Memories for Life: A Review of the Science and Technology

This paper discusses scientific, social and technological aspects of memory. Recent developments in our understanding of memory processes and mechanisms, and their digital implementation, have placed the encoding, storage, management and retrieval of information at the forefront of several fields of research. At the same time, the divisions between the biological, physical and the digital worlds seem to be dissolving. Hence opportunities for interdisciplinary research into memory are being created, between the life sciences, social sciences and physical sciences. Such research may benefit from immediate application into information management technology as a testbed. The paper describes one initiative, Memories for Life, as a potential common problem space for the various interested disciplines

Using Protege for automatic ontology instantiation

This paper gives an overview on the use of Protégé in the Artequakt system, which integrated Protégé with a set of natural language tools to automatically extract knowledge about artists from web documents and instantiate a given ontology. Protégé was also linked to structured templates that generate documents from the knowledge fragments it maintains

Web based knowledge extraction and consolidation for automatic ontology instantiation

The Web is probably the largest and richest information repository available today. Search engines are the common access routes to this valuable source. However, the role of these search engines is often limited to the retrieval of lists of potentially relevant documents. The burden of analysing the returned documents and identifying the knowledge of interest is therefore left to the user. The Artequakt system aims to deploy natural language tools to automatically ex-tract and consolidate knowledge from web documents and instantiate a given ontology, which dictates the type and form of knowledge to extract. Artequakt focuses on the domain of artists, and uses the harvested knowledge to gen-erate tailored biographies. This paper describes the latest developments of the system and discusses the problem of knowledge consolidation

Automatic extraction of knowledge from web documents

A large amount of digital information available is written as text documents in the form of web pages, reports, papers, emails, etc. Extracting the knowledge of interest from such documents from multiple sources in a timely fashion is therefore crucial. This paper provides an update on the Artequakt system which uses natural language tools to automatically extract knowledge about artists from multiple documents based on a predefined ontology. The ontology represents the type and form of knowledge to extract. This knowledge is then used to generate tailored biographies. The information extraction process of Artequakt is detailed and evaluated in this paper

Generating adaptive hypertext content from the semantic web

Accessing and extracting knowledge from online documents is crucial for therealisation of the Semantic Web and the provision of advanced knowledge services. The Artequakt project is an ongoing investigation tackling these issues to facilitate the creation of tailored biographies from information harvested from the web. In this paper we will present the methods we currently use to model, consolidate and store knowledge extracted from the web so that it can be re-purposed as adaptive content. We look at how Semantic Web technology could be used within this process and also how such techniques might be used to provide content to be published via the Semantic Web

Development of a core outcome set for use in determining the overall success of gastroschisis treatment.

Background: Gastroschisis research is limited in quality by the presence of significant heterogeneity in outcome measure reporting (PloS One 10(1):e0116908, 2015). Using core outcome sets in research is one proposed method for addressing this problem (Trials 13:103, 2012; Clin Rheumatol 33(9):1313-1322, 2014; Health Serv Res Policy 17(1):1-2, 2012). Ultimately, standardising outcome measure reporting will improve research quality and translate into improvements in patient care.Methods/design: Candidate outcome measures have been identified through systematic reviews. These outcome measures will form the starting point for an online, three-phase Delphi process that will be carried out in parallel by three panels of experts. Panel 1 is a neonatal panel, panel 2 is a non-neonatal panel and panel 3 is a lay panel.In round 1, experts will be asked to score the previously identified outcome measures from 1–9 based on how important they think the measures are in determining the overall success of their/their child’s/their patient’s gastroschisis treatment.In round 2, experts will be presented with the same list of outcome measures and with graphical representations of how their panel scored that outcome in round 1. They will be asked to re-score the outcome measure taking into account how important other members of their panel felt it to be. In round 3, experts will again be asked to re-score each outcome measure, but this time they will receive a graphical representation of the distribution of scores from all three panels which they should take into account when re-scoring.Following round 3 of the Delphi process, 40 experts will be invited to attend a face-to-face consensus meeting. Participants will be invited in a purposive manner to obtain balance between the different panels. The results of the Delphi process will be discussed, and outcomes re-scored. Outcome measures where?&gt;?70 % of the participants at the meeting scored them as 7–9 and?&lt;?15 % scored them as 1–3 will form the core outcome set.Discussion: Development of a core outcome set will help to reduce the heterogeneity of the outcome measure reporting in gastroschisis. This will increase the quality of research taking place and ultimately improve care provided to infants with gastroschisis.<br/

Application of the matched nested case-control design to the secondary analysis of trial data

Background: A nested case-control study is an efficient design that can be embedded within an existing cohort study or randomised trial. It has a number of advantages compared to the conventional case-control design, and has the potential to answer important research questions using untapped prospectively collected data. Methods: We demonstrate the utility of the matched nested case-control design by applying it to a secondary analysis of the Abnormal Doppler Enteral Prescription Trial. We investigated the role of milk feed type and changes in milk feed type in the development of necrotising enterocolitis in a group of 398 high risk growth-restricted preterm infants. Results: Using matching, we were able to generate a comparable sample of controls selected from the same population as the cases. In contrast to the standard case-control design, exposure status was ascertained prior to the outcome event occurring and the comparison between the cases and matched controls could be made at the point at which the event occurred. This enabled us to reliably investigate the temporal relationship between feed type and necrotising enterocolitis. Conclusions: A matched nested case-control study can be used to identify credible associations in a secondary analysis of clinical trial data where the exposure of interest was not randomised, and has several advantages over a standard case-control design. This method offers the potential to make reliable inferences in scenarios where it would be unethical or impractical to perform a randomised clinical trial.</br

Recombinant expression and characterisation of the oxygen-sensitive 2-enoate reductase from Clostridium sporogenes

‘Ene’-reductases have attracted significant attention for the preparation of chemical intermediates and biologically active products. To date, research has been focussed primarily on Old Yellow Enzyme-like proteins, due to their ease of handling, whereas 2-enoate reductases from clostridia have received much less attention, because of their oxygen sensitivity and a lack of suitable expression systems. A hypothetical 2-enoate reductase gene, fldZ, was identified in Clostridium sporogenes DSM 795. The encoded protein shares a high degree of homology to clostridial FMN- and FAD-dependent 2-enoate reductases, including the cinnamic acid reductase proposed to be involved in amino acid metabolism in proteolytic clostridia. The gene was cloned and overexpressed in Escherichia coli. Successful expression depended on the use of strictly anaerobic conditions for both growth and enzyme preparation, since FldZ was oxygen-sensitive. The enzyme reduced aromatic enoates, such as cinnamic acid or p-coumaric acid, but not short chain unsaturated aliphatic acids. The b,b-disubstituted nitroalkene, (E)-1-nitro-2-phenylpropene, was reduced to enantiopure (R)-1-nitro-2-phenylpropane with a yield of 90 %. By contrast, the a,b-disubstituted nitroalkene, (E)-2-nitro-1-phenylpropene, was reduced with a moderate yield of 56% and poor enantioselectivity (16% ee for (S)-2-nitro-1-phenylpropane). The availability of an expression system for this recombinant clostridial 2-enoate reductase will facilitate future characterisation of this unusual class of ‘ene’-reductases, and expand the biocatalytic toolbox available for enantioselective hydrogenation of carbon-carbon double bonds