| 1. |
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| 2. |
- Labit, B., et al.
(författare)
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Dependence on plasma shape and plasma fueling for small edge-localized mode regimes in TCV and ASDEX Upgrade
- 2019
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:8
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Tidskriftsartikel (refereegranskat)abstract
- © 2019 Institute of Physics Publishing. All rights reserved. Within the EUROfusion MST1 work package, a series of experiments has been conducted on AUG and TCV devices to disentangle the role of plasma fueling and plasma shape for the onset of small ELM regimes. On both devices, small ELM regimes with high confinement are achieved if and only if two conditions are fulfilled at the same time. Firstly, the plasma density at the separatrix must be large enough (ne,sep/nG ∼ 0.3), leading to a pressure profile flattening at the separatrix, which stabilizes type-I ELMs. Secondly, the magnetic configuration has to be close to a double null (DN), leading to a reduction of the magnetic shear in the extreme vicinity of the separatrix. As a consequence, its stabilizing effect on ballooning modes is weakened.
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| 3. |
- Pantazis, N, et al.
(författare)
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Determining the likely place of HIV acquisition for migrants in Europe combining subject-specific information and biomarkers data
- 2019
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Ingår i: Statistical methods in medical research. - : SAGE Publications. - 1477-0334 .- 0962-2802. ; 28:7, s. 1979-1997
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Tidskriftsartikel (refereegranskat)abstract
- In most HIV-positive individuals, infection time is only known to lie between the time an individual started being at risk for HIV and diagnosis time. However, a more accurate estimate of infection time is very important in certain cases. For example, one of the objectives of the Advancing Migrant Access to Health Services in Europe (aMASE) study was to determine if HIV-positive migrants, diagnosed in Europe, were infected pre- or post-migration. We propose a method to derive subject-specific estimates of unknown infection times using information from HIV biomarkers’ measurements, demographic, clinical, and behavioral data. We assume that CD4 cell count (CD4) and HIV-RNA viral load trends after HIV infection follow a bivariate linear mixed model. Using post-diagnosis CD4 and viral load measurements and applying the Bayes’ rule, we derived the posterior distribution of the HIV infection time, whereas the prior distribution was informed by AIDS status at diagnosis and behavioral data. Parameters of the CD4–viral load and time-to-AIDS models were estimated using data from a large study of individuals with known HIV infection times (CASCADE). Simulations showed substantial predictive ability (e.g. 84% of the infections were correctly classified as pre- or post-migration). Application to the aMASE study ( n = 2009) showed that 47% of African migrants and 67% to 72% of migrants from other regions were most likely infected post-migration. Applying a Bayesian method based on bivariate modeling of CD4 and viral load, and subject-specific information, we found that the majority of HIV-positive migrants in aMASE were most likely infected after their migration to Europe.
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| 4. |
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| 5. |
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| 6. |
- Abudurexiti, A, et al.
(författare)
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Taxonomy of the order Bunyavirales: update 2019
- 2019
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Ingår i: Archives of virology. - : Springer Science and Business Media LLC. - 1432-8798 .- 0304-8608. ; 164:7, s. 1949-1965
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Tidskriftsartikel (refereegranskat)
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| 7. |
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Pellinen, T, et al.
(författare)
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ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer
- 2018
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8:1, s. 2338-
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Tidskriftsartikel (refereegranskat)abstract
- Caveolin-1 (CAV1) is over-expressed in prostate cancer (PCa) and is associated with adverse prognosis, but the molecular mechanisms linking CAV1 expression to disease progression are poorly understood. Extensive gene expression correlation analysis, quantitative multiplex imaging of clinical samples, and analysis of the CAV1-dependent transcriptome, supported that CAV1 re-programmes TGFβ signalling from tumour suppressive to oncogenic (i.e. induction of SLUG, PAI-1 and suppression of CDH1, DSP, CDKN1A). Supporting such a role, CAV1 knockdown led to growth arrest and inhibition of cell invasion in prostate cancer cell lines. Rationalized RNAi screening and high-content microscopy in search for CAV1 upstream regulators revealed integrin beta1 (ITGB1) and integrin associated proteins as CAV1 regulators. Our work suggests TGFβ signalling and beta1 integrins as potential therapeutic targets in PCa over-expressing CAV1, and contributes to better understand the paradoxical dual role of TGFβ in tumour biology.
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| 12. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 13. |
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| 14. |
- Milani, Diogo, et al.
(författare)
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Satellite DNAs Unveil Clues about the Ancestry and Composition of B Chromosomes in Three Grasshopper Species
- 2018
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 9:11
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Tidskriftsartikel (refereegranskat)abstract
- Supernumerary (B) chromosomes are dispensable genomic elements occurring frequently among grasshoppers. Most B chromosomes are enriched with repetitive DNAs, including satellite DNAs (satDNAs) that could be implicated in their evolution. Although studied in some species, the specific ancestry of B chromosomes is difficult to ascertain and it was determined in only a few examples. Here we used bioinformatics and cytogenetics to characterize the composition and putative ancestry of B chromosomes in three grasshopper species, Rhammatocerus brasiliensis, Schistocerca rubiginosa, and Xyleus discoideus angulatus. Using the RepeatExplorer pipeline we searched for the most abundant satDNAs in Illumina sequenced reads, and then we generated probes used in fluorescent in situ hybridization (FISH) to determine chromosomal position. We used this information to infer ancestry and the events that likely occurred at the origin of B chromosomes. We found twelve, nine, and eighteen satDNA families in the genomes of R. brasiliensis, S. rubiginosa, and X. d. angulatus, respectively. Some satDNAs revealed clustered organization on A and B chromosomes varying in number of sites and position along chromosomes. We did not find specific satDNA occurring in the B chromosome. The satDNAs shared among A and B chromosomes support the idea of putative intraspecific ancestry from small autosomes in the three species, i.e., pair S11 in R. brasiliensis, pair S9 in S. rubiginosa, and pair S10 in X. d. angulatus. The possibility of involvement of other chromosomal pairs in B chromosome origin is also hypothesized. Finally, we discussed particular aspects in composition, origin, and evolution of the B chromosome for each species.
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| 15. |
- Agić, Heda, 1989-, et al.
(författare)
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Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway
- 2019
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstatten.
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| 16. |
- Cerveny, S., et al.
(författare)
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Evidence of Coupling between the Motions of Water and Peptides
- 2016
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 7:20, s. 4093-4098
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Tidskriftsartikel (refereegranskat)abstract
- Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid L-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins. This implies that the crucial role of water for protein dynamics can be extended to other types of macromolecular systems, where water is also able to determine their conformational fluctuations. Using the energy landscape picture of macromolecules, the thermodynamic criterion for such solvent-slaved macromolecular motions may be that the macromolecules need the entropy contribution from the solvent to overcome the enthalpy barriers between different conformational substates.
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| 17. |
- Combarro Palacios, Izaskun, et al.
(författare)
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Motions of water and solutes-Slaving versus plasticization phenomena
- 2019
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 1089-7690 .- 0021-9606. ; 150:12
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Tidskriftsartikel (refereegranskat)abstract
- It is well-accepted that hydration water is crucial for the structure, dynamics, and function of proteins. However, the exact role of water for the motions and functions of proteins is still debated. Experiments have shown that protein and water dynamics are strongly coupled but with water motions occurring on a considerably faster time scale (the so-called slaving behavior). On the other hand, water also reduces the conformational entropy of proteins and thereby acts as a plasticizer of them. In this work, we analyze the dynamics (using broadband dielectric spectroscopy) of some specific non-biological water solutions in a broad concentration range to elucidate the role of water in the dynamics of the solutes. Our results demonstrate that at low water concentrations (less than 5 wt. %), the plasticization phenomenon prevails for all the materials analyzed. However, at higher water concentrations, two different scenarios can be observed: the slaving phenomenon or plasticization, depending on the solute analyzed. These results generalize the slaving phenomenon to some, but not all, non-biological solutions and allow us to analyze the key factors for observing the slaving behavior in protein solutions as well as to reshaping the slaving concept.
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| 18. |
- Esteso, V., et al.
(författare)
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Trapping of Gas Bubbles in Water at a Finite Distance below a Water-Solid Interface
- 2019
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 35:12, s. 4218-4223
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Tidskriftsartikel (refereegranskat)abstract
- Gas bubbles in a water-filled cavity move upward because of buoyancy. Near the roof, additional forces come into play, such as Lifshitz, double layer, and hydrodynamic forces. Below uncharged metallic surfaces, repulsive Lifshitz forces combined with buoyancy forces provide a way to trap micrometer-sized bubbles. We demonstrate how bubbles of this size can be stably trapped at experimentally accessible distances, the distances being tunable with the surface material. By contrast, large bubbles (≥100 μm) are usually pushed toward the roof by buoyancy forces and adhere to the surface. Gas bubbles with radii ranging from 1 to 10 μm can be trapped at equilibrium distances from 190 to 35 nm. As a model for rock, sand grains, and biosurfaces, we consider dielectric materials such as silica and polystyrene, whereas aluminium, gold, and silver are the examples of metal surfaces. Finally, we demonstrate that the presence of surface charges further strengthens the trapping by inducing ion adsorption forces.
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| 19. |
- Grundstrom, M., et al.
(författare)
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Oak pollen seasonality and severity across Europe and modelling the season start using a generalized phenological model
- 2019
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 663, s. 527-536
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Tidskriftsartikel (refereegranskat)abstract
- Oak pollen seasons are relatively unexplored in large parts of Europe despite producing allergens and being a common tree in both continental and northern parts. Many studies are concentrated only on the Iberian Peninsula. In this study, the seasonal pattern of oak pollen in Europe was analysed using 10 observation sites, ranging from Spain to Sweden. The magnitude of peaks and annual pollen integral together with season-length were studied and substantially higher pollen levels and longer seasons were found in Spain. Two northern sites in Denmark and Sweden showed high oak pollen peaks together with two sites in Spain and United Kingdom. The study also tested four common definitions of season start and applied a generalized phenological model for computing the start of the pollen season. The most accurate definition for a European-wide description of the observed oak pollen start was when the cumulative daily average pollen count reached 50 grains per cubic meter. For the modelling of the start a thermal time method based on Growing Degree Day (GDD) was implemented, utilizing daily temperatures and a generalized approach to identify model parameters applicable to all included sites. GDD values varied between sites and generally followed a decreasing gradient from south to north, with some exceptions. Modelled onsets with base temperatures below 7 degrees C matched well with observed onsets and 76% of the predictions differed <= 4 days compared to observed onsets when using a base temperature of 2 degrees C. Base temperatures above 7 degrees C frequently predicted onsets differing >1 week from the observed. This general approach can be extended to a larger area where pollen observations are non-existent. The presented work will increase the understanding of oak pollen variation in Europe and provide knowledge of its phenology, which is a critical aspect both for modelling purposes on large-scale and assessing the human exposure to oak allergens. (C) 2019 The Authors. Published by Elsevier B.V.
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| 20. |
- Jensen, Soren, et al.
(författare)
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New occurrences of Palaeopascichnus from the Stahpogieddi Formation, Arctic Norway, and their bearing on the age of the Varanger Ice Age
- 2018
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Ingår i: Canadian journal of earth sciences (Print). - : CANADIAN SCIENCE PUBLISHING, NRC RESEARCH PRESS. - 0008-4077 .- 1480-3313. ; 55:11, s. 1253-1261
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Tidskriftsartikel (refereegranskat)abstract
- We report on new occurrences of the late Ediacaran problematicum Palaeopascichnus (Protista?) from the Stahpogieddi Formation, Arctic Norway. The stratigraphically lowest occurrences are in beds transitional between the Lillevannet and Indreelva members: the highest in the second cycle of the Manndrapselva Member, stratigraphically close to the lowest occurrences of Cambrian-type trace fossils. This establishes a long stratigraphical range of Palaeopascichnus on the Digermulen Peninsula, as has been previously documented from Newfoundland, South Australia, and elsewhere in Baltica. The age range of Palaeopascichnus in Avalonia and Baltica is from similar to 565 to 541 Ma. Since the transition from the Mortensnes Formation to the Stahpogieddi Formation is without a major break in sedimentation, this supports the inference that the underlying glacigenic Mortensnes Formation is ca. 580 Ma, and therefore Gaskiers-equivalent, or younger.
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| 21. |
- Jensen, Soren, et al.
(författare)
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Scratch circles from the Ediacaran and Cambrian of Arctic Norway and southern Africa, with a review of scratch circle occurrences
- 2018
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Ingår i: Bulletin of Geosciences. - : CZECH GEOLOGICAL SURVEY. - 1214-1119 .- 1802-8225. ; 93:3, s. 287-304
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Forskningsöversikt (refereegranskat)abstract
- Scratch circles - bedding plane parallel sedimentary structures formed by the passive rotation of a tethered organism into the surrounding sediment - are relatively rare in the geological record. Here new occurrences of scratch circles are described from the Ediacaran-Cambrian Stahpogieddi Formation, Digermulen Peninsula, Arctic Norway, and from the Ediacaran Nudaus and Urusis formations, Nama Group, of southern Africa. A literature survey confirms a previously noted concentration of scratch circles reported from shallow marine upper Ediacaran-lower Cambrian and paralic Carboniferous rocks. Scratch circle identification and nomenclature are discussed. The stratigraphical range of the trace fossils Treptichnus pedum and Gyrolithes isp. in the Stahpogieddi Formation are extended downward. Combined with earlier reports of Harlaniella podolica this adds new precision to the placement of the Ediacaran-Cambrian boundary on the Digermulen Peninsula.
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| 22. |
- Meinhold, Guido, et al.
(författare)
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First record of carbonates with spherulites and cone-in-cone structures from the Precambrian of Arctic Norway, and their palaeoenvironmental significance
- 2019
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Ingår i: Precambrian Research. - : Elsevier BV. - 0301-9268 .- 1872-7433. ; 328, s. 99-110
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Tidskriftsartikel (refereegranskat)abstract
- We report for the first time carbonates from the upper Ediacaran sedimentary succession of Finnmark, Arctic Norway. Carbonates occur as calcareous siliciclastic beds, lenses, and concretions, some with calcite spherulites and cone-in-cone (CIC) calcite, in a mudrock to fine-grained sandstone succession from approximately 3 m to 26 m above the base of the 2nd cycle of the Manndrapselva Member of the Stahpogieddi Formation (Vestertana Group). They occur c. 40 m below the Ediacaran-Cambrian boundary, which is well defined by trace fossils. Thin-section petrography and scanning micro X-ray fluorescence elemental mapping reveal a layered composition of the calcareous sedimentary rocks. In some of those, well-developed nested cones of CIC calcite form the outer layer. Thin clay coatings outline individual cones. The inner layers are composed of (1) carbonate with calcite spherulites (grainstone) and (2) thinly laminated fine-grained calcareous siliciclastics (mudstone and wackestone) indicated by elevated concentrations of Al, Si, Fe, and Ti. The inner siliciclastic layers contain framboidal pyrite and probably organic matter. Formation of calcite spherulites took place probably at the sediment-water interface either in a coastal littoral environment or in situ in the sublittoral zone under high alkaline conditions whereas CIC calcite formed during burial diagenesis and clearly in pre-Caledonian time before metamorphism and cleavage formation. This new record of carbonates with calcite spherulites and CIC structures from the Ediacaran of Arctic Norway adds to their rare occurrences in the geological record.
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| 23. |
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| 24. |
- Seinfeld, S., et al.
(författare)
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Influence of music on anxiety induced by fear of heights in virtual reality
- 2016
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Ingår i: Frontiers in Psychology. - : Frontiers Research Foundation. - 1664-1078. ; 6:JAN
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Tidskriftsartikel (refereegranskat)abstract
- Music is a potent mood regulator that can induce relaxation and reduce anxiety in different situations. While several studies demonstrate that certain types of music have a subjective anxiolytic effect, the reported results from physiological responses are less conclusive. Virtual reality allows us to study diverse scenarios of real life under strict experimental control while preserving high ecological validity. We aimed to study the modulating effect of music on the anxiety responses triggered by an immersive virtual reality scenario designed to induce fear of heights. Subjects experienced a virtual scenario depicting an exterior elevator platform ascending and descending the total height of its 350 meters tall supporting structure. Participants were allocated to either a group that experienced the elevator ride with background music or without, in a between-groups design. Furthermore, each group included participants with different degrees of fear of heights, ranging from low to high fear. Recordings of heart rate, galvanic skin response, body balance, and head movements were obtained during the experiments. Subjective anxiety was measured by means of three questionnaires. The scenario produced significant changes in subjective and physiological measures, confirming its efficacy as a stressor. A significant increase in state anxiety was found between pre and post-assessment in the silence group, but not in the music group, indicating that post-stress recovery was faster in the musical group. Results suggest that music can ameliorate the subjective anxiety produced by fear of heights.
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| 25. |
- Stewart, Joshua D., et al.
(författare)
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Research Priorities to Support Effective Manta and Devil Ray Conservation
- 2018
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 5, s. 1-27
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Forskningsöversikt (refereegranskat)abstract
- Manta and devil rays are filter-feeding elasmobranchs that are found circumglobally in tropical and subtropical waters. Although relatively understudied for most of the Twentieth century, public awareness and scientific research on these species has increased dramatically in recent years. Much of this attention has been in response to targeted fisheries, international trade in mobulid products, and a growing concern over the fate of exploited populations. Despite progress in mobulid research, major knowledge gaps still exist, hindering the development of effective management and conservation strategies. We assembled 30 leaders and emerging experts in the fields of mobulid biology, ecology, and conservation to identify pressing knowledge gaps that must be filled to facilitate improved science-based management of these vulnerable species. We highlight focal research topics in the subject areas of taxonomy and diversity, life history, reproduction and nursery areas, population trends, bycatch and fisheries, spatial dynamics and movements, foraging and diving, pollution and contaminants, and sub-lethal impacts. Mobulid rays remain a poorly studied group, and therefore our list of important knowledge gaps is extensive. However, we hope that this identification of high priority knowledge gaps will stimulate and focus future mobulid research.
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| 26. |
- Ueda, Kiyoshi, et al.
(författare)
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Roadmap on photonic, electronic and atomic collision physics : I. Light-matter interaction
- 2019
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Ingår i: Journal of Physics B. - : IOP PUBLISHING LTD. - 0953-4075 .- 1361-6455. ; 52:17
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Tidskriftsartikel (refereegranskat)abstract
- We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. In Roadmap I, we focus on the light-matter interaction. In this area, studies of ultrafast electronic and molecular dynamics have been rapidly growing, with the advent of new light sources such as attosecond lasers and x-ray free electron lasers. In parallel, experiments with established synchrotron radiation sources and femtosecond lasers using cutting-edge detection schemes are revealing new scientific insights that have never been exploited. Relevant theories are also being rapidly developed. Target samples for photon-impact experiments are expanding from atoms and small molecules to complex systems such as biomolecules, fullerene, clusters and solids. This Roadmap aims to look back along the road, explaining the development of these fields, and look forward, collecting contributions from twenty leading groups from the field.
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