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This deliverable complements "D10.5 SoBigData e-Infrastructure software release 1" by describing how such a software has been deployed to serve the current needs of the SoBigData community. In particular, it describes how such a software has been exploited to make available the components envisaged in "D10.2 SoBigData e-Infrastructure release plan 1", i.e. the SoBigData portal (and the underlying Virtual Organisation), the SoBigData Catalogue, and the SoBigData Virtual Research Environments.

This report describes the PARTHENOS e-infrastructure architecture: the hardware and the services. Hardware is organized as a dynamic cloud of virtual machines, supporting computation and storage, while the services are organized into e-infrastructure middleware, storage, and end user services.

In this study we analyse the solutions offered by scientific data repositories to research data publishing. In particular, we focus on generalist repositories, i.e., repositories supporting the deposition of any research data. We have analysed the current practices promoted by such repositories with respect to 8 key aspects in data publishing, i.e., dataset formatting, documentation, licensing, publication costs, validation, availability, discovery and access, and citation.

Information and communication technology (ICT) advances in research infrastructures are continuously changing the way research and scientific communication are performed. Scientists, funders, and organisations are moving the paradigm of Research Publishing well beyond traditional articles. The aim is to pursue an holistic approach where publishing includes any product (e.g. publications, datasets, experiments, software, web sites, blogs) resulting from a research activity and relevant to the interpretation, evaluation, and reuse of the activity or part of it. We show that the implementation of this vision is today mainly inspired by literature scientific communication workflows, which separate the "where" research is conducted from the "where" research is published and shared. We claim that this model cannot fit well with scientific communication practice envisaged in Science 2.0 settings and propose a new class of scientific data repositories, denominated "Science 2.0 Repositories" (SciRepos), as a possible solution. SciRepos address the data pub lishing issues by blurring the distinction between research life-cycle and research publishing. They enable effective scientific communication workflows by making research products creation and publishing occur "within" the research infrastructure and "during" the research activities. We present the benefits resulting from Publishing in SciRepos and define a Reference Model and a Reference Architecture for a SciRepo platform, a general purpose platform facilitating the realisation of a SciRepo over any ICT-based research infrastructure environment with limited costs and efforts if compared with from-scratch approaches.

The purpose of data publishing is to release research data for others to use. However, its implementation remains an open issue. 'Science 2.0 Repositories' (SciRepos) address the publishing requirements arising in Science 2.0 by blurring the distinction between research life-cycle and research publishing. SciRepos interface with the ICT services of research infrastructures to intercept and publish research products while providing researchers with social networking tools for discovery, notification, sharing, discussion, and assessment of research products.

Friuli Venezia Giulia holds the higest row incidence rate for breast carcinoma in Italy (218%00) and Trieste, where live 125.000 women (105.000 women of age below 75) has the highest incidence rate among the other provinces of the region (220%00). The risk of developing breast carcinoma seems to be correlated with many different factors. The goal of this study is to focus on same specific breast carcinoma risk factors in the Trieste population.

This document reports on activities related to the gCube system integration, testing, distribution and documentation performed during the third reporting period of iMarine project.

Modern science calls for innovative practices to facilitate research collaborations that span institutions, disciplines, and countries. Scientists and practitioners are called to produce enhanced forms of scientific communication thus to make it possible for others to identify errors, to support, reject or refine theories and to reuse data for further understanding and knowledge. This scenario can benefit a lot from Internet-based services aiming at providing individual users having at their disposal scarce resources with interaction-oriented facilities, i.e., social computing, and elastic access to facilities on demand, i.e., cloud computing. In this paper, we present the D4Science approach that by leveraging social computing and cloud computing realises an integrated web-based working environment where scientists have at their fingertips what is needed to accomplish a scientific investigation. In particular, we present the large array of collaboration-oriented facilities obtained by integrating social networking paradigms with virtual research environments.

Modern science calls for innovative practices to facilitate research collaborations spanning institutions, disciplines, and countries. Paradigms such as cloud computing and social computing represent a new opportunity for individuals with scant resources, to participate in science. The D4Science.org Hybrid Data Infrastructure combines these two paradigms with Virtual Research Environments in order to offer a large array of collaboration-oriented facilities as-a-Service.

ICT advances in research infrastructures are continuously changing the way research and scientific communication are performed. Scientists, funders, and organizations are moving the paradigm of "research publishing" well beyond traditional articles. The aim is to pursue an holistic approach where publishing includes any product (e.g. publications, datasets, experiments, software, web sites, blogs) resulting from a research activity and relevant to the interpretation, evaluation, and reuse of the activity or part of it. The implementation of this vision is today mainly inspired by literature scientific communication workflows, which separate the "where" research is conducted from the "where" research is published and shared. In this paper we claim that this model cannot fit well with modern scientific communication practice. We present the idea of Research Infrastructure Scientific Communication (RISC) systems, which meet modern research publishing requirements by blurring the distinction between research life-cycle and research publishing. Finally, we present the implementation of a RISC system, running in the context of the D4Science research infrastructure.

Scientific activities are nowadays highly multidisciplinary, involve researchers of different institutions, and need innovative working environments. In this context, the Networked Multimedia Information Systems Laboratory (NeMIS) of the CNR Institute of Information Science and Technology (ISTI) has designed and realized an approach for the creation and management of Virtual Research Environments based on Hybrid Data Infrastructures. Such environments, accessible through a web browser, offer the whole set of resources necessary to fully respond to the needs of a specific application context (data, services and computational resources). These resources are dynamically acquired by means of an infrastructure that is capable of interfacing with existing services and Grid/Cloud infrastructures. This approach has been successfully applied in application contexts ranging from managing of catch statistics to the production of species distribution maps based on probabilistic models taking into account environmental factors.

Modern science call for innovative practices to facilitate research collaborations that span institutions, disciplines, and countries. Scientists and practitioners are called to produce enhanced forms of scientific communication thus to make it possible for others to identify errors, to support, reject or refine theories and to reuse data for further understanding and knowledge. This scenario can benefit a lot from Internet-based services aiming at providing individual users having at their disposal scarce resources with interaction-oriented facilities, i.e., social computing, and elastic access to facilities on demand, i.e., cloud computing. In this paper, we present the Hybrid Data Infrastructure, D4Science, developed to serve the needs of various communities of practice yet based on a technology which is domain agnostic. By leveraging social computing and cloud computing D4Science realises an integrated web-based working environment where scientists have at their fingertips what is needed to accomplish a scientific investigation. We present the large scale data management and processing facilities obtained through the use of services compliant with the cloud paradigms. Moreover, we present the large array of collaboration-oriented facilities obtained by integrating social networking paradigms with virtual research environments.

Modern science communication requires innovative environment and means for providing stakeholders with scientific outcomes. Research objects are emerging as replacements of traditional "documents" in scientific communication. These objects are multi-media and multi-part objects that aggregate all the "pieces" that contribute to a research result. Supporting these objects has gone beyond the capacity of traditional technological approaches based on locally specialized data management facilities. In this article we present an environment for producing "live research objects" by exploiting the capabilities offered by a Data Infrastructure. Such environment includes: (i) a workspace where users can organize and share with their co-workers very different items in a file-system-like environment; (ii) an editing framework where users can define the structure of a live research object and compile objects that comply with one of the defined templates; and (iii) a workflow engine where users can define the workflow governing the production of a live research object by specifying the phases and the relative responsible actors(s).

Infrastruttura per: (i) la registrazione, monitoring e mantenimento di risorse di calcolo, servizi e dati condivise secondo certe politiche e (ii) la creazione di ambienti virtuali di supporto alla collaborazione scientifica che si basano sull'uso di queste risorse.

Large scale Digital Library e-Infrastructures are emerging as a new approach for facilitating the development of Digital Libraries (DLs) serving diverse user communities with specific and continuously evolving requirements. Such an approach promotes the building of large-scale DLs via the dynamic, automated management of highly-distributed DL resources - e.g. collections of information objects, services, computing and storage resources - and enforcing controlled sharing of such resources across different DLs. This paper discusses an extensible and new approach for User Interfaces development, facilitating the sharing and reuse of UI resources, i.e. user interface constituents. In particular a design model and a concrete implementation, carried out in the context of DILIGENT and D4Science projects is presented in detail.

The SYRMEP (SYnchrotron Radiation for MEdical Physics) imaging system is based on the combination of a monochromatic laminar X-ray beam, with a laminar high-efficiency pixel silicon detector. The use of synchrotron radiation X-rays has the advantage of minimizing the radiation dose delivered to the sample because it is possible to choose the best energy for the considered radiological examination. The high efficiency of the detector (about 90% in 18-28 keV energy range) also lowers this dose figure. Since the detector is capable of single-photon counting, the information contained in the beam is fully exploited, leading to high contrast resolution. The present phase of the SYRMEP project involves a systematic study of in vitro breast tissue samples. The same samples are then imaged by means of a conventional mammographic Mo anode tube used in the common diagnostic practice and recorded on film/screen system. The comparison of the two imaging modalities shows the advantages, with special regard to contrast resolution, of the SYRMEP imaging system compared with conventional film-screen devices.

NAVIGATOR is an Italian regional project boosting precision medicine in oncology with the aim of making it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project’s goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e., standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.

Background: Conservative therapies for patients affected by Peripheral Arterial Occlusive Disease (PAOD) aim first to correct the risk factors and to slow down the disease progression. Among these, exercise has positive effects on blood flow, muscle metabolism and well demonstrated systemic effects. These include reduction of chronic inflammation markers, improvement of walking mechanics and heart function. Controlled physical training increases the ability to perform the daily activities improving life expectancy of these patients. The aim of this study is to evaluate the effects and the effectiveness of physical training performed in thermal water compared to traditional treadmill walking exercise. Methods: 98 patients affected by lib stage PAOD, according to Leriche-Fontaine classification, were enrolled. Patients were randomized into two groups: the first arm carried out an intensive training program under medical supervision (group A); the second one carried out a rehabilitative exercise associated with crenotherapy (group B). The following parameters were detected: Ankle-Brachial pressure index (ABI), actual claudication distance (ACD), maximum walking distance (MWD), flow mediated dilatation (FMD) and the intima-media thickness (IMT). All patients underwent Doppler echocardiography and complete biochemical assay. RESULTS: In both groups, there was a statistically significant improvement of lipidaemia compared to baseline. When compared with each other, the two groups did not show statistically significant differences. There were no significant differences between the two groups regarding echocardiographic findings. Vascular reactivity study showed a statistically significant improvement of FMD after 3 months of exercise in both groups. In crenotherapy group (B) FMD values were significantly higher than the treadmill ones (A). In both groups a statistically significant improvement in ACD was observed Conclusions: Our experience shows that crenotherapy has similar effects compared to traditional physical training in the treatment of PAOD, being equally well tolerated and safe; it gives an advantage over conventional physical training in terms of ACD and MWD improvement, although not statistically significant, and it is extremely welcome to patients compared to traditional physical training.

The efficacy and safety of nonionic dimeric contrast media in subjects with impaired renal function is largely unknown. The present study was aimed at determining the risk of tubular nephrotoxicity in patients with mild to moderate renal insufficiency who underwent intravenous urography (IVU) with the nonionic dimeric contrast agent iodixanol (Visipaque, Nycomed Imaging, Oslo, Norway). In a double-blind protocol 64 patients (55 males; mean age 68.3 years) with serum creatinine between 135 and 265 micromol/l who were to undergo IVU were randomized to receive iodixanol (a nonionic dimer) or iopromide (a nonionic monomer), 600 mg I/kg b. w. Renal function was evaluated before and 1 h, 6 h, 24 h, 48 h and 7 days after IVU with analysis of serum creatinine, urinary enzymes alanylaminopeptidase and N-acetyl-beta-glucosaminidase, and urinary microproteins alpha-1-microglobulin and albumin. Renal function remained stable in both contrast medium groups during the follow-up period. No statistically significant differences were observed between the monomer and the dimer in terms of urinary enzyme and microprotein excretion or serum creatinine. Transient radiocontrast-induced nephropathy developed in 1 patient who had received iodixanol. The administration of the nonionic dimeric contrast medium iodixanol, or of the nonionic monomer iopromide, entailed a low nephrotoxic potential in patients with mild to moderate renal insufficiency undergoing excretory urography.

Phase contrast x-ray imaging is a powerful technique for the detection of low-contrast details in weakly absorbing objects. This method is of possible relevance in the field of diagnostic radiology. In fact, imaging low-contrast details within soft tissue does not give satisfactory results in conventional x-ray absorption radiology, mammography being a typical example. Nevertheless, up to now all applications of the phase contrast technique, carried out on thin samples, have required radiation doses substantially higher than those delivered in conventional radiological examinations. To demonstrate the applicability of the method to mammography we produced phase contrast images of objects a few centimetres thick while delivering radiation doses lower than or comparable to doses needed in standard mammographic examinations (typically approximately 1 mGy mean glandular dose (MGD)). We show images of a custom mammographic phantom and of two specimens of human breast tissue obtained at the SYRMEP bending magnet beamline at Elettra, the Trieste synchrotron radiation facility. The introduction of an intensifier screen enabled us to obtain phase contrast images of these thick samples with radiation doses comparable to those used in mammography. Low absorbing details such as 50 microm thick nylon wires or thin calcium deposits (approximately 50 microm) within breast tissue, invisible with conventional techniques, are detected by means of the proposed method. We also find that the use of a bending magnet radiation source relaxes the previously reported requirements on source size for phase contrast imaging. Finally, the consistency of the results has been checked by theoretical simulations carried out for the purposes of this experiment.

Non-ionic dimers induce less diuresis than non-ionic monomers, resulting in increased opacification of the urinary tract in intravenous (i.v.) urography. This double blind, comparative, randomized, parallel trial compared the efficacy of iodixanol (non-ionic dimer) and iopromide (non-ionic monomer) in 100 patients with mild to moderate renal insufficiency (serum creatinine of 135 to 265 mumol l-1) who underwent i.v. urography. A total dose of 600 mgI kg-1 bw of iodixanol (320 mgI ml-1) or iopromide (300 mgI ml-1) was injected. Radiographs were blindly evaluated by three radiologists who analysed different parameters (renal border visualization, nephrogram density, calyceal filling and density, papillary blush detection, delineation of collecting ducts, renal pelvis opacification, visualization of ureters, bladder density, bladder distention). Densitometric evaluation on the renal pelvis and bladder was also performed. Iodixanol showed better filling and density of the calyces (p = 0.004), more frequent detection of papillary blush (p = 0.003) and better opacification of the renal pelvis (p = 0.006). No significant differences between the two contrast media were found in regard to other parameters. In conclusion, the results confirmed theoretical expectations. The non-ionic dimer iodixanol is to be preferred to a non-ionic monomer such as iopromide in i.v. urography on patients with impaired renal function.