| 1. |
- Aidas, Kestutis, et al.
(author)
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The Dalton quantum chemistry program system
- 2014
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In: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Journal article (peer-reviewed)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 2. |
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| 3. |
- McDevitt, Allan D., et al.
(author)
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Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
- 2022
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:3, s. 993-1006
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Journal article (peer-reviewed)abstract
- Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.
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| 4. |
- Norén, Karin, et al.
(author)
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Genetic footprints reveal geographic patterns of expansion in Fennoscandian red foxes
- 2015
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In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 21:9, s. 3299-3312
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Journal article (peer-reviewed)abstract
- Population expansions of boreal species are among the most substantial ecological consequences of climate change, potentially transforming both structure and processes of northern ecosystems. Despite their importance, little is known about expansion dynamics of boreal species. Red foxes (Vulpes vulpes) are forecasted to become a keystone species in northern Europe, a process stemming from population expansions that began in the 19th century. To identify the relative roles of geographic and demographic factors and the sources of northern European red fox population expansion, we genotyped 21 microsatellite loci in modern and historical (1835–1941) Fennoscandian red foxes. Using Bayesian clustering and Bayesian inference of migration rates, we identified high connectivity and asymmetric migration rates across the region, consistent with source-sink dynamics, whereby more recently colonized sampling regions received immigrants from multiple sources. There were no clear clines in allele frequency or genetic diversity as would be expected from a unidirectional range expansion from south to north. Instead, migration inferences, demographic models and comparison to historical red fox genotypes suggested that the population expansion of the red fox is a consequence of dispersal from multiple sources, as well as in situ demographic growth. Together, these findings provide a rare glimpse into the anatomy of a boreal range expansion and enable informed predictions about future changes in boreal communities.
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| 5. |
- Roos, Anna, 1961-, et al.
(author)
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High prevalence of Müllerian duct remnant cysts on the spermatic duct in wild Eurasian otters (Lutra lutra) from Sweden
- 2013
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:12, s. e84660-
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Journal article (peer-reviewed)abstract
- The spermatic ducts (vasa deferentia) of 235 otters (Lutra lutra) found dead between 1999 and 2012 in Sweden were examined for presence of paraductular cysts. Single or multiple elongated uni- or bilateral cysts parallel to the spermatic duct were noted in 72% of the examined males. The cysts were adjacent to, but did not communicate with the lumen of the spermatic duct, and were usually located within a few centimeters of the testis and epididymis. The cysts are proposed to be congenital Mullerian duct remnants. Other morphologic abnormalities in the reproductive organs were not noted within this study. Possible causes of the incomplete regression of the embryonic female gonadal duct are exposure to environmental contaminants such as elevated concentrations of estrogen-like compounds (endocrine disrupting chemicals), inbreeding, or a naturally occurring anatomic defect. No obvious geographical pattern was observed for otters with or without cysts. This is the first study and description of cysts on the spermatic duct in otters.
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| 6. |
- Söderlund, Robert, et al.
(author)
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Prevalence and genomic characteristics of zoonotic gastro-intestinal pathogens and ESBL/pAmpC producing Enterobacteriaceae among Swedish corvid birds
- 2019
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In: Infection Ecology & Epidemiology. - : Taylor & Francis. - 2000-8686. ; 9:1
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Journal article (peer-reviewed)abstract
- Introduction: Wild birds pose a potential threat to animal and human health by spreading infectious diseases. In the present study, we studied the occurrence of bacterial zoonotic pathogens as well as enterobacteria with transferrable antimicrobial resistance genes among Swedish corvids.Materials and methods: Intestines from 66 jackdaws, crows, rooks and magpies from the vicinity of livestock farms at 14 locations in 7 counties were analysed by direct culture or PCR screening followed by culture. Isolates were investigated by whole-genome sequencing.Results and discussion: Campylobacter jejuni were detected in 82% and Yersinia in 3% of the birds. ESBL-producing E. coli were found in one sample (2%) and carried bla CTX-M-55. No Enterobacteriaceae with transferable carbapenem resistance were identified. No Salmonella or E. coli O157:H7 were found, but PCR analysis for enterohaemorrhagic E. coli virulence genes revealed 35% positive samples for intimin, 9% for verotoxin 1 and 17% for verotoxin 2. C. jejuni isolates from corvids were compared to previously published isolates from Swedish sources by multi-locus sequence typing based on genome sequences. All corvid C. jejuni isolates formed a cluster, intermingled with human and chicken isolates. Our results indicate that C. jejuni is ubiquitous among Swedish corvid birds, with sporadic transmission to poultry and humans.
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