system based on Optical Beacons, a set of external and well-controlled pulsed light sources located throughout the detector, is described. This calibration system takes into account the optical properties of sea water, which is used as the detection volume of the ANTARES telescope. The design, tests, construction and first results of the two types of beacons, LED and laser-based, are presented.Comment: 21 pages, 18 figures, submitted to Nucl. Instr. and Meth. Phys. Res.

Chronology of the sedimentary processes during the postglacial sea level rise in two estuaries of the Algarve coast, Southern Portugal

Four profiles of estuarine sediments obtained from boreholes drilled in the Algarve, Southern Portugal were studied in order to reconstruct the process of sediment accumulation driven by the postglacial sea level rise. In addition to the sedimentological analysis, the Foraminifera Index of Marine Influence (FIMI) permitted assessment of the nature and organization of sedimentary facies in the BelicheeGuadiana and Gilão-Almargem estuaries. The Beliche- Guadiana CM5 and Almargem G2 profiles accumulated in a sheltered environment, with the former presenting an almost continuous record of the sea level rise since ca 13 000 cal yr BP. The G1 and G3 profiles from the Gilão-Almargem area represent a more discontinuous record of the last 8000 years, which accumulated in the more dynamic environment of an outer estuary. The integration of all radiocarbon ages of dated levels, led to an estimate of sediment accumulation rates. Assuming a constant position of the sediment surface with respect to the tidal range and a negligible compaction of sediment, the sea level rose at the rate of 7 mm yr ^-1 in the period from 13 000 to 7500 cal yr BP. This process slowed down to ca 0.9 mm yr 1 from 7500 cal yr BP until the present. The marked historical change in the rate of sediment accumulation in these estuaries also occurred with the accumulation of organic matter and is, therefore, important data for global biogeochemical models of carbon. The main obstacle to obtain higher temporal resolution of the sedimentary processes was the intense anaerobic respiration of organic matter via sulphate reduction, which did not allow any accumulation of peat and, furthermore, led to erasure of the palaeontological record by acid formed from the subsequent oxidation of sulphides.FORMOSE- Sources and Retention of Organic Matter in the Estuarine Zones, PRAXIS XXI program of Portuguese Science and Technology Foundation and project MEGASIG, INTERREG IIIa program of the European Union