Using Grammar-Based Genetic Programming for Mining Disjointness Axioms Involving Complex Class Expressions

International audienceIn the context of the Semantic Web, learning implicit knowledge in terms of axioms from Linked Open Data has been the object of much current research. In this paper, we propose a method based on grammar-based genetic programming to automatically discover disjoint-ness axioms between concepts from the Web of Data. A training-testing model is also implemented to overcome the lack of benchmarks and comparable research. The acquisition of axioms is performed on a small sample of DBpedia with the help of a Grammatical Evolution algorithm. The accuracy evaluation of mined axioms is carried out on the whole DBpe-dia. Experimental results show that the proposed method gives high accuracy in mining class disjointness axioms involving complex expressions

Outflows from the high-mass protostars NGC 7538 IRS1/2 observed with bispectrum speckle interferometry -- Signatures of flow precession

NGC 7538 IRS1 is a high-mass (approx. 30 M_sun) protostar with a CO outflow, an associated UCHII region, and a linear methanol maser structure, which might trace a Keplerian-rotating circumstellar disk. The directions of the various associated axes are misaligned with each other. We investigate the near-infrared morphology of the source to clarify the relations among the various axes. K'-band bispectrum speckle interferometry was performed at two 6-meter-class telescopes -- the BTA 6m telescope and the 6.5m MMT. Complementary IRAC images from the Spitzer Space Telescope Archive were used to relate the structures detected with the outflow at larger scales. High-dynamic range images show fan-shaped outflow structure in which we detect 18 stars and several blobs of diffuse emission. We interpret the misalignment of various outflow axes in the context of a disk precession model, including numerical hydrodynamic simulations of the molecular emission. The precession period is approx. 280 years and its half-opening angle is 40 degrees. A possible triggering mechanism is non-coplanar tidal interaction of an (undiscovered) close companion with the circumbinary protostellar disk. Our observations resolve the nearby massive protostar NGC 7538 IRS2 as a close binary with separation of 195 mas. We find indications for shock interaction between the outflow activities in IRS1 and IRS2. Indications of outflow precession have been discovered to date in a number of massive protostars, all with large precession angles 20--45 degrees. This might explain the difference between the outflow widths in low- and high-mass stars and add support to a common collimation mechanism.Comment: 20 pages; 8 figures; Accepted by A&A on April 10, 2006; Image quality reduced due to astro-ph file size limitations; Please download a version with high-quality images from http://www.mpifr-bonn.mpg.de/staff/tpreibis/ngc7538.pd

Magnetism, entropy, and the first nano-machines

The efficiency of bio-molecular motors stems from reversible interactions $\sim$ $k_B T$; weak bonds stabilizing intermediate states (enabling $direct$ conversion of chemical into mechanical energy). For their (unknown) origins, we suggest that a magnetically structured phase (MSP) formed via accretion of super-paramagnetic particles (S-PPs) by magnetic rocks on the Hadean Ocean floor had hosted motor-like diffusion of ligand-bound S-PPs through its template-layers; its ramifications range from optical activity to quantum coherence. A gentle flux gradient offers both detailed-balance breaking non-equilibrium and $asymmetry$ to a magnetic dipole, undergoing infinitesimal spin-alignment changes. Periodic perturbation of this background by local H-fields of template-partners can lead to periodic high and low-template affinity states, due to the dipole's magnetic degree of freedom. An accompanying magnetocaloric effect allows interchange between system-entropy and bath temperature. We speculate on a magnetic reproducer in a setting close to the mound-scenario of Russell and coworkers that could evolve bio- ratchets.Comment: 17 pages, 1 figur

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Atrial fibrillation affects more than 33 million people worldwide and increases the risk of stroke, heart failure, and death. Fourteen genetic loci have been associated with atrial fibrillation in European and Asian ancestry groups. To further define the genetic basis of atrial fibrillation, we performed large-scale, trans-ancestry meta-analyses of common and rare variant association studies. The genome-wide association studies (GWAS) included 17,931 individuals with atrial fibrillation and 115,142 referents; the exome-wide association studies (ExWAS) and rare variant association studies (RVAS) involved 22,346 cases and 132,086 referents. We identified 12 new genetic loci that exceeded genome-wide significance, implicating genes involved in cardiac electrical and structural remodeling. Our results nearly double the number of known genetic loci for atrial fibrillation, provide insights into the molecular basis of atrial fibrillation, and may facilitate the identification of new potential targets for drug discovery

Multiple Loci Are Associated with White Blood Cell Phenotypes

White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count—6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count—17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count—6p21, 19p13 at EPS15L1; monocyte count—2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse ancestral backgrounds

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Genetic correlations and genome-wide associations of cortical structure in general population samples of 22,824 adults

Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprises 22,824 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging

Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

Peer reviewe

Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting

OBJECTIVE: To explore genetic and lifestyle risk factors of MRI-defined brain infarcts (BI) in large population-based cohorts.METHODS: We performed meta-analyses of genome-wide association studies (GWAS) and examined associations of vascular risk factors and their genetic risk scores (GRS) with MRI-defined BI and a subset of BI, namely, small subcortical BI (SSBI), in 18 population-based cohorts (n = 20,949) from 5 ethnicities (3,726 with BI, 2,021 with SSBI). Top loci were followed up in 7 population-based cohorts (n = 6,862; 1,483 with BI, 630 with SBBI), and we tested associations with related phenotypes including ischemic stroke and pathologically defined BI.RESULTS: The mean prevalence was 17.7% for BI and 10.5% for SSBI, steeply rising after age 65. Two loci showed genome-wide significant association with BI: FBN2, p = 1.77 × 10-8; and LINC00539/ZDHHC20, p = 5.82 × 10-9. Both have been associated with blood pressure (BP)-related phenotypes, but did not replicate in the smaller follow-up sample or show associations with related phenotypes. Age- and sex-adjusted associations with BI and SSBI were observed for BP traits (p value for BI, p [BI] = 9.38 × 10-25; p [SSBI] = 5.23 × 10-14 for hypertension), smoking (p [BI] = 4.4 × 10-10; p [SSBI] = 1.2 × 10-4), diabetes (p [BI] = 1.7 × 10-8; p [SSBI] = 2.8 × 10-3), previous cardiovascular disease (p [BI] = 1.0 × 10-18; p [SSBI] = 2.3 × 10-7), stroke (p [BI] = 3.9 × 10-69; p [SSBI] = 3.2 × 10-24), and MRI-defined white matter hyperintensity burden (p [BI] = 1.43 × 10-157; p [SSBI] = 3.16 × 10-106), but not with body mass index or cholesterol. GRS of BP traits were associated with BI and SSBI (p ≤ 0.0022), without indication of directional pleiotropy.CONCLUSION: In this multiethnic GWAS meta-analysis, including over 20,000 population-based participants, we identified genetic risk loci for BI requiring validation once additional large datasets become available. High BP, including genetically determined, was the most significant modifiable, causal risk factor for BI.</p