| 1. |
- Karlsson, Edvin, et al.
(author)
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The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia
- 2013
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 15:2, s. 634-645
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Journal article (peer-reviewed)abstract
- Previous studies of the causative agent of tularaemia, Francisella tularensis have identified phylogeographic patterns suggestive of environmental maintenance reservoirs. To investigate the phylogeography of tularaemia in Sweden, we selected 163 clinical isolates obtained during 1995-2009 in 10 counties and sequenced one isolate's genome to identify new genetic markers. An improved typing scheme based on two indels and nine SNPs was developed using hydrolysis or TaqMan MGB probe assays. The results showed that much of the known global genetic diversity of F. tularensis subsp. holarctica is present in Sweden. Thirteen of the 163 isolates belonged to a new genetic group that is basal to all other known members of the major genetic clade B.I, which is spread across the Eurosiberian region. One hundred and twenty-five of the 163 Swedish isolates belonged to B.I, but individual clades' frequencies differed from county to county (P < 0.001). Subsequent analyses revealed a correlation between genotype variation over time and recurrent outbreaks at specific places, supporting the 'maintenance reservoir' environmental maintenance hypothesis. Most importantly, the findings reveal the presence of diverse source populations of F. tularensis subsp. holarctica in Sweden and suggest a historical spread of the disease from Scandinavia to other parts of Eurosiberia.
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| 2. |
- Lärkeryd, Adrian, et al.
(author)
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CanSNPer : a hierarchical genotype classifier of clonal pathogens
- 2014
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In: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 30:12, s. 1762-1764
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Journal article (peer-reviewed)abstract
- Advances in typing methodologies have recently reformed the field of molecular epidemiology of pathogens. The falling cost of sequencing technologies is creating a deluge of whole genome sequencing data that burdens bioinformatics resources and tool development. In particular, single nucleotide polymorphisms in core genomes of pathogens are recognized as the most important markers for inferring genetic relationships because they are evolutionarily stable and amenable to high-throughput detection methods. Sequence data will provide an excellent opportunity to extend our understanding of infectious disease when the challenge of extracting knowledge from available sequence resources is met. Here, we present an efficient and user-friendly genotype classification pipeline, CanSNPer, based on an easily expandable database of predefined canonical single nucleotide polymorphisms.
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| 3. |
- Martin, Natalia, et al.
(author)
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Intrinsic Ligand Effect Governing the Catalytic Activity of Pd Oxide Thin Films
- 2014
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In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 4:10, s. 3330-3334
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Journal article (peer-reviewed)abstract
- High-pressure X-ray photoelectron spectroscopy, mass spectrometry, and density functional theory calculations have been combined to study methane oxidation over Pd(100). The measurements reveal a high activity when a two-layer PdO(101) oriented film is formed. Although a one-layer PdO(101) film exhibits a similar surface structure, no or very little activity is observed. The calculations show that the presence of an oxygen atom directly below the coordinatively unsaturated Pd atom in the two-layer PdO(101) film is crucial for efficient methane dissociation, demonstrating a ligand effect that may be broadly important in determining the catalytic properties of oxide thin films.
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| 4. |
- Månsson, Sven, et al.
(author)
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Quantification of low fat contents: a comparison of MR imaging and spectroscopy methods at 1.5 and 3 T.
- 2012
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In: Magnetic Resonance Imaging. - : Elsevier BV. - 1873-5894 .- 0730-725X.
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Journal article (peer-reviewed)abstract
- Magnetic resonance spectroscopy (MRS) has long been considered the golden standard for non-invasive measurement of tissue fat content. With improved techniques for fat/water separation, imaging has become an alternative to MRS for fat quantification. Several imaging models have been proposed, but their performance relative to MRS at very low fat contents is yet not fully established. In this work, imaging and spectroscopy were compared at 1.5 T and 3 T in phantoms with 0-3% fat fraction (FF). We propose a multispectral model with individual a priori R(2) relaxation rates for water and fat, and a common unknown R(2)' relaxation. Magnitude and complex image reconstructions were also compared. Best accuracy was obtained with the imaging method at 1.5 T. At 3 T, the FFs were underestimated due to larger fat-water phase shifts. Agreement between measured and true FF was excellent for the imaging method at 1.5 T (imaging: FF(meas)=0.98 FF(true)-0.01%, spectroscopy: FF(meas)=0.77 FF(true)+0.08%), and fair at 3 T (imaging: FF(meas)=0.91 FF(true)-0.19%, spectroscopy: FF(meas)=0.79 FF(true)+0.02%). The imaging method was able to quantify FFs down to approx. 0.5%. We conclude that the suggested imaging model is capable of fat quantification with accuracy and precision similar to or better than spectroscopy and offers an improvement vs. a model with a common R(2)* relaxation only.
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