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

Ballistic spin field-effect transistors: Multichannel effects

We study a ballistic spin field-effect transistor (SFET) with special attention to the issue of multi-channel effects. The conductance modulation of the SFET as a function of the Rashba spin-orbit coupling strength is numerically examined for the number of channels ranging from a few to close to 100. Even with the ideal spin injector and collector, the conductance modulation ratio, defined as the ratio between the maximum and minimum conductances, decays rapidly and approaches one with the increase of the channel number. It turns out that the decay is considerably faster when the Rashba spin-orbit coupling is larger. Effects of the electronic coherence are also examined in the multi-channel regime and it is found that the coherent Fabry-Perot-like interference in the multi-channel regime gives rise to a nested peak structure. For a nonideal spin injector/collector structure, which consists of a conventional metallic ferromagnet-thin insulator-2DEG heterostructure, the Rashba-coupling-induced conductance modulation is strongly affected by large resonance peaks that arise from the electron confinement effect of the insulators. Finally scattering effects are briefly addressed and it is found that in the weakly diffusive regime, the positions of the resonance peaks fluctuate, making the conductance modulation signal sample-dependent.Comment: 18 pages, 15 figure

Application of Recent Developments in Deep Learning to ANN-based Automatic Berthing Systems

Previous studies on Artificial Neural Network (ANN)-based automatic berthing showed considerable increases in performance by training ANNs with a set of berthing datasets. However, the berthing performance deteriorated when an extrapolated initial position was given. To overcome the extrapolation problem and improve the training performance, recent developments in Deep Learning (DL) are adopted in this paper. Recent activation functions, weight initialization methods, input data-scaling methods, a higher number of hidden layers, and Batch Normalization (BN) are considered, and their effectiveness has been analyzed based on loss functions, berthing performance histories, and berthing trajectories. Finally, it is shown that the use of recent activation and weight initialization method results in faster training convergence and a higher number of hidden layers. This leads to a better berthing performance over the training dataset. It is found that application of the BN can overcome the extrapolated initial position problem

UNDER-APPRECIATED VIOLIN REPERTOIRE OF THE TWENTIETH CENTURY

From the countless number of works in the violin repertoire, only a relatively few are chosen to be played regularly. For instance, the premier of Beethoven’s Violin Concerto was not successful, and the work was neglected until the late 19th century, when it was revived by Joachim. I strongly believed that we should not stop discovering and bringing forgotten and under-appreciated masterpieces to our audience so that we may prevent these works from being buried permanently. This was the purpose and the title of my dissertation project. Selections for my dissertation programs consisted of works by relatively unknown composers or lesser-known pieces by well-known composers. In addition, I did try to make the program as varied as possible: I played a violin concerto and solo violin piece as well as regular violin sonatas. As I looked for such works, and prepared all the recitals it often occurred to me that I was getting lost in the midst of thousands of under- appreciated treasures which I felt the need to rescue. Furthermore, all of them were the kinds of works that definitely required much more of my time and effort to research and to learn than standard repertoire that could be easily heard in recordings and read about, for the limited accessible information about them and technical difficulties. Therefore, I basically selected the pieces for the three dissertation recitals among those works I most wanted to learn immediately. My project included Arvo Pärt’s Fratres for Violin and Piano, Béla Bartók’s Sonata No.2 for Violin and Piano, Ottorino Respighi’s Violin Sonata, Leoš Janáček’s Violin Sonata, Carl Nielsen’s Violin Concerto, Karl Goldmark’s Ballade, Karol Szymanowski’s Violin Sonata, Krzysztof Penderecki’s Cadenza for Solo Violin, and André Previn’s Tango Song and Dance. The pianists for these performances were Juny Jung and Hyun Jung Kim for the first two recitals, and Hye Jin Lee for the last one. My thirst for researching and playing hidden treasures of the past for my audiences will not end after I complete my degree, and I am sure that this project will go on throughout my whole musical life

Microfluidic system for high throughput characterisation of echogenic particles

Echogenic particles, such as microbubbles and volatile liquid micro/nano droplets, have shown considerable potential in a variety of clinical diagnostic and therapeutic applications. The accurate prediction of their response to ultrasound excitation is however extremely challenging, and this has hindered the optimisation of techniques such as quantitative ultrasound imaging and targeted drug delivery. Existing characterisation techniques, such as ultra-high speed microscopy provide important insights, but suffer from a number of limitations; most significantly difficulty in obtaining large data sets suitable for statistical analysis and the need to physically constrain the particles, thereby altering their dynamics. Here a microfluidic system is presented that overcomes these challenges to enable the measurement of single echogenic particle response to ultrasound excitation. A co-axial flow focusing device is used to direct a continuous stream of unconstrained particles through the combined focal region of an ultrasound transducer and a laser. Both the optical and acoustic scatter from individual particles are then simultaneously recorded. Calibration of the device and example results for different types of echogenic particle are presented, demonstrating a high throughput of up to 20 particles per second and the ability to resolve changes in particle radius down to 0.1 ?m with an uncertainty of less than 3%

Hepatocellular Carcinoma after Transcatheter Arterial Chemoembolization: Difficulties on Imaging Follow-up

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Cdk5 Phosphorylates Dopamine D2 Receptor and Attenuates Downstream Signaling

The dopamine D2 receptor (DRD2) is a key receptor that mediates dopamine-associated brain functions such as mood, reward, and emotion. Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase whose function has been implicated in the brain reward circuit. In this study, we revealed that the serine 321 residue (S321) in the third intracellular loop of DRD2 (D2i3) is a novel regulatory site of Cdk5. Cdk5-dependent phosphorylation of S321 in the D2i3 was observed in in vitro and cell culture systems. We further observed that the phosphorylation of S321 impaired the agonist-stimulated surface expression of DRD2 and decreased G protein coupling to DRD2. Moreover, the downstream cAMP pathway was affected in the heterologous system and in primary neuronal cultures from p35 knockout embryos likely due to the reduced inhibitory activity of DRD2. These results indicate that Cdk5-mediated phosphorylation of S321 inhibits DRD2 function, providing a novel regulatory mechanism for dopamine signaling.X111111sciescopu

Biologically and acoustically compatible chamber for studying ultrasound-mediated delivery of therapeutic compounds

Ultrasound (US), in combination with microbubbles, has been found to be a potential alternative to viral therapies for transfecting biological cells. The translation of this technique to the clinical environment, however, requires robust and systematic optimization of the acoustic parameters needed to achieve a desired therapeutic effect. Currently, a variety of different devices have been developed to transfect cells in vitro, resulting in a lack of standardized experimental conditions and difficulty in comparing results from different laboratories. To overcome this limitation, we propose an easy-to-fabricate and cost-effective device for application in US-mediated delivery of therapeutic compounds. It comprises a commercially available cell culture dish coupled with a silicon-based "lid" developed in-house that enables the device to be immersed in a water bath for US exposure. Described here are the design of the device, characterization of the sound field and fluid dynamics inside the chamber and an example protocol for a therapeutic delivery experiment