| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
- 2022
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Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 239-244
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.
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| 2. |
- Sun, Bing, et al.
(författare)
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Ion transport in polycarbonate based solid polymer electrolytes : experimental and computational investigations
- 2016
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 18:14, s. 9504-9513
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Tidskriftsartikel (refereegranskat)abstract
- Among the alternative host materials for solid polymer electrolytes (SPEs), polycarbonates have recently shown promising functionality in all-solid-state lithium batteries from ambient to elevated temperatures. While the computational and experimental investigations of ion conduction in conventional polyethers have been extensive, the ion transport in polycarbonates has been much less studied. The present work investigates the ionic transport behavior in SPEs based on poly(trimethylene carbonate) (PTMC) and its co-polymer with epsilon-caprolactone (CL) via both experimental and computational approaches. FTIR spectra indicated a preferential local coordination between Li+ and ester carbonyl oxygen atoms in the P(TMC20CL80) co-polymer SPE. Diffusion NMR revealed that the co-polymer SPE also displays higher ion mobilities than PTMC. For both systems, locally oriented polymer domains, a few hundred nanometers in size and with limited connections between them, were inferred from the NMR spin relaxation and diffusion data. Potentiostatic polarization experiments revealed notably higher cationic transference numbers in the polycarbonate based SPEs as compared to conventional polyether based SPEs. In addition, MD simulations provided atomic-scale insight into the structure-dynamics properties, including confirmation of a preferential Li+-carbonyl oxygen atom coordination, with a preference in coordination to the ester based monomers. A coupling of the Li-ion dynamics to the polymer chain dynamics was indicated by both simulations and experiments.
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| 3. |
- 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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| 4. |
- Björk, Mats, 1960-, et al.
(författare)
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Methane emissions from macrophyte beach wrack on Baltic seashores
- 2023
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Ingår i: Ambio. - : Springer Nature. - 0044-7447 .- 1654-7209. ; 52:1, s. 171-181
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Tidskriftsartikel (refereegranskat)abstract
- Beach wrack of marine macrophytes is a natural component of many beaches. To test if such wrack emits the potent greenhouse gas methane, field measurements were made at different seasons on beach wrack depositions of different ages, exposure, and distance from the water. Methane emissions varied greatly, from 0 to 176 mg CH4-C m−2 day−1, with a clear positive correlation between emission and temperature. Dry wrack had lower emissions than wet. Using temperature data from 2016 to 2020, seasonal changes in fluxes were calculated for a natural wrack accumulation area. Such calculated average emissions were close to zero during winter, but peaked in summer, with very high emissions when daily temperatures exceeded 20 °C. We conclude that waterlogged beach wrack significantly contributes to greenhouse gas emissions and that emissions might drastically increase with increasing global temperatures. When beach wrack is collected into heaps away from the water, the emissions are however close to zero.
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| 5. |
- Guo, Y., et al.
(författare)
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Reversible Structural Isomerization of Nature's Water Oxidation Catalyst Prior to O-O Bond Formation
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:26, s. 11736-11747
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic water oxidation is catalyzed by a manganese-calcium oxide cluster, which experiences five "S-states" during a light-driven reaction cycle. The unique "distorted chair"-like geometry of the Mn4CaO5(6)cluster shows structural flexibility that has been frequently proposed to involve "open" and "closed"-cubane forms from the S1 to S3states. The isomers are interconvertible in the S1 and S2states, while in the S3state, the open-cubane structure is observed to dominate inThermosynechococcus elongatus (cyanobacteria) samples. In this work, using density functional theory calculations, we go beyond the S3+Yzstate to the S3nYz•→ S4+Yzstep, and report for the first time that the reversible isomerism, which is suppressed in the S3+Yzstate, is fully recovered in the ensuing S3nYz•state due to the proton release from a manganese-bound water ligand. The altered coordination strength of the manganese-ligand facilitates formation of the closed-cubane form, in a dynamic equilibrium with the open-cubane form. This tautomerism immediately preceding dioxygen formation may constitute the rate limiting step for O2formation, and exert a significant influence on the water oxidation mechanism in photosystem II.
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| 6. |
- Atai, F., et al.
(författare)
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Super-Macdonald Polynomials: Orthogonality and Hilbert Space Interpretation
- 2021
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Ingår i: Communications in Mathematical Physics. - : Springer Science and Business Media LLC. - 0010-3616 .- 1432-0916. ; 388:1, s. 435-468
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Tidskriftsartikel (refereegranskat)abstract
- The super-Macdonald polynomials, introduced by Sergeev andVeselov (Commun Math Phys 288: 653-675, 2009), generalise the Macdonald polynomials to (arbitrary numbers of) two kinds of variables, and they are eigenfunctions of the deformed Macdonald-Ruijsenaars operators introduced by the same authors in Sergeev and Veselov (CommunMath Phys 245: 249-278, 2004). We introduce a Hermitian form on the algebra spanned by the super-Macdonald polynomials, prove their orthogonality, compute their (quadratic) norms explicitly, and establish a corresponding Hilbert space interpretation of the super-Macdonald polynomials and deformed MacdonaldRuijsenaars operators. This allows for a quantum mechanical interpretation of the models defined by the deformedMacdonald-Ruijsenaars operators. Motivated by recent results in the nonrelativistic (q -> 1) case, we propose that these models describe the particles and anti-particles of an underlying relativistic quantum field theory, thus providing a natural generalisation of the trigonometric Ruijsenaars model.
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| 7. |
- Benn, J., et al.
(författare)
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Currents and Finite Elements as Tools for Shape Space
- 2019
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Ingår i: Journal of Mathematical Imaging and Vision. - : Springer Science and Business Media LLC. - 0924-9907 .- 1573-7683. ; 61:8, s. 1197-1220
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Tidskriftsartikel (refereegranskat)abstract
- The nonlinear spaces of shapes (unparameterized immersed curves or submanifolds) are of interest for many applications in image analysis, such as the identification of shapes that are similar modulo the action of some group. In this paper, we study a general representation of shapes as currents, which are based on linear spaces and are suitable for numerical discretization, being robust to noise. We develop the theory of currents for shape spaces by considering both the analytic and numerical aspects of the problem. In particular, we study the analytical properties of the current map and the norm that it induces on shapes. We determine the conditions under which the current determines the shape. We then provide a finite element-based discretization of the currents that is a practical computational tool for shapes. Finally, we demonstrate this approach on a variety of examples.
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| 8. |
- Cavalcante, Larissa Lopes, et al.
(författare)
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Analysis of fossil plant cuticles using vibrational spectroscopy: A new preparation protocol
- 2023
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Ingår i: Review of Palaeobotany and Palynology. - : Elsevier. - 0034-6667 .- 1879-0615. ; 316
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Tidskriftsartikel (refereegranskat)abstract
- Analyses for organic “fingerprints” on fossilized plant cuticles and pollen hold valuable chemotaxonomic and palaeoclimatic information, and are thus becoming more utilized by palaeobotanists. Plant cuticle and pollen composition are generally analyzed after standard treatments with several chemical reagents for mineral and mesophyll removal. However, the potential alterations on the fossil composition caused by the different cleaning reagents used are still poorly understood. We tested the effects of commonly used palaeobotanical processing methods on the spectra of fossilized cuticles from successions of Late Triassic to Early Jurassic age, including the gymnosperms Lepidopteris, Ginkgoites, Podozamites, Ptilozamites and Pterophyllum astartense. Our study shows that standard chemical processing caused chemical alterations that might lead to erroneous interpretation of the infrared (IR) spectra. The difference in pH caused by HCl induces changes in the proportion between the two bands at ~1720 and 1600 cm 1 (carboxylate and C-C stretch of aromatic compounds) indicating that the band at ~1610 cm 1 at least partially corresponds to carboxylate instead of C-C stretch of aromatic compounds. Interestingly, despite being used in high concentration, HF did not cause changes in the chemical composition of the cuticles. The most alarming changes were caused by the use of Schulze ’s solution, which resulted in the addition of both NO2 and (O)NO2 compounds in the cuticle. Consequently, a new protocol using H2CO3, HF, and H2O2 for preparing fossil plant cuticles aimed for chemical analyses is proposed, which provides an effective substitute to the conventional methods. In particular, a less aggressive and more sustainable alternative to Schulze’s solution is shown to be hydrogen peroxide, which causes only minor alteration of the fossil cuticle ’s chemical composition. Future work should carefully follow protocols, having in mind the impacts of different solutions used to treat leaves and other palaeobotanical material such as palynomorphs with aims to enable the direct comparison of spectra obtained in different studies.
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| 9. |
- da Cruz, Vinicius Vaz, et al.
(författare)
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Nuclear dynamics in resonant inelastic X-ray scattering and X-ray absorption of methanol
- 2019
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 150:23
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Tidskriftsartikel (refereegranskat)abstract
- We report on a combined theoretical and experimental study of core-excitation spectra of gas and liquid phase methanol as obtained with the use of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray scattering (RIXS). The electronic transitions are studied with computational methods that include strict and extended second-order algebraic diagrammatic construction [ADC(2) and ADC(2)-x], restricted active space second-order perturbation theory, and time-dependent density functional theory-providing a complete assignment of the near oxygen K-edge XAS. We show that multimode nuclear dynamics is of crucial importance for explaining the available experimental XAS and RIXS spectra. The multimode nuclear motion was considered in a recently developed "mixed representation" where dissociative states and highly excited vibrational modes are accurately treated with a time-dependent wave packet technique, while the remaining active vibrational modes are described using Franck-Condon amplitudes. Particular attention is paid to the polarization dependence of RIXS and the effects of the isotopic substitution on the RIXS profile in the case of dissociative core-excited states. Our approach predicts the splitting of the 2a RIXS peak to be due to an interplay between molecular and pseudo-atomic features arising in the course of transitions between dissociative core- and valence-excited states. The dynamical nature of the splitting of the 2a peak in RIXS of liquid methanol near pre-edge core excitation is shown. The theoretical results are in good agreement with our liquid phase measurements and gas phase experimental data available from the literature. (C) 2019 Author(s).
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| 10. |
- Emami, S. Noushin, et al.
(författare)
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A key malaria metabolite modulates vector blood seeking, feeding, and susceptibility to infection
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 355:6329
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Tidskriftsartikel (refereegranskat)abstract
- Malaria infection renders humans more attractive to Anopheles gambiae sensu lato mosquitoes than uninfected people. The mechanisms remain unknown. We found that an isoprenoid precursor produced by Plasmodium falciparum, (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), affects A. gambiae s. l. blood meal seeking and feeding behaviors as well as susceptibility to infection. HMBPP acts indirectly by triggering human red blood cells to increase the release of CO2, aldehydes, and monoterpenes, which together enhance vector attraction and stimulate vector feeding. When offered in a blood meal, HMBPP modulates neural, antimalarial, and oogenic gene transcription without affecting mosquito survival or fecundity; in a P. falciparum-infected blood meal, sporogony is increased.
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