| 1. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 2. |
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Beale, S. B., et al.
(author)
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Combined two-phase co-flow and counter-flow in a gas channel/porous transport layer assembly
- 2020. - 9
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In: PRiME 2020 : Polymer Electrolyte Fuel Cells and Electrolyzers 20 (PEFC and E 20) - Polymer Electrolyte Fuel Cells and Electrolyzers 20 (PEFC and E 20). - : The Electrochemical Society. - 1938-5862 .- 1938-6737. - 9781607685395 ; 98:9, s. 305-315
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Conference paper (peer-reviewed)abstract
- This paper considers a detailed numerical analysis of combined liquid-gas co-flow in a gas channel, with liquid-gas counter-flow in a porous transport layer, as is typically found on the cathode side of a polymer electrolyte fuel cell. The geometry is obtained by digital reconstruction of nano-computer tomography images. From this, the domain is tessellated with an unstructured castellated or octree mesh, upon which the equations of mass and momentum are solved by means of a volume of fluid method. Liquid water is produced from an electrode where gaseous oxygen is simultaneously consumed by electrochemical reduction; Liquid-gas counter flow in the porous transport layer results in liquid drops being entrained in co-flow in the gas channels and convected by the gas downstream.
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| 5. |
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| 6. |
- Beale, M. A., et al.
(author)
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Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis
- 2021
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In: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 6:12
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Journal article (peer-reviewed)abstract
- Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p.pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides. Global syphilis prevalence has been increasing. Sequencing and analysis of a global collection of 726 Treponema pallidum samples reveal globally circulating lineages linked to a rapid expansion occurring since the end of the twentieth century.
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| 7. |
- Zhang, S., et al.
(author)
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Polymer electrolyte fuel cell modeling - A comparison of two models with different levels of complexity
- 2020
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In: International Journal of Hydrogen Energy. - : Elsevier BV. - 0360-3199. ; 45:38, s. 19761-19777
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Journal article (peer-reviewed)abstract
- The modeling of fuel cells requires the coupling of fluid transport with electro-chemical reactions. There are two approaches commonly used. Firstly, the electrodes can be treated as two planes, where the potential gradient can be considered as being locally one-dimensional. In this case a two dimensional current density distribution is obtained. Secondly, the two electrode layers can be spatially resolved and the protonic and electronic potentials obtained by solving a pair of coupled Poisson equations. The latter approach requires much higher computational resources, because a higher spatial resolution is required and a large set of model parameters is required. On the other hand, much more detailed local information can be obtained by this method. The motivation for this study was to compare the results quantitively with detailed experimental data for a high temperature polymer electrolyte fuel cell with a geometric area of 200 cm2. Both model approaches show very good agreement with measured local current density distributions. The second model is able to provide a deeper insight into the current density variation through the membrane and catalyst layers and reveals points with local extremes. The present results are specific for high temperature polymer electrolyte fuel cells but the conclusions may readily be applied to the modeling of other high temperature fuel cell types.
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| 8. |
- Beale, M., et al.
(author)
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CONTEMPORARY SYPHILIS IS CHARACTERISED BY RAPID GLOBAL SPREAD OF PANDEMIC TREPONEMA PALLIDUM LINEAGES
- 2021
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In: Sexually Transmitted Infections. - : BMJ Publishing Group Ltd. - 1368-4973 .- 1472-3263. ; 97:Suppl. 1, s. A17-A17
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Journal article (other academic/artistic)abstract
- Background: Syphilis is an important sexually transmitted infection caused by the bacterium Treponema pallidum subspecies pallidum. The last two decades have seen syphilis incidence rise in many high-income countries, yet the evolutionary and epidemiological relationships that underpin this are poorly understood, as is the global T. pallidum population structure.Methods: We assembled a geographically and temporally diverse collection of clinical and laboratory samples, performing direct sequencing on the majority, and combining these with 133 publicly available sequences to compile a dataset comprising 726 T. pallidum genomes. We analysed the resulting genomes using detailed phylogenetic analysis and clustering.Results: We show that syphilis globally can be described by only two deeply branching lineages, Nichols and SS14. We show that both of these lineages can be found circulatingcon currently in 12 of the 23 countries sampled. To provide further phylodynamic resolution we subdivided Treponema pallidum subspecies pallidum into 17 distinct sublineages. Importantly, like SS14, we provide evidence that two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analysis showed that recent isolates circulating in 14 different countries were genetically identical in their core genome to those from other countries, suggesting frequent exchange through international transmission pathways. This contrasts with the majority of samples collected prior to 1983, which are phylogenetically distinct from these more recently isolated sublineages. Bayesian temporal analysis provided evidence of a population bottleneck and decline occurring during the late 1990s, followed by a rapid population expansion a decade later. This was driven by the dominant T. pallidum sublineages circulating today, many of which are resistant to macrolides.Conclusion: Combined we show that the population of contemporary syphilis in high-income countries has undergone a recent and rapid global expansion. This dataset will provide a framework for future characterisation and epidemiological investigation of syphilis populations.
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| 9. |
- Cellini, Andrea, 1991, et al.
(author)
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Structural basis of the radical pair state in photolyases and cryptochromes
- 2022
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In: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; , s. 4889-4892
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Journal article (peer-reviewed)abstract
- We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes.
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| 10. |
- Yang, Danan, et al.
(author)
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Numerical Reconstruction of Proton Exchange Membrane Fuel Cell Gas Diffusion Layers
- 2023
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In: ; , s. 49-61
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Conference paper (peer-reviewed)abstract
- Stochastic reconstruction is widely employed for effective and flexible imitation of Gas Diffusion Layers (GDLs), e.g., to facilitate the study of their properties. However, the reconstruction often overlooks crucial factors such as fiber curvature, fiber stack arrangement, and fiber anisotropy. Consequently, the impact of these structural characteristics remains poorly understood. In this study, an in-house reconstruction procedure is developed based on the periodic surface model. This procedure enables the generation of GDLs with either straight or curved fibers, layer-by-layer or random arrangement, and different probabilities of through-plane fiber orientation angles. The porosity, domain size, and fiber diameter are extracted from an experimental image-based GDL and utilized as input data for the reconstruction. Furthermore, the different GDLs are compared in terms of pore size distribution and through-plane porosity distribution. It is concluded that introducing proper selections of these fiber features gives the reconstruction more realistic properties.
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