OnTheFly: a tool for automated document-based text annotation, data linking and network generation

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database

A Smartphone Application Designed to Engage the Elderly in Home-Based Rehabilitation

As life expectancy increases, it is imperative that the elderly take advantage of the benefits of technology to remain active and independent. Mobile health applications are widely used nowadays as they promote a healthy lifestyle and self-management of diseases, opening new horizons in the interactive health service delivery. However, adapting these applications to the needs and requirements of the elderly is still a challenge. This article presents a smartphone application that is part of a multifactorial intervention to support older people with balance disorders. The application aims to enable users to self-evaluate their activity and progress, to communicate with each other and, through strategically selected motivational features, to engage with the system with undiminished interest for a long period of time. Mock-up interfaces were evaluated in semi-structured focus groups and interviews that were performed across three European countries. Further evaluation in the form of four pilot studies with 160 participants will be performed and qualitative and quantitative measures will be used to process the feedback about the use of the application

jClust: a clustering and visualization toolbox

jClust is a user-friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity propagation, Bron–Kerbosch, MULIC, Restricted neighborhood search cluster algorithm, Markov clustering and Spectral clustering, while the supported filtering procedures are haircut, outside–inside, best neighbors and density control operations. The combination of a simple input file format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for data analysis and information extraction

Binary systems of neutral mesons in Quantum Field Theory

Quasi-degenerate binary systems of neutral mesons of the kaon type are investigated in Quantum Field Theory (QFT). General constraints cast by analyticity and discrete symmetries P, C, CP, TCP on the propagator (and on its spectral function) are deduced. Its poles are the physical masses; this unambiguously defines the propagating eigenstates. It is diagonalized and its spectrum thoroughly investigated. The role of ``spurious'' states, of zero norm at the poles, is emphasized, in particular for unitarity and for the realization of TCP symmetry. The K_L-K_S mass splitting triggers a tiny difference between their CP violating parameters \epsilon_L and \epsilon_S, without any violation of TCP. A constant mass matrix like used in Quantum Mechanics (QM) can only be introduced in a linear approximation to the inverse propagator, which respects its analyticity and positivity properties; it is however unable to faithfully describe all features of neutral mesons as we determine them in QFT, nor to provide any sensible parameterization of eventual effects of TCP violation. The suitable way to diagonalize the propagator makes use of a bi-orthogonal basis; it is inequivalent to a bi-unitary transformation (unless the propagator is normal, which cannot occur here). Problems linked with the existence of different ``in'' and ``out'' eigenstates are smoothed out. We study phenomenological consequences of the differences between the QFT and QM treatments. The non-vanishing of semi-leptonic asymmetry \delta_S - \delta_L does not signal, unlike usually claimed, TCP violation, while A_TCP keeps vanishing when TCP is realized. We provide expressions invariant by the rephasing of K0 and K0bar.Comment: 44 pages, 2 figures. Version to appear in Int. J. Mod. Phys.

Kaon decay interferometry as meson dynamics probes

We discuss the time dependent interferences between $K_L$ and $K_S$ in the decays in $3\pi$ and $\pi\pi\gamma$, to be studied at interferometry machines such as the $\phi$-factory and LEAR. We emphasize the possibilities and the advantages of using interferences, in comparison with width measurements, to obtain information both on $CP$ conserving and $CP$ violating amplitudes. Comparison with present data and suggestions for future experiments are made.Comment: 15 pages, in RevTex, Report INFNNA-IV-93-31, UTS-DFT-93-2

ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings.

Motivation: The prediction of receptor—ligand pairings is an important area of research as intercellular communications are mediated by the successful interaction of these key proteins. As the exhaustive assaying of receptor—ligand pairs is impractical, a computational approach to predict pairings is necessary. We propose a workflow to carry out this interaction prediction task, using a text mining approach in conjunction with a state of the art prediction method, as well as a widely accessible and comprehensive dataset. Among several modern classifiers, random forests have been found to be the best at this prediction task. The training of this classifier was carried out using an experimentally validated dataset of Database of Ligand-Receptor Partners (DLRP) receptor—ligand pairs. New examples, co-cited with the training receptors and ligands, are then classified using the trained classifier. After applying our method, we find that we are able to successfully predict receptor—ligand pairs within the GPCR family with a balanced accuracy of 0.96. Upon further inspection, we find several supported interactions that were not present in the Database of Interacting Proteins (DIPdatabase). We have measured the balanced accuracy of our method resulting in high quality predictions stored in the available database ReLiance. Availability: http://homes.esat.kuleuven.be/?bioiuser/ReLianceDB/ index.php Contact: [email protected]; ernesto.iacucci@gmail. com Supplementary information: Supplementary data are available at Bioinformatics onlin

UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.

The in-depth study of protein-protein interactions (PPIs) is of key importance for understanding how cells operate. Therefore, in the past few years, many experimental as well as computational approaches have been developed for the identification and discovery of such interactions. Here, we present UniReD, a user-friendly, computational prediction tool which analyses biomedical literature in order to extract known protein associations and suggest undocumented ones. As a proof of concept, we demonstrate its usefulness by experimentally validating six predicted interactions and by benchmarking it against public databases of experimentally validated PPIs succeeding a high coverage. We believe that UniReD can become an important and intuitive resource for experimental biologists in their quest for finding novel associations within a protein network and a useful tool to complement experimental approaches (e.g. mass spectrometry) by producing sorted lists of candidate proteins for further experimental validation. UniReD is available at http://bioinformatics.med.uoc.gr/unired/

Tests of the Equivalence Principle with Neutral Kaons

We test the Principle of Equivalence for particles and antiparticles, using CPLEAR data on tagged K0 and K0bar decays into pi^+ pi^-. For the first time, we search for possible annual, monthly and diurnal modulations of the observables |eta_{+-}| and phi_{+-}, that could be correlated with variations in astrophysical potentials. Within the accuracy of CPLEAR, the measured values of |eta_{+-}| and phi_{+-} are found not to be correlated with changes of the gravitational potential. We analyze data assuming effective scalar, vector and tensor interactions, and we conclude that the Principle of Equivalence between particles and antiparticles holds to a level of 6.5, 4.3 and 1.8 x 10^{-9}, respectively, for scalar, vector and tensor potentials originating from the Sun with a range much greater than the distance Earth-Sun. We also study energy-dependent effects that might arise from vector or tensor interactions. Finally, we compile upper limits on the gravitational coupling difference between K0 and K0bar as a function of the scalar, vector and tensor interaction range.Comment: 15 pages latex 2e, five figures, one style file (cernart.csl) incorporate

The influence of the Evros River on the recent sedimentation of the inner shelf of the NE Aegean Sea

Abstract The transboundary Evros River discharges into the Alexandroupolis Gulf, located in the inner shelf of the northeastern Aegean Sea, where it has formed an extended delta. Grain-size and mineralogical analyses of five sediment cores, collected in the subaqueous delta, provide the following information about recent sedimentation processes in the northeastern part of the Aegean shelf: (a) river mouth deposits, consisting of coarse-grained sediments, are mainly deposited in front of the active mouth, whilst some sandy material is expected to be transported alongshore by nearshore currents; (b) delta front deposits are characterised by fine-grained sediments that include evidence of human activities which have taken place, in a more intense way, since the 1950s; and (c) prodelta deposits are represented by almost uniform riverine mud that cover the pre-existed relict sands of the shelf, indicating also the limit (some 15 km to the SW) of the influence of riverine sedimentation on the seabed of the inner shelf of the Alexandroupolis Gulf