| 1. |
- Eriksson, Olivia, et al.
(författare)
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Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35:2, s. 284-292
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours.Results: We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building.
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| 2. |
- Reckermann, M., et al.
(författare)
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Human impacts and their interactions in the Baltic Sea region
- 2022
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Ingår i: Earth Syst. Dynam.. - : Copernicus GmbH. - 2190-4987 .- 2190-4979. ; 13:1, s. 1-80
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Forskningsöversikt (refereegranskat)abstract
- Coastal environments, in particular heavily populated semi-enclosed marginal seas and coasts like the Baltic Sea region, are strongly affected by human activities. A multitude of human impacts, including climate change, affect the different compartments of the environment, and these effects interact with each other. As part of the Baltic Earth Assessment Reports (BEAR), we present an inventory and discussion of different human-induced factors and processes affecting the environment of the Baltic Sea region, and their interrelations. Some are naturally occurring and modified by human activities (i.e. climate change, coastal processes, hypoxia, acidification, submarine groundwater discharges, marine ecosystems, non-indigenous species, land use and land cover), some are completely human-induced (i.e. agriculture, aquaculture, fisheries, river regulations, offshore wind farms, shipping, chemical contamination, dumped warfare agents, marine litter and microplastics, tourism, and coastal management), and they are all interrelated to different degrees. We present a general description and analysis of the state of knowledge on these interrelations. Our main insight is that climate change has an overarching, integrating impact on all of the other factors and can be interpreted as a background effect, which has different implications for the other factors. Impacts on the environment and the human sphere can be roughly allocated to anthropogenic drivers such as food production, energy production, transport, industry and economy. The findings from this inventory of available information and analysis of the different factors and their interactions in the Baltic Sea region can largely be transferred to other comparable marginal and coastal seas in the world.
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| 3. |
- Hedlund, Artur, et al.
(författare)
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Microstructures of cellulose coagulated in water and alcohols from 1-ethyl-3-methylimidazolium acetate : contrasting coagulation mechanisms
- 2019
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Ingår i: Cellulose. - : Springer Science and Business Media LLC. - 0969-0239 .- 1572-882X. ; 26:3, s. 1545-1563
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: Coagulation of cellulose solutions is a process whereby many useful materials with variable microstructures and properties can be produced. This study investigates the complexity of the phase separation that generates the structural heterogeneity of such materials. The ionic liquid, 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), and a co-solvent, dimethylsulfoxide (DMSO), are used to dissolve microcrystalline cellulose in concentrations from 5 to 25 wt%. The solutions are coagulated in water or 2-propanol (2PrOH). The coagulated material is then washed and solvent exchanged (water → 2PrOH → butanone → cyclohexane) in order to preserve the generated microstructures upon subsequent drying before analysis. Sweep electron microscopy images of 50 k magnification reveal open-pore fibrillar structures. The crystalline constituents of those fibrils are estimated using wide-angle X-ray spectroscopy and specific surface area data. It is found that the crystalline order or crystallite size is reduced by an increase in cellulose concentration, by the use of the co-solvent DMSO, or by the use of 2PrOH instead of water as the coagulant. Because previous theories cannot explain these trends, an alternative explanation is presented here focused on solid–liquid versus liquid–liquid phase separations. Graphical abstract: [Figure not available: see fulltext.].
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| 4. |
- Zhang, Chu, et al.
(författare)
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Steps and catalytic reactions : CO oxidation with preadsorbed O on Rh(553)
- 2022
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Ingår i: Surface Science. - : Elsevier BV. - 0039-6028 .- 1879-2758. ; 715
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Tidskriftsartikel (refereegranskat)abstract
- Industrial catalysts are often comprised of nanoparticles supported on high-surface-area oxides, in order to maximise the catalytically active surface area and thereby utilise the active material better. These nanoparticles expose steps and corners that, due to low coordination to neighboring atoms, are more reactive and, as a consequence, are often assumed to have higher catalytic activity. We have investigated the reaction between CO and preadsorbed O on a stepped Rh(553) surface, and show that CO oxidation indeed occurs faster than on the flat Rh(111) surface at the same temperature. However, we do find that this is not a result of reactions at the step sites but rather at the terrace sites close to the steps, due to in-plane relaxation enabled by the step. This insight can provide ways to optimize the shape of the nanoparticles to further improve the activity of certain reactions.
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| 5. |
- Anderbrant, Olle, et al.
(författare)
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Pheromone of the elm bark beetle Scolytus laevis (Coleoptera Scolytidae) : stereoisomers of 4-methyl-3-heptanol reduce interspecific competition
- 2010
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Ingår i: Chemoecology. - : Springer Science and Business Media LLC. - 0937-7409 .- 1423-0445. ; 20:3, s. 179-187
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Tidskriftsartikel (refereegranskat)abstract
- Stereoisomers of 4-methyl-3-heptanol (MH) are pheromone components of several Scolytus bark beetles. The elm bark beetle Scolytus laevis (Coleoptera: Scolytidae) has in previous studies been caught in traps baited with commercial MH containing all four stereoisomers, but the lure has been considered a weak attractant. In this study, we addressed the question whether stereospecific responses by S. laevis to stereoisomers of MH might contribute to its niche separation from other sympatric Scolytus species. Using GC-MS, we analyzed extracts of hindguts and abdomens from male and female S. laevis and the sympatric S. triarmatus. We also tested all four MH-stereoisomers individually and in combinations in the field to determine their role for S. laevis. All four stereoisomers were synthesized via a boronic ester method with 1,2-dicyclohexylethanediol as chiral director. In addition, the (3S,4R)-stereoisomer of MH was prepared through enantioselective, lipase-mediated transesterification of a mixture of the four stereoisomers of MH. Females of both species contained small amounts of syn-MH, and males contained trace amounts of anti-MH. The anti stereoisomer (3R,4S)-MH was attractive to male and female S. laevis, whereas the syn stereoisomer (3S,4S)-MH acted as an inhibitor or deterrent and reduced the catch when added to the attractive isomer. The syn isomer is the main aggregation pheromone component of the larger and sympatric S. scolytus and possibly also of S. triarmatus. The avoidance response of S. laevis to the (3S,4S)-stereoisomer may reduce interspecific competition for host trees.
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| 6. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 7. |
- Bergkvist, Bo, et al.
(författare)
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Pools and fluxes of carbon in three Norway spruce ecosystems along a climatic gradient in Sweden
- 2008
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 89:1, s. 7-25
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an integrated analysis of organic carbon (C) pools in soils and vegetation, within-ecosystem fluxes and net ecosystem exchange (NEE) in three 40-year old Norway spruce stands along a north-south climatic gradient in Sweden, measured 2001-2004. A process-orientated ecosystem model (CoupModel), previously parameterised on a regional dataset, was used for the analysis. Pools of soil organic carbon (SOC) and tree growth rates were highest at the southernmost site (1.6 and 2.0-fold, respectively). Tree litter production (litterfall and root litter) was also highest in the south, with about half coming from fine roots (< 1 mm) at all sites. However, when the litter input from the forest floor vegetation was included, the difference in total litter input rate between the sites almost disappeared (190-233 g C m(-2) year(-1)). We propose that a higher N deposition and N availability in the south result in a slower turnover of soil organic matter than in the north. This effect seems to overshadow the effect of temperature. At the southern site, 19% of the total litter input to the O horizon was leached to the mineral soil as dissolved organic carbon, while at the two northern sites the corresponding figure was approx. 9%. The CoupModel accurately described general C cycling behaviour in these ecosystems, reproducing the differences between north and south. The simulated changes in SOC pools during the measurement period were small, ranging from -8 g C m(-2) year(-1) in the north to +9 g C m(-2) year(-1) in the south. In contrast, NEE and tree growth measurements at the northernmost site suggest that the soil lost about 90 g C m(-2) year(-1).
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| 8. |
- Rahman, Mohammad A., et al.
(författare)
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Regeneration of Assembled, Molecular-Motor-Based Bionanodevices
- 2019
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 19:10, s. 7155-7163
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Tidskriftsartikel (refereegranskat)abstract
- The guided gliding of cytoskeletal filaments, driven by biomolecular motors on nano/microstructured chips, enables novel applications in biosensing and biocomputation. However, expensive and time-consuming chip production hampers the developments. It is therefore important to establish protocols to regenerate the chips, preferably without the need to dismantle the assembled microfluidic devices which contain the structured chips. We here describe a novel method toward this end. Specifically, we use the small, nonselective proteolytic enzyme, proteinase K to cleave all surface-adsorbed proteins, including myosin and kinesin motors. Subsequently, we apply a detergent (5% SDS or 0.05% Triton X100) to remove the protein remnants. After this procedure, fresh motor proteins and filaments can be added for new experiments. Both, silanized glass surfaces for actin-myosin motility and pure glass surfaces for microtubule-kinesin motility were repeatedly regenerated using this approach. Moreover, we demonstrate the applicability of the method for the regeneration of nano/microstructured silicon-based chips with selectively functionalized areas for supporting or suppressing gliding motility for both motor systems. The results substantiate the versatility and a promising broad use of the method for regenerating a wide range of protein-based nano/microdevices.
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| 9. |
- Couto, Rafael Carvalho, et al.
(författare)
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The carbon and oxygen K-edge NEXAFS spectra of CO
- 2020
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 22:28, s. 16215-16223
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Tidskriftsartikel (refereegranskat)abstract
- We present and analyze high resolution near edge X-ray absorption fine structure (NEXAFS) spectra of CO+ at the carbon and oxygen K-edges. The spectra show a wealth of features that appear very differently at the two K-edges. The analysis of these features can be divided into three parts; (i) repopulation transition to the open shell orbital – here the C(1s) or O(1s) to 5σ transition, where the normal core hole state is reached from a different initial state and different interaction than in X-ray photoelectron spectroscopy; (ii) spin coupled split valence bands corresponding to C(1s) or O(1s) to π* transitions; (iii) remainder weak and long progressions towards the double ionization potentials containing a manifold of peaks. These parts, none of which has correspondence in NEXAFS spectra of neutral molecules, are dictated by the localization of the singly occupied 5σ orbital, adding a dimension of chemistry to the ionic NEXAFS technique.
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| 10. |
- Hao, Meng-Shu, et al.
(författare)
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The Ca2+-Regulation of the Mitochondrial External NADPH Dehydrogenase in Plants Is Controlled by Cytosolic pH
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:9
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Tidskriftsartikel (refereegranskat)abstract
- NADPH is a key reductant carrier that maintains internal redox and antioxidant status, and that links biosynthetic, catabolic and signalling pathways. Plants have a mitochondrial external NADPH oxidation pathway, which depends on Ca2+ and pH in vitro, but concentrations of Ca2+ needed are not known. We have determined the K-0.5(Ca2+) of the external NADPH dehydrogenase from Solanum tuberosum mitochondria and membranes of E. coli expressing Arabidopsis thaliana NDB1 over the physiological pH range using O-2 and decylubiquinone as electron acceptors. The K-0.5(Ca2+) of NADPH oxidation was generally higher than for NADH oxidation, and unlike the latter, it depended on pH. At pH 7.5, K-0.5(Ca2+) for NADPH oxidation was high (approximate to 100 mu M), yet 20-fold lower K-0.5(Ca2+) values were determined at pH 6.8. Lower K-0.5(Ca2+) values were observed with decylubiquinone than with O-2 as terminal electron acceptor. NADPH oxidation responded to changes in Ca2+ concentrations more rapidly than NADH oxidation did. Thus, cytosolic acidification is an important activator of external NADPH oxidation, by decreasing the Ca2+-requirements for NDB1. The results are discussed in relation to the present knowledge on how whole cell NADPH redox homeostasis is affected in plants modified for the NDB1 gene.
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