Challenges for the representation of morphology in ontology lexicons

Recent years have experienced a growing trend in the publication of language resources as Linguistic Linked Data (LLD) to enhance their discovery, reuse and the interoperability of tools that consume language data. To this aim, the OntoLex-lemon model has emerged as a de facto standard to represent lexical data on the Web. However, traditional dictionaries contain a considerable amount of morphological information which is not straightforwardly representable as LLD within the current model. In order to fill this gap a new Morphology Module of OntoLex-lemon is currently being developed. This paper presents the results of this model as on-going work as well as the underlying challenges that emerged during the module development. Based on the MMoOn Core ontology, it aims to account for a wide range of morphological information, ranging from endings to derive whole paradigms to the decomposition and generation of lexical entries which is in compliance to other OntoLex-lemon modules and facilitates the encoding of complex morphological data in ontology lexicons

Colony-Level Effects of Amygdalin on Honeybees and Their Microbes

Amygdalin, a cyanogenic glycoside, is found in the nectar and pollen of almond trees, as well as in a variety of other crops, such as cherries, nectarines, apples and others. It is inevitable that western honeybees (Apis mellifera) consistently consume amygdalin during almond pollination season because almond crops are almost exclusively pollinated by honeybees. This study tests the effects of a field-relevant concentration of amygdalin on honeybee microbes and the activities of key honeybee genes. We executed a two-month field trial providing sucrose solutions with or without amygdalin ad libitum to free-flying honeybee colonies. We collected adult worker bees at four time points and used RNA sequencing technology and our HoloBee database to assess global changes in microbes and honeybee transcripts. Our hypothesis was that amygdalin will negatively affect bee microbes and possibly immune gene regulation. Using a log2 fold-change cutoff at two and intraday comparisons, we show no large change of bacterial counts, fungal counts or key bee immune gene transcripts, due to amygdalin treatment in relation to the control. However, relatively large titer decreases in the amygdalin treatment relative to the control were found for several viruses. Chronic bee paralysis virus levels had a sharp decrease (−14.4) with titers then remaining less than the control, Black queen cell virus titers were lower at three time points (\u3c−2) and Deformed wing virus titers were lower at two time points (\u3c−6) in amygdalin-fed compared to sucrose-fed colonies. Titers of Lotmaria passim were lower in the treatment group at three of the four dates (\u3c−4). In contrast, Sacbrood virus had two dates with relative increases in its titers (\u3e2). Overall, viral titers appeared to fluctuate more so than bacteria, as observed by highly inconstant patterns between treatment and control and throughout the season. Our results suggest that amygdalin consumption may reduce several honeybee viruses without affecting other microbes or colony-level expression of immune genes

Evolutionary relationships among barley and <i>Arabidopsis</i> core circadian clock and clock-associated genes

The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens. We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number (e.g. gene duplications among the various species). We propose that the common ancestor of barley and Arabidopsis had two-thirds of the key clock components identified in Arabidopsis prior to the separation of the monocot/dicot groups. After this separation, multiple independent gene duplication events took place in both monocot and dicot ancestors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00239-015-9665-0) contains supplementary material, which is available to authorized users

The impact of Galactic synchrotron emission on CMB anisotropy measurements. I. Angular power spectrum analysis of total intensity all-sky surveys

Galactic foreground emission is a limiting factor for precise cosmic microwave background (CMB) anisotropy measurements. We perform an angular power spectrum analysis (APS) of all-sky total intensity maps at 408 MHz and 1420 MHz, which are dominated by synchrotron emission out of the Galactic plane. We subtract the brighter sources from the maps. We study the APS as a function of Galactic latitude by considering various cuts and as a function of sky position by dividing the sky into patches of about 15 deg x 15 deg in size. The APS of the Galactic radio diffuse synchrotron emission is best fitted by a power law, $C_{\ell} \sim k \ell^{\alpha}$, with $\alpha \in [-3.0,-2.6]$, where the lower values of $\alpha$ typically correspond to the higher latitudes. Nevertheless, the analysis of the patches reveals that strong local variations exist. The mean APS for $\ell \in [20,40]$ is used to determine the mean spectral index between 408 MHz and 1420 MHz, which is then adopted to extrapolate the synchrotron APS results to the microwave range. A simple extrapolation to 23 GHz of the synchrotron emission APS found at 408 and 1420 MHz does not explain all the power in the WMAP synchrotron component even at middle/high Galactic latitudes. This suggests a significant microwave contribution (of about 50% of the signal) by other components such as free-free or spinning dust emission. The comparison between the extrapolated synchrotron APS and the CMB APS shows that a mask excluding the regions with $|b_{gal}| \lesssim 5^{\circ}$ would reduce the foreground fluctuations to about half of the cosmological ones at 70 GHz even at the lowest multipoles. We discuss the main implications of our analysis for the cosmological exploitation of microwave temperature anisotropy maps.Comment: 15 pages, 20 figures, Astronomy & Astrophysics, accepte

Optics and Quantum Electronics

Contains table of contents for Section 2 and reports on twenty research projects.Charles S. Draper Laboratory Contract DL-H-404179Joint Services Electronics Program Contract DAALO3-89-C-0001National Sciences Foundation Grant EET 87-00474National Science Foundation Grant EET 88-15834U.S. Air Force - Office of Scientific Research Contract F49620-88-C-0089National Science Foundation Grant ECS 85-52701International Business Machines CorporationMassachusetts General Hospital Contract N00014-86K-0117National Institutes of Health Grant 2-RO1-GM35459U.S. Department of Energy Grant DE-FG02-89-ER14012Lawrence Livermore National Laboratory Subcontract B04870

Optics and Quantum Electronics

Contains table of contents for Section 2 and reports on eleven research projects.Joint Services Electronics Program Contract DAAL03-89-C-0001National Science Foundation Grant EET 87-00474U.S. Air Force - Office of Scientific Research Contract F49620-88-C-0089Charles S. Draper Laboratory Contract DL-H-404179National Center for Integrated PhotonicsNational Science Foundation Grant ECS 87-18417NEC Research InstituteNational Science Foundation Grant ECS 85-52701Medical Free Electron Laser Program Contract N00014-86-K-0117National Institutes of Health Grant 5-RO1-GM35459Lawrence Livermore National Laboratory Contract B048704U.S. Department of Energy Grant DE-FG02-89-ER14012Columbia University Contract P016310

Planck intermediate results XVI. Profile likelihoods for cosmological parameters

We explore the 2013 Planck likelihood function with a high-precision multi-dimensional minimizer (Minuit). This allows a refinement of the CDM best-fit solution with respect to previously-released results, and the construction of frequentist confidence intervals using profile likelihoods. The agreement with the cosmological results from the Bayesian framework is excellent, demonstrating the robustness of the Planck results to the statistical methodology. We investigate the inclusion of neutrino masses, where more significant differences may appear due to the non-Gaussian nature of the posterior mass distribution. By applying the Feldman-Cousins prescription, we again obtain results very similar to those of the Bayesian methodology. However, the profile-likelihood analysis of the cosmic microwave background (CMB) combination (Planck+WP+highL) reveals a minimum well within the unphysical negative-mass region. We show that inclusion of the Planck CMB-lensing information regularizes this issue, and provide a robust frequentist upper limit \u3c3mv 640:26 eV (95% confidence) from the CMB+lensing+BAO data combination. \ua9 ESO 2014

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder

Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data