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

Smart Roadside System for Driver Assistance and Safety Warnings: Framework and Applications

The use of newly emerging sensor technologies in traditional roadway systems can provide real-time traffic services to drivers through Telematics and Intelligent Transport Systems (ITSs). This paper introduces a smart roadside system that utilizes various sensors for driver assistance and traffic safety warnings. This paper shows two road application models for a smart roadside system and sensors: a red-light violation warning system for signalized intersections, and a speed advisory system for highways. Evaluation results for the two services are then shown using a micro-simulation method. In the given real-time applications for drivers, the framework and certain algorithms produce a very efficient solution with respect to the roadway type features and sensor type use

CFTR Gating II: Effects of Nucleotide Binding on the Stability of Open States

Previously, we demonstrated that ADP inhibits cystic fibrosis transmembrane conductance regulator (CFTR) opening by competing with ATP for a binding site presumably in the COOH-terminal nucleotide binding domain (NBD2). We also found that the open time of the channel is shortened in the presence of ADP. To further study this effect of ADP on the open state, we have used two CFTR mutants (D1370N and E1371S); both have longer open times because of impaired ATP hydrolysis at NBD2. Single-channel kinetic analysis of ΔR/D1370N-CFTR shows unequivocally that the open time of this mutant channel is decreased by ADP. ΔR/E1371S-CFTR channels can be locked open by millimolar ATP with a time constant of ∼100 s, estimated from current relaxation upon nucleotide removal. ADP induces a shorter locked-open state, suggesting that binding of ADP at a second site decreases the locked-open time. To test the functional consequence of the occupancy of this second nucleotide binding site, we changed the [ATP] and performed similar relaxation analysis for E1371S-CFTR channels. Two locked-open time constants can be discerned and the relative distribution of each component is altered by changing [ATP] so that increasing [ATP] shifts the relative distribution to the longer locked-open state. Single-channel kinetic analysis for ΔR/E1371S-CFTR confirms an [ATP]-dependent shift of the distribution of two locked-open time constants. These results support the idea that occupancy of a second ATP binding site stabilizes the locked-open state. This binding site likely resides in the NH(2)-terminal nucleotide binding domain (NBD1) because introducing the K464A mutation, which decreases ATP binding affinity at NBD1, into E1371S-CFTR shortens the relaxation time constant. These results suggest that the binding energy of nucleotide at NBD1 contributes to the overall energetics of the open channel conformation

Functional neural differentiation of human adipose tissue-derived stem cells using bFGF and forskolin

<p>Abstract</p> <p>Background</p> <p>Adult mesenchymal stem cells (MSCs) derived from adipose tissue have the capacity to differentiate into mesenchymal as well as endodermal and ectodermal cell lineage <it>in vitro</it>. We characterized the multipotent ability of human adipose tissue-derived stem cells (hADSCs) as MSCs and investigated the neural differentiation potential of these cells.</p> <p>Results</p> <p>Human ADSCs from earlobe fat maintained self-renewing capacity and differentiated into adipocytes, osteoblasts, or chondrocytes under specific culture conditions. Following neural induction with bFGF and forskolin, hADSCs were differentiated into various types of neural cells including neurons and glia <it>in vitro</it>. In neural differentiated-hADSCs (NI-hADSCs), the immunoreactivities for neural stem cell marker (nestin), neuronal markers (Tuj1, MAP2, NFL, NFM, NFH, NSE, and NeuN), astrocyte marker (GFAP), and oligodendrocyte marker (CNPase) were significantly increased than in the primary hADSCs. RT-PCR analysis demonstrated that the mRNA levels encoding for ABCG2, nestin, Tuj1, MAP2, NFL, NFM, NSE, GAP43, SNAP25, GFAP, and CNPase were also highly increased in NI-hADSCs. Moreover, NI-hADSCs acquired neuron-like functions characterized by the display of voltage-dependent tetrodotoxin (TTX)-sensitive sodium currents, outward potassium currents, and prominent negative resting membrane potentials under whole-cell patch clamp recordings. Further examination by RT-PCR showed that NI-hADSCs expressed high level of ionic channel genes for sodium (SCN5A), potassium (MaxiK, Kv4.2, and EAG2), and calcium channels (CACNA1C and CACNA1G), which were expressed constitutively in the primary hADSCs. In addition, we demonstrated that Kv4.3 and Eag1, potassium channel genes, and NE-Na, a TTX-sensitive sodium channel gene, were highly induced following neural differentiation.</p> <p>Conclusions</p> <p>These combined results indicate that hADSCs have the same self-renewing capacity and multipotency as stem cells, and can be differentiated into functional neurons using bFGF and forskolin.</p

Itch and Janus Kinase Inhibitors

Itch is a common skin symptom, with complex aetiology and pathogenesis. It is mediated by 2 pathways, the histaminergic and non-histaminergic pathways. Chronic itch is understood to be processed by the latter and is difficult to treat with traditional pruritus therapies. The Janus kinase and signal transducer and activator of transcription pathway is a signalling mechanism that regulates gene expression through various cytokines. Janus kinase inhibitors, which have been tested and used for several autoimmune diseases, have also been shown to be effective for itch through clinical trials and case reports. Janus kinase inhibitors could be a good choice for pruritus in atopic dermatitis, psoriasis, and other diseases, such as prurigo nodularis and lichen planus, with rapid itch relief compared with conventional treatments. The most common adverse effects reported include nasopharyngitis, acne, and elevated blood creatine phosphokinase levels. Janus kinase inhibitors are currently prescribed with warnings about a potential increase in malignancies and cardiovascular diseases and usage in people of older ages. This review aims to provide knowledge about itch and the Janus kinase and signal transducer and activator of transcription pathway and to analyse the current evidence for itch relief by Janus kinase inhibitors

Grouping-matrix based Graph Pooling with Adaptive Number of Clusters

Graph pooling is a crucial operation for encoding hierarchical structures within graphs. Most existing graph pooling approaches formulate the problem as a node clustering task which effectively captures the graph topology. Conventional methods ask users to specify an appropriate number of clusters as a hyperparameter, then assume that all input graphs share the same number of clusters. In inductive settings where the number of clusters can vary, however, the model should be able to represent this variation in its pooling layers in order to learn suitable clusters. Thus we propose GMPool, a novel differentiable graph pooling architecture that automatically determines the appropriate number of clusters based on the input data. The main intuition involves a grouping matrix defined as a quadratic form of the pooling operator, which induces use of binary classification probabilities of pairwise combinations of nodes. GMPool obtains the pooling operator by first computing the grouping matrix, then decomposing it. Extensive evaluations on molecular property prediction tasks demonstrate that our method outperforms conventional methods.Comment: 10 pages, 3 figure

Isolated Weakness of Middle, Ring, and Little Fingers due to a Small Cortical Infarction in the Medial Precentral Gyrus

Small cortical strokes can produce predominant isolated weakness in a particular group of fingers: radial or ulnar. The traditional views are of point-to-point representations of each finger to neurons located in the precentral gyrus of the motor cortex such that the neurons of the radial fingers are located laterally and those of the ulnar fingers are located medially. We present a case of isolated weakness of middle, ring, and little fingers due to a small cortical infarction in the medial precentral gyrus

Differences in Clinical Outcomes Between Patients With ST-Elevation Versus Non-ST-Elevation Acute Myocardial Infarction in Korea

In Korea, the incidence of acute myocardial infarction has been increasing rapidly. Twelve-month clinical outcomes for 13,133 patients with acute myocardial infarction enrolled in the nationwide prospective Korea Acute Myocardial Infarction Registry study were analyzed according to the presence or absence of ST-segment elevation. Patients with ST-segment elevation myocardial infarction (STEMI) were younger, more likely to be men and smokers, and had poorer left ventricular function with a higher incidence of cardiac death compared to patients with non-ST-segment elevation myocardial infarction (NSTEMI). NSTEMI patients had a higher prevalence of 3-vessel and left main coronary artery disease with complex lesions, and were more likely to have co-morbidities. The in-hospital and 1-month survival rates were higher in NSTEMI patients than in STEMI patients. However, 12-month survival rates was not different between the two groups. In conclusion, NSTEMI patients have worse clinical outcomes than STEMI patients, and therefore should be treated more intensively during clinical follow-up