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Sökning: LAR1:gu > Tidskriftsartikel > Chalmers tekniska högskola

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1.
  • 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.
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3.
  • Abarenkov, Kessy, et al. (författare)
  • Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
  • 2016
  • Ingår i: MycoKeys. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
  • Tidskriftsartikel (refereegranskat)abstract
    • Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data - for example, "retrieve all fungal sequences recovered from bathrooms" - a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http:// gensc.org/ mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http:// its. mycologylab.org).
4.
  • Abbas, Aamer, 1973-, et al. (författare)
  • Characterization and mapping of carotenoids in the algae Dunaliella and Phaeodactylum using Raman and target orthogonal partial least squares.
  • 2011
  • Ingår i: Chemometrics and Intelligent Laboratory Systems. - 0169-7439. ; 107:1, s. 174-177
  • Tidskriftsartikel (refereegranskat)abstract
    • A method was developed for the characterisation of carotenoid pigments in algal species using Raman spectroscopy in combination with multivariate hyperspectral analysis. Target orthogonal partial least squares (T-OPLS) operates by designating one known reference spectrum as the target. The target spectrum is put as the single y column in an OPLS regression model where the X matrix consists of the unfolded image spectra as variables in its columns. The spectral shape of the OPLS first orthogonal target score enabled us to verify the peak positions of the standard, and detect new peaks, not present in the reference standard. It was shown that the mixture of carotenoids present in the algae did not fully match the reference spectrum, however, the method provided enough information to make an analysis possible also in this case. The image results were constructed from the OPLS loading vectors that were showing a correlation map for the reference spectrum from the predictive loadings and maps of the occurrence of deviations from the orthogonal loadings.
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