Processing SPARQL queries with regular expressions in RDF databases

Background: As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results: In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions: Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.X113sciescopu

Developing a Hybrid Dictionary-based Bio-entity Recognition Technique

Background: Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. Methods: This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. Results: The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. Conclusions: The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall.X1133Ysciescopu

Evidence of the influence of phonon density on Tm³⁺ upconversion luminescence in tellurite and germanate glasses

Author name used in this publication: C. L. MakAuthor name used in this publication: W. L. TsuiAuthor name used in this publication: K. H. Wong2001-2002 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Effect of Silicon Content on Carbide Precipitation and Low-Temperature Toughness of Pressure Vessel Steels

Cr – Mn – Mo – Ni pressure vessel steels containing 0.54 and 1.55% Si are studied. Metallographic and fractographic analyses of the steels after tempering at 650 and 700°C are performed. The impact toughness at – 30°C and the hardness of the steels are determined. The mass fraction of the carbide phase in the steels is computed with the help of the J-MatPro 4.0 software

QRS changes and QT intervals on 12-lead ECGs in patients receiving biventricular pacing for congestive heart failure

published_or_final_versio

Ocean temperature and salinity components of the Madden-Julian oscillation observed by Argo floats

New diagnostics of the Madden-Julian Oscillation (MJO) cycle in ocean temperature and, for the first time, salinity are presented. The MJO composites are based on 4 years of gridded Argo float data from 2003 to 2006, and extend from the surface to 1,400 m depth in the tropical Indian and Pacific Oceans. The MJO surface salinity anomalies are consistent with precipitation minus evaporation fluxes in the Indian Ocean, and with anomalous zonal advection in the Pacific. The Argo sea surface temperature and thermocline depth anomalies are consistent with previous studies using other data sets. The near-surface density changes due to salinity are comparable to, and partially offset, those due to temperature, emphasising the importance of including salinity as well as temperature changes in mixed-layer modelling of tropical intraseasonal processes. The MJO-forced equatorial Kelvin wave that propagates along the thermocline in the Pacific extends down into the deep ocean, to at least 1,400 m. Coherent, statistically significant, MJO temperature and salinity anomalies are also present in the deep Indian Ocean

Temperature dependence of the electronic structure of the J(eff)=12 Mott insulator Sr2IrO4 studied by optical spectroscopy

We investigated the temperature-dependent evolution of the electronic structure of the J(eff)=1/2 Mott insulator Sr2IrO4 using optical spectroscopy. The optical conductivity spectra sigma(omega) of this compound has recently been found to exhibit two d-d transitions associated with the transition between the J(eff)=1/2 and J(eff)=3/2 bands due to the cooperation of the electron correlation and spin-orbit coupling. As the temperature increases, the two peaks show significant changes resulting in a decrease in the Mott gap. The experimental observations are compared with the results of first-principles calculation in consideration of increasing bandwidth. We discuss the effect of the temperature change in the electronic structure of Sr2IrO4 in terms of local lattice distortion, excitonic effect, electron-phonon coupling, and magnetic ordering.open69575

Delayed treatment of basilar thrombosis in a patient with a basilar aneurysm: a case report

<p>Abstract</p> <p>Introduction</p> <p>Acute occlusion of the basilar artery is a neurological emergency that has a high risk of severe disability and mortality. Delayed thrombolysis or endovascular therapy has been performed with some success in patients who present after 3 hours of symptom onset. Here we present the first case of delayed intra-arterial thrombolysis of a basilar artery thrombosis associated with a large saccular aneurysm.</p> <p>Case presentation</p> <p>A 73-year-old Caucasian man with a history of smoking and alcohol abuse presented to the Emergency Department complaining of diplopia and mild slurred speech and who progressed over 12 hours to coma and quadriparesis. He was found to have a large basilar tip aneurysm putting him at high risk for hemorrhage with lytic treatment.</p> <p>Conclusion</p> <p>The treatment options for basilar thrombosis are discussed. Aggressive treatment options should be considered despite long durations of clinical symptoms in basilar thrombosis, even in extremely high risk patients.</p