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  • A, Komonen, et al. (författare)
  • Insects associated with fruit bodies of the wood-decaying fungus Oak mazegill (Daedalea quercina) in mixed oak forests in southern Sweden
  • 2012
  • Ingår i: Entomologisk Tidskrift. - 0013-886X. ; 133:4, s. 173-181
  • Tidskriftsartikel (refereegranskat)abstract
    • Polypores host species rich insect assemblages, but relatively few polypore species have been studied in detail. We investigated insect assemblages associated with the fruit bodies of Daedalea quercina, a specialist species on oak in southern Sweden. Fruit bodies (n = 228) were collected from 25 nature reserves and woodland key habitats, and were taken into the laboratory to collect emerging insects. A total of 245 insect individuals were recorded, belonging to at least 45 species. The numerically dominant fungivores were the tineid moths Montescardia tessulatella (n = 38 individuals) and Nemapogon fungivorellus (n = 10) and the coleopteran Ennearthron cornutum (Ciidae) (n = 44). Altogether 40 individuals of hymenopteran parasitoids were recorded, belonging to Braconidae (Exothecinae, Microgastrinae and Rogadinae, altogether 6 spp.), Ichneumonidae (Banchinae, Cryptinae and Orthocentrinae, altogether 4 spp.), Torymidae (1 sp.), Perilampidae (1 sp.) and Scelionidae (1 sp.). Most of the remaining insect species are not specifically associated with fruit bodies, but occupy many types of decaying material. In conclusion, D. quercina hosted a low number of insect individuals in general and only a few coleopteran species. The fungus apparently has only one specialist species, N. fungivorellus, which is a near-threatened (NT) species on the Swedish red list; the record from Norra Vi is the first from the Jönköping. The overall low number of insect individuals and the dominance of Lepidoptera among the fungivores is possibly explained by the tough fruit bodies of D. quercina, which only moths are able to utilize; fruit bodies which had already started to rot were devoid of moths.
  • A. Nojima, et al. (författare)
  • Calculational aspects of electron-phonon coupling at surfaces
  • 2008
  • Ingår i: J. Phys: Condens. Matter. - 1361-648X. ; 20
  • Tidskriftsartikel (refereegranskat)abstract
    • We study the validity of two frequently used approximations in calculations of electron–phonon coupling at surfaces. The rigid-ion approximation is a standard approximation used for the bulk metals. On the basis of density functional theory calculations, we find that for Be this approximation is as valid for surface atoms as for bulk atoms. In addition, the slab method for calculations of a phonon induced surface state lifetime is examined. The convergence of the electron–phonon matrix element with respect to the thickness of the slab is studied for several systems. When the number of slab layers is increased, the net effect of decreasing overlap and increasing number of final states depends strongly on the decay length of the surface state wavefunction and the band structure.
  • A.O., Tillmar, et al. (författare)
  • Using X-chromosomal markers in relationship testing: : How to calculate likelihood ratios taking linkage and linkage disequilibrium into account
  • 2011
  • Ingår i: Forensic Science International : Genetics. - Elsevier. - 1872-4973. ; 5:5, s. 506-511
  • Tidskriftsartikel (refereegranskat)abstract
    • X-chromosomal markers in forensic genetics have become more widely used during the recent years, particularly for relationship testing. Linkage and linkage disequilibrium (LD) must typically be accounted for when using close X-chromosomal markers. Thus, when producing the weight-of-evidence, given by a DNA-analysis with markers that are linked, the normally used product rule is invalid. Here we present an efficient model for calculating likelihood ratio (LR) with markers on the X-chromosome which are linked and in LD. Furthermore, the model was applied on several cases based on data from the eight X-chromosomal loci included in the Mentype® Argus X-8 (Biotype). Using a simulation approach we showed that the use of X-chromosome data can offer valuable information for choosing between the alternatives in each of the cases we studied, and that the LR can be high in several cases. We demonstrated that when linkage and LD were disregarded, as opposed to taken into account, the difference in calculated LR could be considerable. When these differences were large, the estimated haplotype frequencies often had a strong impact and we present a method to estimate haplotype frequencies. Our conclusion is that linkage and LD should be accounted for when using the tested set of markers, and the presented model is an efficient way of doing so.
  • A, Teschendorff, et al. (författare)
  • The dynamics of DNA methylation covariation patterns in carcinogenesis
  • 2014
  • Ingår i: PLoS Computational Biology. - 1553-734X. ; 10:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Recently it has been observed that cancer tissue is characterised by an increased variability in DNA methylation patterns. However, how the correlative patterns in genome-wide DNA methylation change during the carcinogenic progress has not yet been explored. Here we study genome-wide inter-CpG correlations in DNA methylation, in addition to single site variability, during cervical carcinogenesis. We demonstrate how the study of changes in DNA methylation covariation patterns across normal, intra-epithelial neoplasia and invasive cancer allows the identification of CpG sites that indicate the risk of neoplastic transformation in stages prior to neoplasia. Importantly, we show that the covariation in DNA methylation at these risk CpG loci is maximal immediately prior to the onset of cancer, supporting the view that high epigenetic diversity in normal cells increases the risk of cancer. Consistent with this, we observe that invasive cancers exhibit increased covariation in DNA methylation at the risk CpG sites relative to normal tissue, but lower levels relative to pre-cancerous lesions. We further show that the identified risk CpG sites undergo preferential DNA methylation changes in relation to human papilloma virus infection and age. Results are validated in independent data including prospectively collected samples prior to neoplastic transformation. Our data are consistent with a phase transition model of carcinogenesis, in which epigenetic diversity is maximal prior to the onset of cancer. The model and algorithm proposed here may allow, in future, network biomarkers predicting the risk of neoplastic transformation to be identified.
  • Aalto, Susanne, 1964-, et al. (författare)
  • 13CO 1-0 imaging of the Medusa merger, NGC 4194. Large scale variations in molecular cloud properties
  • 2010
  • Ingår i: Astronomy and Astrophysics. - 0004-6361. ; 522
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims. Studying molecular gas properties in merging galaxies gives important clues to the onset and evolution of interaction-triggered starbursts. The (CO)-C-12/(CO)-C-13 line intensity ratio can be used as a tracer of how dynamics and star formation processes impact the gas properties. The Medusa merger (NGC 4194) is particularly interesting to study since its L-FIR/L-CO ratio rivals that of ultraluminous galaxies (ULIRGs), despite the comparatively modest luminosity, indicating an exceptionally high star formation efficiency (SFE) in the Medusa merger. Methods. High resolution OVRO (Owens Valley Radio Observatory) observations of the (CO)-C-13 1-0 have been obtained and compared with matched resolution OVRO (CO)-C-12 1-0 data to investigate the molecular gas cloud properties in the Medusa merger. Results. Interferometric observations of (CO)-C-12 and (CO)-C-13 1-0 in the Medusa (NGC 4194) merger show the (CO)-C-12 (CO)-C-13 1-0 intensity ratio (R) increases from normal, quiescent values (7-10) in the outer parts (r > 2 kpc) of the galaxy to high (16 to > 40) values in the central (r < 1 kpc) starburst region. In the central two kpc there is an east-west gradient in R where the line ratio changes by more than a factor of three over 5 '' (945 pc). The integrated (CO)-C-13 emission peaks in the north-western starburst region while the central (CO)-C-12 emission is strongly associated with the prominent crossing dust-lane. Conclusions. We discuss the central east-west gradient in R in the context of gas properties in the starburst and the central dust lane. We suggest that the central gradient in R is mainly caused by diffuse gas in the dust lane. In this scenario, the actual molecular mass distribution is better traced by the (CO)-C-13 1-0 emission than the (CO)-C-12. The possibilities of temperature and abundance gradients are also discussed. We compare the central gas properties of the Medusa to those of other minor mergers and suggest that the extreme and transient phase of the Medusa star formation activity has similar traits to those of high-redshift galaxies.
  • Aalto, Susanne, 1964- (författare)
  • Chemistry in luminous AGN and starburst galaxies
  • 2008
  • Ingår i: Astrophysics and Space Science. - 0004-640X. ; 313:1-3, s. 273-278
  • Tidskriftsartikel (refereegranskat)abstract
    • Molecular line emission is a useful tool for probing the highly obscured inner kpc of starburst galaxies and buried AGNs. Molecular line ratios serve as diagnostic tools of the physical conditions of the gas-but also of its chemical properties. Both provide important clues to the type and evolutionary stage of the nuclear activity. While CO emission remains the main tracer for molecular distribution and dynamics, molecules such as HCN, HNC, HCO+, CN and HC3N are useful for probing the properties of the denser (n greater than or similar to 10(4) cm(-3)), star-forming gas. Here I discuss current views on how line emission from these species can be interpreted in luminous galaxies. HNC, HCO+ and CN are all species that can be associated both with photon dominated regions (PDRs) in starbursts-as well as X-ray dominated regions (XDRs) associated with AGN activity. HC3N line emission may identify galaxies where the starburst is in the early stage of its evolution.
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