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

Sequence learning in Associative Neuronal-Astrocytic Network

The neuronal paradigm of studying the brain has left us with limitations in both our understanding of how neurons process information to achieve biological intelligence and how such knowledge may be translated into artificial intelligence and its most brain-derived branch, neuromorphic computing. Overturning our fundamental assumptions of how the brain works, the recent exploration of astrocytes is revealing that these long-neglected brain cells dynamically regulate learning by interacting with neuronal activity at the synaptic level. Following recent experimental evidence, we designed an associative, Hopfield-type, neuronal-astrocytic network and analyzed the dynamics of the interaction between neurons and astrocytes. We show that astrocytes were sufficient to trigger transitions between learned memories in the neuronal component of the network. Further, we mathematically derived the timing of the transitions that was governed by the dynamics of the calcium-dependent slow-currents in the astrocytic processes. Overall, we provide a brain-morphic mechanism for sequence learning that is inspired by, and aligns with, recent experimental findings. To evaluate our model, we emulated astrocytic atrophy and showed that memory recall becomes significantly impaired after a critical point of affected astrocytes was reached. This brain-inspired and brain-validated approach supports our ongoing efforts to incorporate non-neuronal computing elements in neuromorphic information processing.Comment: 8 pages, 5 figure

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

Advanced load-shift system: an experimental validation of the ac-dc converter as shunt active power filter

This paper presents a load-shift system with advanced functionalities to interface the power grid (PG). When compared with the conventional approach, an advanced load-shift system (aLSS) permits the compensation of power quality (PQ) problems for the grid-side, namely problems related to current harmonics, current imbalance, and power factor. The proposed aLSS is composed by a bidirectional ac-dc converter to interface the PG and by a bidirectional dc-dc converter to interface an energy storage system (ESS). Since the main innovation is related with the PG interface, the focus of this work is on the analysis of the ac-dc converter, which is based on a three-phase four-leg converter. A theoretical study and the details concerning the control algorithm are presented and discussed along the paper. A laboratory prototype of the proposed aLSS was developed and the details of implementation are described in the paper. Experimental results obtained with the developed prototype prove that the aLSS contributes for the technology progress in this area, validating a new concept of operation concerning the PQ on the PG side.This work has been supported by FCT – Fundação para a Ciência e Tecnologia with-in the Project Scope: UID/CEC/00319/2019. This work has been supported by the FCT Project QUALITY4POWER PTDC/EEI-EEE/28813/2017, and by the FCT Project newERA4GRIDs PTDC/EEI-EEE/30283/2017

Weight management: a comparison of existing dietary approaches in a work-site setting

<b>OBJECTIVES:</b> (1) To compare the effectiveness a 2512 kJ (600 kcal) daily energy deficit diet (ED) with a 6279 kJ (1500 kcal) generalized low-calorie diet (GLC) over a 24 week period (12 weeks weight loss plus 12 weeks weight maintenance). (2) To determine if the inclusion of lean red meat at least five times per week as part of a slimming diet is compatible with weight loss in comparison with a diet that excludes lean red meat. DESIGN: Randomized controlled trial. <b>SETTING:</b> Large petrochemical work-site. <b>PARTICIPANTS:</b> One-hundred and twenty-two men aged between 18 and 55 y. <b>MAIN OUTCOME MEASURES:</b> Weight loss and maintenance of weight loss. <b>INTERVENTION:</b> Eligible volunteers were randomized to one of the four diet=meat combinations (ED meat, ED no meat, GLC meat, GLC no meat). One-third of subjects in each diet/meat combination were randomized to an initial control period prior to receiving dietary advice. All subjects attended for review every 2 weeks during the weight loss period. For the 12 week structured weight maintenance phase, individualized energy prescriptions were re-calculated for the ED group as 1.4 (activity factor)x basal metabolic rate. Healthy eating advice was reviewed with subjects in the GLC group. All subjects were contacted by electronic mail at 2 week intervals and anthropometric and dietary information requested. <b>RESULTS:</b> No difference was evident between diet groups in mean weight loss at 12 weeks (4.3 (s.d. 3.4) kg ED group vs 5.0 (s.d. 3.5) kg GLC group, P=0.34). Mean weight loss was closer to the intended weight loss in the 2512 kJ (600 kcal) ED group. The dropout rate was also lower than the GLC group. The inclusion of lean red meat in the diet on at least five occasions per week did not impair weight loss. Mean weight gain following 12 weeks weight maintenance was þ1.1 (s.d. 1.8) kg, P<0.0001. No differences were found between groups. <b>CONCLUSIONS:</b> This study has shown that the individualized 2512 kJ (600 kcal) ED approach was no more effective in terms of weight loss than the 6279 kJ (1500 kcal) GLC approach. However the ED approach might be considered preferable as compliance was better with this less demanding prescription. In terms of weight loss the elimination of red meat from the diet is unnecessary. The weight maintenance intervention was designed as a low-input approach, however weight regain was significant and weight maintenance strategies require further development

Spin and Chirality Effects in Antler-Topology Processes at High Energy e+e−e^+e^- Colliders

We perform a model-independent investigation of spin and chirality correlation effects in the antler-topology processes $e^+e^-\to\mathcal{P}^+\mathcal{P}^-\to (\ell^+ \mathcal{D}^0) (\ell^-\mathcal{\bar{D}}^0)$ at high energy $e^+e^-$ colliders with polarized beams. Generally the production process $e^+e^-\to\mathcal{P}^+\mathcal{P}^-$ can occur not only through the $s$-channel exchange of vector bosons, $\mathcal{V}^0$, including the neutral Standard Model (SM) gauge bosons, $\gamma$ and $Z$, but also through the $s$- and $t$-channel exchanges of new neutral states, $\mathcal{S}^0$ and $\mathcal{T}^0$, and the $u$-channel exchange of new doubly-charged states, $\mathcal{U}^{--}$. The general set of (non-chiral) three-point couplings of the new particles and leptons allowed in a renormalizable quantum field theory is considered. The general spin and chirality analysis is based on the threshold behavior of the excitation curves for $\mathcal{P}^+\mathcal{P}^-$ pair production in $e^+e^-$ collisions with longitudinal and transverse polarized beams, the angular distributions in the production process and also the production-decay angular correlations. In the first step, we present the observables in the helicity formalism. Subsequently, we show how a set of observables can be designed for determining the spins and chiral structures of the new particles without any model assumptions. Finally, taking into account a typical set of approximately chiral invariant scenarios, we demonstrate how the spin and chirality effects can be probed experimentally at a high energy $e^+e^-$ collider.Comment: 50 pages, 14 figures, 6 tables, matches version published in EPJ

Facile Synthesis of High Quality Graphene Nanoribbons

Graphene nanoribbons have attracted attention for their novel electronic and spin transport properties1-6, and because nanoribbons less than 10 nm wide have a band gap that can be used to make field effect transistors. However, producing nanoribbons of very high quality, or in high volumes, remains a challenge. Here, we show that pristine few-layer nanoribbons can be produced by unzipping mildly gas-phase oxidized multiwalled carbon nanotube using mechanical sonication in an organic solvent. The nanoribbons exhibit very high quality, with smooth edges (as seen by high-resolution transmission electron microscopy), low ratios of disorder to graphitic Raman bands, and the highest electrical conductance and mobility reported to date (up to 5e2/h and 1500 cm2/Vs for ribbons 10-20 nm in width). Further, at low temperature, the nanoribbons exhibit phase coherent transport and Fabry-Perot interference, suggesting minimal defects and edge roughness. The yield of nanoribbons was ~2% of the starting raw nanotube soot material, which was significantly higher than previous methods capable of producing high quality narrow nanoribbons1. The relatively high yield synthesis of pristine graphene nanoribbons will make these materials easily accessible for a wide range of fundamental and practical applications.Comment: Nature Nanotechnology in pres

Pay-it-forward dual gonorrhea/chlamydia test uptake among men who have sex with men in China: a pragmatic, quasi-experimental study

Background: Chinese men who have sex with men (MSM) rarely receive gonorrhea/chlamydia testing. The purpose of this pilot study was to evaluate a pay-it-forward strategy to increase gonorrhea/chlamydia testing among MSM. Pay-it-forward has one person receive a gift, then asks the same person if they would like to give a gift to another person. Methods: We used a quasi-experimental pragmatic study to compare a pay-it-forward model to standard of care at two HIV testing sites for MSM. A pay-it-forward program was implemented for three months, during which men were offered free gonorrhea/chlamydia testing and given the option of donating money toward testing for future participants. Both sites then switched to standard of care for three months, offering dual testing at the standard price. We compared test uptake and financial costs in the two groups. Findings: 408 men were included in this study. 203 men were offered pay-it-forward, and 205 were offered standard of care. Overall, 109 (109/203, 53·7%) men received gonorrhea/chlamydia testing in the pay-it-forward group and 12 (12/205, 5·9%) men received gonorrhea/chlamydia testing in the standard of care group (adjusted odds ratio 19·73, 95%CI 10·02-38·85). This was a first gonorrhea or chlamydia test for 86% (104/121) of men. 89% (97/109) of men in the pay-it-forward group donated some amount. The incremental unit cost per test in the pay-it-forward group was 67 USD, compared to 503 USD in the standard of care group. Interpretation: Pay-it-forward may be a sustainable model for expanding integrated HIV testing services among MSM in China

Measurements of neutral vector resonance in Higgsless models at the LHC

In Higgsless models, new vector resonances appear to restore the unitarity of the W_L W_L scattering amplitude without the Higgs boson. In the ideal delocalized three site Higgsless model, one of large prodcution cross section of the neutral vector resonance (Z') at the Large Hadron Collider is the W-associated production, pp \to Z'W \to WWW. Although the dileptonic decay channnel, l\nu l'\nu 'jj, is experimentally clean to search for the Z' signals, it is difficult to reconstruct the Z' invariant mass due to the two neutrinos in the final state. We study collider signatures of Z' using the M_{T2}-Assisted On-Shell (MAOS) reconstruction of the missing neutrino momenta. We show the prospect of the Z' mass determination in the channel, l\nu l'\nu 'jj, at the Large Hadron Collider.Comment: 16 pages, 6 figures, 5 tables; v2: references added, minor corrections, version published in JHE