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

Effect of leaning angle of gecko-inspired slanted polymer nanohairs on dry adhesion

We present analysis of adhesion properties of angled polymer nanohairs with a wide range of leaning angles from 0?? to 45?? and ultraviolet (UV)-curable polyurethane acrylate (PUA) materials of two different elastic moduli (19.8 and 320 MPa). It is demonstrated that shear adhesion and adhesion hysteresis can be greatly enhanced by increasing the leaning angle of nanohairs both for soft and hard materials due to increased contact area and reduced structural stiffness.open211

Cholinergic neurons in the dorsomedial hypothalamus regulate mouse brown adipose tissue metabolism.

OBJECTIVE: Brown adipose tissue (BAT) thermogenesis is critical in maintaining body temperature. The dorsomedial hypothalamus (DMH) integrates cutaneous thermosensory signals and regulates adaptive thermogenesis. Here, we study the function and synaptic connectivity of input from DMH cholinergic neurons to sympathetic premotor neurons in the raphe pallidus (Rpa). METHODS: In order to selectively manipulate DMH cholinergic neuron activity, we generated transgenic mice expressing channelrhodopsin fused to yellow fluorescent protein (YFP) in cholinergic neurons (choline acetyltransferase (ChAT)-Cre::ChR2-YFP) with the Cre-LoxP technique. In addition, we used an adeno-associated virus carrying the Cre recombinase gene to delete the floxed Chat gene in the DMH. Physiological studies in response to optogenetic stimulation of DMH cholinergic neurons were combined with gene expression and immunocytochemical analyses. RESULTS: A subset of DMH neurons are ChAT-immunopositive neurons. The activity of these neurons is elevated by warm ambient temperature. A phenotype-specific neuronal tracing shows that DMH cholinergic neurons directly project to serotonergic neurons in the Rpa. Optical stimulation of DMH cholinergic neurons decreases BAT activity, which is associated with reduced body core temperature. Furthermore, elevated DMH cholinergic neuron activity decreases the expression of BAT uncoupling protein 1 (Ucp1) and peroxisome proliferator-activated receptor γ coactivator 1 α (Pgc1α) mRNAs, markers of BAT activity. Injection of M2-selective muscarinic receptor antagonists into the 4th ventricle abolishes the effect of optical stimulation. Single cell qRT-PCR analysis of retrogradely identified BAT-projecting neurons in the Rpa shows that all M2 receptor-expressing neurons contain tryptophan hydroxylase 2. In animals lacking the Chat gene in the DMH, exposure to warm temperature reduces neither BAT Ucp1 nor Pgc1α mRNA expression. CONCLUSION: DMH cholinergic neurons directly send efferent signals to sympathetic premotor neurons in the Rpa. Elevated cholinergic input to this area reduces BAT activity through activation of M2 mAChRs on serotonergic neurons. Therefore, the direct DMH(ACh)-Rpa(5-HT) pathway may mediate physiological heat-defense responses to elevated environmental temperature.We thank Althea Cavanaugh and Licheng Wu for technical supports. This work was supported by NIDDK (RO1DK092246) to Y.-H.J. and New York obesity nutrition research center to J.H.J.This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S2212877815000617

The Synergistic Effect of Conditional Pten Loss and Oncogenic K-ras Mutation on Endometrial Cancer Development Occurs via Decreased Progesterone Receptor Action

Endometrial cancer is the most common gynecological cancer. Estrogen-dependent endometrioid carcinoma is the most common type of endometrial cancer, and alterations in the expression of PTEN and K-ras have been associated with this disease. To study the roles of Pten and K-ras in endometrial cancer, we generated Pten ablation and oncogenic K-ras mutation in progesterone receptor positive cells (PRcre/+Ptenf/f K-rasG12D). Double mutant mice dramatically accelerated the development of endometrial cancer compared to a single mutation of either gene. Histological analysis showed that all of the 1-month old double mutant female mice developed endometrial cancer with myometrial invasion. The expression of PR was downregulated in double mutant mice compared to a single mutation of either gene which resulted in decreased suppression of estrogen signaling. Therefore, these results suggest a synergistic effect of dysregulation of the Pten and K-ras signaling pathways during endometrial tumorigenesis

Normal and Anomalous Self-Healing Mechanism of Crystalline Calcium Silicate Hydrates

The origin of different stability of crystalline calcium silicate hydrates was investigated. The tobermorite crystal has been used as an analog of cement hydrate that is being mostly manufactured material on earth. Normal tobermorite is thermally unstable and transforms to amorphous at low pressure. Meanwhile, anomalous tobermorite with high Al content does not significantly transform under high pressure or high temperature. Conducted X-ray absorption spectroscopy explains the weak stability of normal tobermorite which was originally hypothesized by the role of zeolitic Ca ions in the cavities of silicate chains. Atomic simulations reproduced the experimentally observed trend of pressure behavior once the ideal structures were modified to account for the Al content as well as the chain defects. The simulations also suggested that the stability of tobermorite under stress could be rationalized as a self-healing mechanism in which the structural instabilities were accommodated by a global sliding of the CaO layer.J.M. acknowledges support by a grant (20SCIP-C159063-01) from Construction Technology Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government. H.M. acknowledges the financial support from the Gobierno Vasco (project IT912-16). The work in San Sebasti ' an (R.D., J.S.D, A.A) was supported by the Spanish Ministry of Science and Innovation with RTI2018-098554-B-I00, PID2019-105488GB-I00 and PCI2019-103657 research grants, the Gobierno Vasco UPV/EHU (Project No. IT-1246-19), and the European Commission from the NRG-STORAGE project (GA 870114). The Institute of Engineering Research in Seoul National University provided research facilities for this work. The Ca-XAS and HPXRD experiments were performed at XAFCA beamline in Singapore Synchrotron Light Source (SSLS) and 12.2.2 beamline in Advanced Light Source (ALS), respectively. The ALS supported by a DOE Office of Science User Facility under contract no. DE-AC02-05CH11231 and the Consortium for Materials Properties Research in Earth Sciences under NSF Cooperative Agreement EAR 1606856. The authors thank Prof. Simon M. Clark, Dr. Yonghua Du, and Dr. Shibo Xi for helpful discussions and beamline experimental supports

Misorientation-angle-dependent electrical transport across molybdenum disulfide grain boundaries

Grain boundaries in monolayer transition metal dichalcogenides have unique atomic defect structures and band dispersion relations that depend on the inter-domain misorientation angle. Here, we explore misorientation angle-dependent electrical transport at grain boundaries in monolayer MoS2 by correlating the atomic defect structures of measured devices analysed with transmission electron microscopy and first-principles calculations. Transmission electron microscopy indicates that grain boundaries are primarily composed of 5–7 dislocation cores with periodicity and additional complex defects formed at high angles, obeying the classical low-angle theory for angles <22°. The inter-domain mobility is minimized for angles <9° and increases nonlinearly by two orders of magnitude before saturating at ∼16 cm2 V−1 s−1 around misorientation angle≈20°. This trend is explained via grain-boundary electrostatic barriers estimated from density functional calculations and experimental tunnelling barrier heights, which are ≈0.5 eV at low angles and ≈0.15 eV at high angles (≥20°)

Lack of association between PRNP 1368 polymorphism and Alzheimer's disease or vascular dementia

<p>Abstract</p> <p>Background</p> <p>Polymorphisms of the prion protein gene (<it>PRNP</it>) at codons 129 and 219 play an important role in the susceptibility to Creutzfeldt-Jakob disease (CJD), and might be associated with other neurodegenerative disorders. Several recent reports indicate that polymorphisms outside the coding region of <it>PRNP </it>modulate the expression of prion protein and are associated with sporadic CJD, although other studies failed to show an association. These reports involved the polymorphism <it>PRNP </it>1368 which is located upstream from <it>PRNP </it>exon 1. In a case-controlled protocol, we assessed the possible association between the <it>PRNP </it>1368 polymorphism and either Alzheimer's disease (AD) or vascular dementia (VaD).</p> <p>Methods</p> <p>To investigate whether the <it>PRNP </it>1368 polymorphism is associated with the occurrence of AD or VaD in the Korean population, we compared the genotype, allele, and haplotype frequencies of the <it>PRNP </it>1368 polymorphism in 152 AD patients and 192 VaD patients with frequencies in 268 healthy Koreans.</p> <p>Results and conclusion</p> <p>Significant differences in genotype, allele and haplotype frequencies of <it>PRNP </it>1368 polymorphism were not observed between AD and normal controls. There were no significant differences in the genotype and allele frequencies of the <it>PRNP </it>1368 polymorphism between Korean VaD patients and normal controls. However, in the haplotype analysis, haplotype Ht5 was significantly over-represented in Korean VaD patients. This was the first genetic association study of a polymorphism outside the coding region of <it>PRNP </it>in relation to AD and VaD.</p

Construction of a 3He magnetic force microscope with a vector magnet

We constructed a He-3 magnetic force microscope operating at the base temperature of 300 mK under a vector magnetic field of 2-2-9 T in the x-y-z direction. Fiber optic interferometry as a detection scheme is employed in which two home-built fiber walkers are used for the alignment between the cantilever and the optical fiber. The noise level of the laser interferometer is close to its thermodynamic limit. The capabilities of the sub-Kelvin and vector field are demonstrated by imaging the coexistence of magnetism and superconductivity in a ferromagnetic superconductor (ErNi2B2C) at T = 500 mK and by probing a dipole shape of a single Abrikosov vortex with an in-plane tip magnetization. (C) 2016 AIP Publishing LLC.open1111sciescopu

Transient upregulation of postsynaptic IP3-gated Ca release underlies short-term potentiation of metabotropic glutamate receptor 1 signaling in cerebellar Purkinje cells

Synaptic plasticity lasting approximately 100 s has been suggested to function as a temporary buffer for neural information. One example of this was reported by Batchelor and Garthwaite (1997), who found that a slow metabotropic glutamate receptor 1 (mGluR1)-evoked EPSP produced by burst stimulation of cerebellar parallel fiber-Purkinje cell synapses could be potentiated by a conditioning stimulus consisting of prior activation of climbing fiber synapses (or injection of depolarizing current) with a delay of up to 90 s. What is the molecular basis of the signal that spans this temporal gap? Here, we show that mGluR1-evoked slow EPSCs evoked by parallel fiber burst test stimuli show a similar form of short-term potentiation (mGluR1-STP) and that this phenomenon is also observed when parallel fiber bursts are replaced by pressure pulses of an exogenous mGluR1 agonist. Ca imaging experiments revealed that cytosolic Ca levels returned to baseline within several seconds after conditioning depolarization, indicating that this cannot underlie mGluR1-STP. To test the hypothesis that transient upregulation of inositol-1,4,5-trisphosphate (IP(3))-gated Ca release underlies this phenomenon, we used local photolytic uncaging of IP(3) to deplete IP(3)-gated Ca stores. IP(3) uncaging in the interval between conditioning depolarization and the test pulse produced a complete blockade of mGluR1-STP, as did blockade of IP(3) receptors with heparin. When Ca transients evoked by IP(3) uncaging were used as a test stimulus, conditioning depolarization produced a large STP of Ca response amplitudes. These data suggest that transient upregulation of postsynaptic IP(3)-gated Ca signaling constitutes a novel form of short-term synaptic plasticity