eTRIKS Analytical Environment: A Modular High Performance Framework for Medical Data Analysis

Translational research is quickly becoming a science driven by big data. Improving patient care, developing personalized therapies and new drugs depend increasingly on an organization's ability to rapidly and intelligently leverage complex molecular and clinical data from a variety of large-scale partner and public sources. As analysing these large-scale datasets becomes computationally increasingly expensive, traditional analytical engines are struggling to provide a timely answer to the questions that biomedical scientists are asking. Designing such a framework is developing for a moving target as the very nature of biomedical research based on big data requires an environment capable of adapting quickly and efficiently in response to evolving questions. The resulting framework consequently must be scalable in face of large amounts of data, flexible, efficient and resilient to failure. In this paper we design the eTRIKS Analytical Environment (eAE), a scalable and modular framework for the efficient management and analysis of large scale medical data, in particular the massive amounts of data produced by high-throughput technologies. We particularly discuss how we design the eAE as a modular and efficient framework enabling us to add new components or replace old ones easily. We further elaborate on its use for a set of challenging big data use cases in medicine and drug discovery

Linking and Harmonizing Forest Spatial Pattern Analyses at European, National and Regional Scales for a Better Characterization of Forest Vulnerability and Resilience

The project ¿Linking and harmonizing the forests spatial pattern analyses at European, national and regional scales for a better characterization of the forests vulnerability and resilience¿ (JRC contract 382391 F1SC) covers one of the seven topics to be studied in the frame of the Regulation (EC) 2152/2003 on the monitoring of forest and environmental interactions, the so-called "Forest Focus" Regulation. It first demonstrates the application of the mathematical morphology based forest spatial pattern analysis tool developed at the Joint Research Centre (GUIDOS); it then develops one index related to potential forest vulnerability, resistance and resilience (FVRR index) on the basis of multi-criteria fuzzy modelling technics. Its final aim is to address linkages between forest spatial pattern and forest ecological functionality with emphasis on forest vulnerability, resistance, resilience. This study was conducted by a European consortium coordinated by the University of Molise (Italy) and included partners from the University of Hamburg (Germany), the European Forest Institute (Finland) and the Forest Research (United Kingdom). The overall supervision of the project and the processing of forest spatial pattern were done by the Joint Research Centre.JRC.DDG.H.7-Land management and natural hazard

Forest Focus Monitoring Database System - Executive Summary Report 2003 Level II Data

This Executive Report presents the results obtained from all processing stages (data reception, validation checks ¿ compliance, conformity, uniformity) for submitted data referring to the monitoring year 2003. This report presents the results at the end of the processing phase after data have been re-submitted in 2007. It presents in addition a brief comment on the data status for each NFC, for the reporting year, with respect to the parameter assessed and including analyses of spatial variability of data and temporal trends of parameters.JRC.H.7-Land management and natural hazard

Forest Focus Monitoring Database System - Technical Report 2003 Level II Data

Forest Focus (Regulation (EC) No 2152/2003) is a Community scheme for harmonized, broad-based, comprehensive and long-term monitoring of European forest ecosystems. Under this scheme the monitoring of air pollution effects on forests is carried out by participating countries on the basis of the systematic network of observation points (Level I) and of the network of observation plots for intensive and continuous monitoring (Level II). According to Article 15(1) of the Forest Focus Regulation Member States shall annually, through the designated authorities and agencies, forward to the Commission geo-referenced data gathered under the scheme, together with a report on them by means of computer telecommunications and/or electronic technology. For managing the data JRC has implemented a Forest Focus Monitoring Database System. This Technical Report presents the results obtained from all processing stages (data reception, validation checks ¿ compliance, conformity, uniformity) for submitted data referring to the monitoring year 2003. This report presents the results at the end of the processing phase after data have been re-submitted in 2007. It presents in addition a brief comment on the data status for each NFC, for the reporting year, with respect to the parameter assessed and including analyses of spatial variability of data and temporal trends of parameters.JRC.H.7-Land management and natural hazard

Immunohistochemical localization of fibronectin as a tool for the age determination of human skin wounds

We analyzed the distribution of fibronectin in routinely embedded tissue specimens from 53 skin wounds and 6 postmortem wounds. In postmortem wounds a faint but focal positive staining was exclusively found at the margin of the specimens which dit not extend into the adjacent stroma. Vital wounds were classified into 3 groups. The first comprising lesions with wound ages ranging from a few seconds to 30 min, the second comprising those with wound ages upt to 3 weeks, and the third group with lesions more than 3 weeks old. Ten out of 17 lesions with a wound age up to 30 min showed a clear positive reaction within the wound area. Three specimens in this group were completely negative, while in 4 additional cases the result was not significantly different from postmortem lesions. These 7 cases were characterized by acute death with extremely short survival times (only seconds). In wounds up to 3 weeks old fibronectin formed a distinct network containing an increasing number of inflammatory cells corresponding to the wound age. In 2 cases with a survival time of 17 days and in all wounds older than 3 weeks fibronectin was restricted to the surface of fibroblasts and to parallel arranged fibers in the granulation tissue without any network structures. We present evidence that fibronectin is a useful marker for vital wounds with a survival time of more than a few minutes. Fibronectin appears before neutrophilic granulocytes migrate into the wound area. Since a faint positive fibronectin staining is seen in postmortem lesions and bleedings, we propose that only those wounds which show strong positive fibronectin staining also extending into the adjacent stroma should be regarded as vital

Clinical-pathological study on β-APP, IL-1β, GFAP, NFL, Spectrin II, 8OHdG, TUNEL, miR-21, miR-16, miR-92 expressions to verify DAI-diagnosis, grade and prognosis

Traumatic brain injury (TBI) is one of the most important death and disability cause, involving substantial costs, also in economic terms, when considering the young age of the involved subject. Aim of this paper is to report a series of patients treated at our institutions, to verify neurological results at six months or survival; in fatal cases we searched for βAPP, GFAP, IL-1β, NFL, Spectrin II, TUNEL and miR-21, miR-16, and miR-92 expressions in brain samples, to verify DAI diagnosis and grade as strong predictor of survival and inflammatory response. Concentrations of 8OHdG as measurement of oxidative stress was performed. Immunoreaction of β-APP, IL-1β, GFAP, NFL, Spectrin II and 8OHdG were significantly increased in the TBI group with respect to control group subjects. Cell apoptosis, measured by TUNEL assay, were significantly higher in the study group than control cases. Results indicated that miR-21, miR-92 and miR-16 have a high predictive power in discriminating trauma brain cases from controls and could represent promising biomarkers as strong predictor of survival, and for the diagnosis of postmortem traumatic brain injury

International Veterinary Epilepsy Task Force recommendations for systematic sampling and processing of brains from epileptic dogs and cats

Traditionally, histological investigations of the epileptic brain are required to identify epileptogenic brain lesions, to evaluate the impact of seizure activity, to search for mechanisms of drug-resistance and to look for comorbidities. For many instances, however, neuropathological studies fail to add substantial data on patients with complete clinical work-up. This may be due to sparse training in epilepsy pathology and or due to lack of neuropathological guidelines for companion animals. The protocols introduced herein shall facilitate systematic sampling and processing of epileptic brains and therefore increase the efficacy, reliability and reproducibility of morphological studies in animals suffering from seizures. Brain dissection protocols of two neuropathological centres with research focus in epilepsy have been optimised with regards to their diagnostic yield and accuracy, their practicability and their feasibility concerning clinical research requirements. The recommended guidelines allow for easy, standardised and ubiquitous collection of brain regions, relevant for seizure generation. Tissues harvested the prescribed way will increase the diagnostic efficacy and provide reliable material for scientific investigations

Ballistic impacts on an anatomically correct synthetic skull with a surrogate skin/soft tissue layer

The aim of this work was to further develop a synthetic model of ballistic head injury by the addition of skin and soft tissue layers to an anatomically correct polyurethane skull filled with gelatine 10% by mass. Six head models were impacted with 7.62 x 39 mm full metal jacket mild steel core (FMJ MSC) bullets with a mean velocity of 652 m/s. The impact events were filmed with high-speed cameras. The models were imaged pre- and post-impact using computed tomography. The models were assessed post impact by two experienced Home Office pathologists and the images assessed by an experienced military radiologist. The findings were scored against real injuries. The entry wounds, exit wounds and fracture patterns were scored positively, but the synthetic skin and soft tissue layer was felt to be too extendable. Further work is ongoing to address this