OPEN DATA IN HEALTH: how knowledge may generate trust

The JRC project on Trust in Digital Interactions (TRUDI) deals with the construction and renewal of confident and trusted relationships between institutions and citizens, addressed as a major and urgent issue to be solved. In this context the JRC is planning a Workshop on “Open Data in Health: how knowledge may generate trust” on November 18, 2014. The workshop aims to investigate some general issues surrounding Open Data in the EU normative perspective, reflect on institutional and civic imaginaries about Open Data, and identify more promising Open Data models to trigger new processes for trust between institutions and citizens in health matters.JRC.G.6-Digital Citizen Securit

GMOREGEX User Guide

This document contains the user manual for the GMOREGEX application. It describes in detail the user functionalities provided by the system to the four different types of users for which the system has been implemented, i.e. the generic (non authenticated) user, the Member States National Competent Authorities user, the Commission user and finally a special type of authenticated user that can add comments or observations to GMO notifications based on the authorisation granted by the Competent Authorities and the Commission users. The GMOREGEX system is a web-based application that enables the electronic support of the GMO notification and authorisation process as defined in Directive 2001/18/EC [DIR.2001/18]. As specified in the Preparatory Report [PR] and in the Global Implementation Plan [GIP], the system has been developed to support the management of document exchange, information dissemination and events tracking related to the authorisation process for the deliberate release of new GMOs for experimental purposes (Part B notifications and associated SNIFs - [SNIF.PARTB]) or for marketing purposes (Part C releases and associated SNIFs and reports - [SNIF.PARTC]). The processes followed in the system are in accordance to "DIRECTIVE 2001/18/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90/220/EEC" and follow the technical specifications and indications contained in the Preparatory Report [PR] and in the Global Implementation Plan [GIP]. This manual is designed to familiarize users with the GMOREGEX system and provide a reference of the system's functionalities and use. The GMOREGEX system includes also the implementation of the GMO Register which supports the storage of information and related documentation of authorised GMOs in the EU, as well as the dissemination of public information to the general public according to the provisions of Art. 31.2 of [DIR.2001/18]. The GMOREGEX system includes also a component that implements the information submission to the Biosafety Clearing House (BCH) in support of the Cartagena Protocol on Biosafety - Regulation (EC) No. 1946/2003 [REG.1946/2003]. The GMOREGEX system supports the following five roles: - Commission user (COM) - Competent Authority (CA) user (this role includes both "LEAD CA" and "Non LEAD CA", a CA is given the role of "LEAD CA" for all notifications that are created by users associated to it) - Authorised External Party (AEP) - Anonymous user (Guest) In addition, and administrator role is defined for administration and management of the system: - System administrator (Admin) From a functional viewpoint, the GMOREGEX system supports the following high-level functionalities: - Creation of a new notification (Part B and Part C) - Management of the lifecycle associated to a new GMO notification (i.e. circulation and publication of information, gathering, sending, collecting and circulation of comments, etc.) - Dissemination/publication of public information associated to an authorised GMO - Submission of information to the BCH Central Portal and publication to a EU-based BCH interface - Reporting - Advanced search facilities The current document is partially based on the documentation generated within the project on the implementation of the system carried out with the collaboration of an external contractor.JRC.I.6-Biotechnology and GMO

Open Data in Health: how knowledge may generate trust

Developed within the context of the JRC project on Trust in Digital Interactions (TRUDI), the Workshop on “Open Data in Health: how knowledge may generate trust” (Ispra, 18 November 2014) aimed to investigate some general issues surrounding Open Data in the EU normative perspective, reflect on institutional and civic imaginaries about Open Data, and identify how trust between institutions and citizens can be improved in health matters. The workshop encompassed three sessions, each asking a different set of questions: a) What is the current state-of-the-art on Open Data, and what does Open Data in health mean? b) Are European policies on Privacy and Open Data conflicting or complementary? c) Do existing portals for Open Data meet citizens’ expectation and which role can be envisaged for the media? This report provides a summary of the topics and arguments presented at the Workshop and offers some recommendations in the still unfolding field of Open Data in Health

Fight against counterfeiting of goods related to IP infringing: Technical report of DG JRC.G.06 on analysis of Due Diligence for fight against counterfeiting of goods related to IP infringing

This report analyses how Due Diligence concepts, which includes Corporate Social Responsibility (CSR) and Supply Chain Management Responsibility (SCMR) can be applied to the fight against counterfeit related to IP infringing. We intentionally decided to limit the study in this report to the market portion of counterfeit products related to IP infringing. Counterfeit products can be a wider set than just IP infringing products.JRC.G.6-Digital Citizen Securit

NADPH oxidase, NOX1, mediates vascular injury in ischemic retinopathy

<b>Aims:</b> Ischemic retinal diseases such as retinopathy of prematurity are major causes of blindness due to damage to the retinal microvasculature. Despite this clinical situation, retinopathy of prematurity is mechanistically poorly understood. Therefore, effective preventative therapies are not available. However, hypoxic-induced increases in reactive oxygen species (ROS) have been suggested to be involved with NADPH oxidases (NOX), the only known dedicated enzymatic source of ROS. Our major aim was to determine the contribution of NOX isoforms (1, 2, and 4) to a rodent model of retinopathy of prematurity. <b>Results:</b> Using a genetic approach, we determined that only mice with a deletion of NOX1, but not NOX2 or NOX4, were protected from retinal neovascularization and vaso-obliteration, adhesion of leukocytes, microglial accumulation, and the increased generation of proangiogenic and proinflammatory factors and ROS. We complemented these studies by showing that the specific NOX inhibitor, GKT137831, reduced vasculopathy and ROS levels in retina. The source of NOX isoforms was evaluated in retinal vascular cells and neuro-glial elements. Microglia, the immune cells of the retina, expressed NOX1, 2, and 4 and responded to hypoxia with increased ROS formation, which was reduced by GKT137831. <b>Innovation:</b> Our studies are the first to identify the NOX1 isoform as having an important role in the pathogenesis of retinopathy of prematurity. <b>Conclusions:</b> Our findings suggest that strategies targeting NOX1 have the potential to be effective treatments for a range of ischemic retinopathie

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study

Background Early mobilisation (EM) is an intervention that may improve the outcome of critically ill patients. There is limited data on EM in COVID-19 patients and its use during the first pandemic wave. Methods This is a pre-planned subanalysis of the ESICM UNITE-COVID, an international multicenter observational study involving critically ill COVID-19 patients in the ICU between February 15th and May 15th, 2020. We analysed variables associated with the initiation of EM (within 72 h of ICU admission) and explored the impact of EM on mortality, ICU and hospital length of stay, as well as discharge location. Statistical analyses were done using (generalised) linear mixed-effect models and ANOVAs. Results Mobilisation data from 4190 patients from 280 ICUs in 45 countries were analysed. 1114 (26.6%) of these patients received mobilisation within 72 h after ICU admission; 3076 (73.4%) did not. In our analysis of factors associated with EM, mechanical ventilation at admission (OR 0.29; 95% CI 0.25, 0.35; p = 0.001), higher age (OR 0.99; 95% CI 0.98, 1.00; p ≤ 0.001), pre-existing asthma (OR 0.84; 95% CI 0.73, 0.98; p = 0.028), and pre-existing kidney disease (OR 0.84; 95% CI 0.71, 0.99; p = 0.036) were negatively associated with the initiation of EM. EM was associated with a higher chance of being discharged home (OR 1.31; 95% CI 1.08, 1.58; p = 0.007) but was not associated with length of stay in ICU (adj. difference 0.91 days; 95% CI − 0.47, 1.37, p = 0.34) and hospital (adj. difference 1.4 days; 95% CI − 0.62, 2.35, p = 0.24) or mortality (OR 0.88; 95% CI 0.7, 1.09, p = 0.24) when adjusted for covariates. Conclusions Our findings demonstrate that a quarter of COVID-19 patients received EM. There was no association found between EM in COVID-19 patients' ICU and hospital length of stay or mortality. However, EM in COVID-19 patients was associated with increased odds of being discharged home rather than to a care facility. Trial registration ClinicalTrials.gov: NCT04836065 (retrospectively registered April 8th 2021)

Linux for Bioinformatics:Dedicated Distribution for Processing of Biological Data - Part 1: Live Distributions

The number of active, widely used and valuable bioinformatics projects at open source software repositories such as bioinformatics.org and sourceforge.net is constantly increasing. Besides historical tools used for the analysis of biological data before Linux became a viable option on the desktop, new projects are started and new tools are being made available to improve the ability to collect, analyse and integrate large collections of data. The development of new or improved algorithms for the analysis of genomic data are fostering the development of new tools. On the other hand, the availability of open source tools with the full access to algorithms and source code and the possibility to modify and improve them, is encouraging a sort of good scientific practice in providing new tools and promotes reproducible research [1]. Important efforts in the past years have been dedicated to making access to data easier and facilitate their analysis improving our knowledge of biology. These efforts have been targeted, for example, at harmonization through the definition of ontologies [24], at integrating databases [23], at devising mechanisms to overcome the typical pattern of creating manual ad-hoc connections among software tools and databases, cutting and pasting queries, creating temporary files and taking notes by providing workflow mechanisms and single access point portals which link smoothly the actions and facilitate reproducible research. [3] [5] [7] [8] [20]. The availability of these enabling tools allows biologists to focus on their research without being distracted by computer problems. In parallel to these efforts, the availability of easy to use live distribution of the GNU/Linux operating system, has facilitated the development of ready made desktop (and server based) solutions which collect in one single CD or DVD an entire operating system equipped with tools for bioinformatics analysis as well as with development environments enabling the further development of new tools. This paper is the first of a two parts survey which reviews the most popular solutions available in the Linux arena providing a desktop environment equipped with applications and development libraries for life scientists.JRC.I.6-Biotechnology and GMO

E-Passports and automated border crossing: a view on interoperability issues

The new electronic passport (also known as biometric passport) was first introduced in the EU in 2006 with Council Regulation No 2252/2004 of 13 December which defined the standards for security features and biometrics in passports and travel documents issued by Member States with the purpose of improving document security and preventing falsification of documents The Regulation further prescribed that as from June 2009, the so called Schengen EU Member States would be issuing second generation electronic passports, i.e. biometric passport with a secondary biometrics: fingerprints in addition to the facial image required by the ICAO Document 9303 and already stored in first generation biometric passports. The paper ourlines the security and privacy characteristics of the electronic passports and illustrates the main issues in interoperability.JRC.DG.G.6-Security technology assessmen