Explorative search of distributed bio-data to answer complex biomedical questions

Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery

GFZ Wireless Seismic Array (GFZ-WISE), a Wireless Mesh Network of Seismic Sensors: New Perspectives for Seismic Noise Array Investigations and Site Monitoring

Over the last few years, the analysis of seismic noise recorded by two dimensional arrays has been confirmed to be capable of deriving the subsoil shear-wave velocity structure down to several hundred meters depth. In fact, using just a few minutes of seismic noise recordings and combining this with the well known horizontal-to-vertical method, it has also been shown that it is possible to investigate the average one dimensional velocity structure below an array of stations in urban areas with a sufficient resolution to depths that would be prohibitive with active source array surveys, while in addition reducing the number of boreholes required to be drilled for site-effect analysis. However, the high cost of standard seismological instrumentation limits the number of sensors generally available for two-dimensional array measurements (i.e., of the order of 10), limiting the resolution in the estimated shear-wave velocity profiles. Therefore, new themes in site-effect estimation research by two-dimensional arrays involve the development and application of low-cost instrumentation, which potentially allows the performance of dense-array measurements, and the development of dedicated signal-analysis procedures for rapid and robust estimation of shear-wave velocity profiles. In this work, we present novel low-cost wireless instrumentation for dense two-dimensional ambient seismic noise array measurements that allows the real–time analysis of the surface-wavefield and the rapid estimation of the local shear-wave velocity structure for site response studies. We first introduce the general philosophy of the new system, as well as the hardware and software that forms the novel instrument, which we have tested in laboratory and field studies

From coherent shocklets to giant collective incoherent shock waves in nonlocal turbulent flows

International audienceUnderstanding turbulent flows arising from random dispersive waves that interact strongly through nonlinearities is a challenging issue in physics. Here we report the observation of a characteristic transition: strengthening the nonlocal character of the nonlinear response drives the system from a fully turbulent regime, featuring a sea of coherent small-scale dispersive shock waves (shocklets) towards the unexpected emergence of a giant collective incoherent shock wave. The front of such global incoherent shock carries most of the stochastic fluctuations and is responsible for a peculiar folding of the local spectrum. Nonlinear optics experiments performed in a solution of graphene nano-flakes clearly highlight this remarkable transition. Our observations shed new light on the role of long-range interactions in strongly nonlinear wave systems operating far from thermodynamic equilibrium, which reveals analogies with, for example, gravitational systems, and establishes a new scenario that can be common to many turbulent flows in photonic quantum fluids, hydrodynamics and Bose–Einstein condensates

Ferroelectric control of the spin texture in germanium telluride

The electrical manipulation of spins in semiconductors, without magnetic fields or auxiliary ferromagnetic materials, represents the holy grail for spintronics. The use of Rashba effect is very attractive because the k-dependent spin-splitting is originated by an electric field. So far only tiny effects in two-dimensional electron gases (2DEG) have been exploited. Recently, GeTe has been predicted to have bulk bands with giant Rashba-like splitting, originated by the inversion symmetry breaking due to ferroelectric polarization. In this work, we show that GeTe(111) surfaces with inwards or outwards ferroelectric polarizations display opposite sense of circulation of spin in bulk Rashba bands, as seen by spin and angular resolved photoemission experiments. Our results represent the first experimental demonstration of ferroelectric control of the spin texture in a semiconductor, a fundamental milestone towards the exploitation of the non-volatile electrically switchable spin texture of GeTe in spintronic devices.Comment: 18 pages, 4 figure

Monitoring the Microseismicity through a Dense Seismic Array and a Similarity Search Detection Technique: Application to the Seismic Monitoring of Collalto Gas-Storage, North Italy

Seismic monitoring in areas where induced earthquakes could occur is a challenging topic for seismologists due to the generally very low signal to noise ratio. Therefore, the seismological community is devoting several efforts to the development of high-quality networks around the areas where fluid injection and storage and geothermal activities take place, also following the national induced seismicity monitoring guidelines. The use of advanced data mining strategies, such as template matching filters, auto-similarity search, and deep-learning approaches, has recently further fostered such monitoring, enhancing the seismic catalogs and lowering the magnitude of completeness of these areas. In this framework, we carried out an experiment where a small-aperture seismic array was installed within the dense seismic network used for monitoring the gas reservoir of Collalto, in North Italy. The continuous velocimetric data, acquired for 25 days, were analysed through the application of the optimized auto-similarity search technique FAST. The array was conceived as a cost-effective network, aimed at integrating, right above the gas storage site, the permanent high-resolution Collalto Seismic Network. The analysis allowed to detect micro-events down to magnitude Ml = −0.4 within a distance of ~15 km from the array. Our results confirmed that the system based on the array installation and the FAST data analysis might contribute to lowering the magnitude of completeness around the site of about 0.7 units