| 1. |
- Schaufler, Katharina, et al.
(författare)
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Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia coli Lineage Sequence Type 648
- 2019
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Ingår i: Antimicrobial Agents and Chemotherapy. - : AMER SOC MICROBIOLOGY. - 0066-4804 .- 1098-6596. ; 63:6
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Tidskriftsartikel (refereegranskat)abstract
- The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and in vivo experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 (n = 107) and ST10 (n = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our in silico, in vitro, and in vivo results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.
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| 2. |
- Simola, U., et al.
(författare)
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Machine learning accelerated likelihood-free event reconstruction in dark matter direct detection
- 2019
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Ingår i: Journal of Instrumentation. - 1748-0221 .- 1748-0221. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Reconstructing the position of an interaction for any dual-phase time projection chamber (TPC) with the best precision is key to directly detecting Dark Matter. Using the likelihood-free framework, a newalgorithm to reconstruct the 2-D (x; y) position and the size of the charge signal (e) of an interaction is presented. The algorithm uses the secondary scintillation light distribution (S2) obtained by simulating events using a waveform generator. To deal with the computational effort required by the likelihood-free approach, we employ the Bayesian Optimization for LikelihoodFree Inference (BOLFI) algorithm. Together with BOLFI, prior distributions for the parameters of interest (x; y; e) and highly informative discrepancy measures to performthe analyses are introduced. We evaluate the quality of the proposed algorithm by a comparison against the currently existing alternative methods using a large-scale simulation study. BOLFI provides a natural probabilistic uncertainty measure for the reconstruction and it improved the accuracy of the reconstruction over the next best algorithm by up to 15% when focusing on events at large radii (R > 30 cm, the outer 37% of the detector). In addition, BOLFI provides the smallest uncertainties among all the tested methods.
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