| 1. |
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- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:2
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Rogers, T J, et al.
(författare)
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Identification of a Duffing oscillator using particle Gibbs with ancestor sampling
- 2019
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Ingår i: Journal of Physics, Conference Series. - : Institute of Physics Publishing (IOPP). - 1742-6588 .- 1742-6596. ; 1264:1
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Tidskriftsartikel (refereegranskat)abstract
- The Duffing oscillator remains a key benchmark in nonlinear systems analysis and poses interesting challenges in nonlinear structural identification. The use of particle methods or sequential Monte Carlo (SMC) is becoming a more common approach for tackling these nonlinear dynamical systems, within structural dynamics and beyond. This paper demonstrates the use of a tailored SMC algorithm within a Markov Chain Monte Carlo (MCMC) scheme to allow inference over the latent states and parameters of the Duffing oscillator in a Bayesian manner. This approach to system identification offers a statistically more rigorous treatment of the problem than the common state-augmentation methods where the parameters of the model are included as additional latent states. It is shown how recent advances in particle MCMC methods, namely the particle Gibbs with ancestor sampling (PG-AS) algorithm is capable of performing efficient Bayesian inference, even in cases where little is known about the system parameters a priori. The advantage of this Bayesian approach is the quantification of uncertainty, not only in the system parameters but also in the states of the model (displacement and velocity) even in the presence of measurement noise.
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| 3. |
- Strassert, Jürgen F H, et al.
(författare)
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Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates
- 2018
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Ingår i: The ISME Journal. - : Macmillan Publishers Ltd.. - 1751-7362 .- 1751-7370. ; 12, s. 304-308
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Tidskriftsartikel (refereegranskat)abstract
- Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.
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| 4. |
- Strassert, Jürgen F. H., et al.
(författare)
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Phylogeny, Evidence for a Cryptic Plastid, and Distribution of Chytriodinium Parasites (Dinophyceae) Infecting Copepods
- 2019
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Ingår i: Journal of Eukaryotic Microbiology. - : Wiley. - 1066-5234 .- 1550-7408. ; 66:4, s. 574-581
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Tidskriftsartikel (refereegranskat)abstract
- Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium, which seemed to be attached to a copepod nauplius, to analyze the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.
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