| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
- Abel, I, et al.
(author)
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Overview of the JET results with the ITER-like wall
- 2013
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In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10, s. 104002-
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Journal article (peer-reviewed)abstract
- Following the completion in May 2011 of the shutdown for the installation of the beryllium wall and the tungsten divertor, the first set of JET campaigns have addressed the investigation of the retention properties and the development of operational scenarios with the new plasma-facing materials. The large reduction in the carbon content (more than a factor ten) led to a much lower Z(eff) (1.2-1.4) during L- and H-mode plasmas, and radiation during the burn-through phase of the plasma initiation with the consequence that breakdown failures are almost absent. Gas balance experiments have shown that the fuel retention rate with the new wall is substantially reduced with respect to the C wall. The re-establishment of the baseline H-mode and hybrid scenarios compatible with the new wall has required an optimization of the control of metallic impurity sources and heat loads. Stable type-I ELMy H-mode regimes with H-98,H-y2 close to 1 and beta(N) similar to 1.6 have been achieved using gas injection. ELM frequency is a key factor for the control of the metallic impurity accumulation. Pedestal temperatures tend to be lower with the new wall, leading to reduced confinement, but nitrogen seeding restores high pedestal temperatures and confinement. Compared with the carbon wall, major disruptions with the new wall show a lower radiated power and a slower current quench. The higher heat loads on Be wall plasma-facing components due to lower radiation made the routine use of massive gas injection for disruption mitigation essential.
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| 4. |
- Romanelli, F, et al.
(author)
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Overview of the JET results
- 2011
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In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 51:9
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Journal article (peer-reviewed)abstract
- Since the last IAEA Conference JET has been in operation for one year with a programmatic focus on the qualification of ITER operating scenarios, the consolidation of ITER design choices and preparation for plasma operation with the ITER-like wall presently being installed in JET. Good progress has been achieved, including stationary ELMy H-mode operation at 4.5 MA. The high confinement hybrid scenario has been extended to high triangularity, lower ρ*and to pulse lengths comparable to the resistive time. The steady-state scenario has also been extended to lower ρ*and ν*and optimized to simultaneously achieve, under stationary conditions, ITER-like values of all other relevant normalized parameters. A dedicated helium campaign has allowed key aspects of plasma control and H-mode operation for the ITER non-activated phase to be evaluated. Effective sawtooth control by fast ions has been demonstrated with3He minority ICRH, a scenario with negligible minority current drive. Edge localized mode (ELM) control studies using external n = 1 and n = 2 perturbation fields have found a resonance effect in ELM frequency for specific q95values. Complete ELM suppression has, however, not been observed, even with an edge Chirikov parameter larger than 1. Pellet ELM pacing has been demonstrated and the minimum pellet size needed to trigger an ELM has been estimated. For both natural and mitigated ELMs a broadening of the divertor ELM-wetted area with increasing ELM size has been found. In disruption studies with massive gas injection up to 50% of the thermal energy could be radiated before, and 20% during, the thermal quench. Halo currents could be reduced by 60% and, using argon/deuterium and neon/deuterium gas mixtures, runaway electron generation could be avoided. Most objectives of the ITER-like ICRH antenna have been demonstrated; matching with closely packed straps, ELM resilience, scattering matrix arc detection and operation at high power density (6.2 MW m-2) and antenna strap voltages (42 kV). Coupling measurements are in very good agreement with TOPICA modelling. © 2011 IAEA, Vienna.
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| 5. |
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| 6. |
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| 7. |
- Downey, Harriet, et al.
(author)
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Training future generations to deliver evidence-based conservation and ecosystem management
- 2021
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In: Ecological Solutions and Evidence. - : Wiley. - 2688-8319. ; 2:1
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Research review (peer-reviewed)abstract
- 1. To be effective, the next generation of conservation practitioners and managers need to be critical thinkers with a deep understanding of how to make evidence-based decisions and of the value of evidence synthesis.2. If, as educators, we do not make these priorities a core part of what we teach, we are failing to prepare our students to make an effective contribution to conservation practice.3. To help overcome this problem we have created open access online teaching materials in multiple languages that are stored in Applied Ecology Resources. So far, 117 educators from 23 countries have acknowledged the importance of this and are already teaching or about to teach skills in appraising or using evidence in conservation decision-making. This includes 145 undergraduate, postgraduate or professional development courses.4. We call for wider teaching of the tools and skills that facilitate evidence-based conservation and also suggest that providing online teaching materials in multiple languages could be beneficial for improving global understanding of other subject areas.
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| 8. |
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| 9. |
- Godhe, Anna, 1967, et al.
(author)
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Intercalibration of classical and molecular techniques for identification of Alexandrium fundyense (Dinophyceae) and estimation of cell densities
- 2007
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In: Harmful Algae. - : Elsevier BV. - 1568-9883. ; 6:1, s. 56-72
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Journal article (peer-reviewed)abstract
- A workshop with the aim to compare classical and molecular techniques for phytoplankton enumeration took place at Kristineberg Marine Research Station, Sweden, in August 2005. Seventeen different techniques - nine classical microscopic-based and eight molecular methods - were compared. Alexandrium fundyense was the target organism in four experiments. Experiment 1 was designed to determine the range of cell densities over which the methods were applicable. Experiment 2 tested the species specificity of the methods by adding Alexandrium ostenfeldii, to samples containing A. fundyense. Experiments 3 and 4 tested the ability of the methods to detect the target organism within a natural phytoplankton community. Most of the methods could detect cells at the lowest concentration tested, 100 cells L-1, but the variance was high for methods using small volumes, such as counting chambers and slides. In general, the precision and reproducibility of the investigated methods increased with increased target cell concentration. Particularly molecular methods were exceptions in that their relative standard deviation did not vary with target cell concentration. Only two of the microscopic methods and three of the molecular methods had a significant linear relationship between their cell count estimates and the A. fundyense concentration in experiment 2, where the objective was to discriminate that species from a morphologically similar and genetically closely related species. None of the investigated methods were affected by the addition of a natural plankton community background matrix in experiment 3. The results of this study are discussed in the context of previous intercomparisons and the difficulties in defining the absolute, true target cell concentration. (c) 2006 Elsevier B.V. All rights reserved.
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| 10. |
- Salfity, M.F., et al.
(author)
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Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimensional phase unwrapping algorithms
- 2006
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In: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 3:8, s. 415-427
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Journal article (peer-reviewed)abstract
- Phase contrast magnetic resonance velocity imaging is a powerful technique for quantitative in vivo blood flow measurement. Current practice normally involves restricting the sensitivity of the technique so as to avoid the problem of the measured phase being 'wrapped' onto the range - π to + π. However, as a result, dynamic range and signal-to-noise ratio are sacrificed. Alternatively, the true phase values can be estimated by a phase unwrapping process which consists of adding integral multiples of 2π to the measured wrapped phase values. In the presence of noise and data undersampling, the phase unwrapping problem becomes non-trivial. In this paper, we investigate the performance of three different phase unwrapping algorithms when applied to three-dimensional (two spatial axes and one time axis) phase contrast datasets. A simple one-dimensional temporal unwrapping algorithm, a more complex and robust three-dimensional unwrapping algorithm and a novel velocity encoding unwrapping algorithm which involves unwrapping along a fourth dimension (the 'velocity encoding' direction) are discussed, and results from the three are presented and compared. It is shown that compared to the traditional approach, both dynamic range and signal-to-noise ratio can be increased by a factor of up to five times, which demonstrates considerable promise for a possible eventual clinical implementation. The results are also of direct relevance to users of any other technique delivering time-varying two-dimensional phase images, such as dynamic speckle interferometry and synthetic aperture radar
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| 11. |
- Waddell, Shona J., et al.
(author)
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Biomimetic oyster shell-replicated topography alters the behaviour of human skeletal stem cells
- 2018
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In: Journal of Tissue Engineering. - : Sage Publications. - 2041-7314. ; 9
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Journal article (peer-reviewed)abstract
- The regenerative potential of skeletal stem cells provides an attractive prospect to generate bone tissue needed for musculoskeletal reparation. A central issue remains efficacious, controlled cell differentiation strategies to aid progression of cell therapies to the clinic. The nacre surface from Pinctada maxima shells is known to enhance bone formation. However, to date, there is a paucity of information on the role of the topography of P. maxima surfaces, nacre and prism. To investigate this, nacre and prism topographical features were replicated onto polycaprolactone and skeletal stem cell behaviour on the surfaces studied. Skeletal stem cells on nacre surfaces exhibited an increase in cell area, increase in expression of osteogenic markers ALP (p<0.05) and OCN (p<0.01) and increased metabolite intensity (p<0.05), indicating a role of nacre surface to induce osteogenic differentiation, while on prism surfaces, skeletal stem cells did not show alterations in cell area or osteogenic marker expression and a decrease in metabolite intensity (p<0.05), demonstrating a distinct role for the prism surface, with the potential to maintain the skeletal stem cell phenotype.
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| 12. |
- Alakpa, Enateri V., et al.
(author)
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The Prismatic Topography of Pinctada maxima Shell Retains Stem Cell Multipotency and Plasticity In Vitro
- 2018
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In: Advanced Biosystems. - : WILEY-V C H VERLAG GMBH. - 2366-7478. ; 2:6
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Journal article (peer-reviewed)abstract
- The shell of the bivalve mollusc Pinctada maxima is composed of the calcium carbonate polymorphs calcite and aragonite (nacre). Mother-of-pearl, or nacre, induces vertebrate cells to undergo osteogenesis and has good osteointegrative qualities in vivo. The calcite counterpart, however, is less researched in terms of the response of vertebrate cells. This study shows that isolation of calcite surface topography from the inherent chemistry allows viable long-term culture of bone marrow derived mesenchymal stem cells (MSCs). Self-renewal is evident from the increased gene expression of the self-renewal markers CD63, CD166, and CD271 indicating that cells cultured on the calcite topography maintain their stem cell phenotype. MSCs also retain their multipotency and can undergo successful differentiation into osteoblasts and adipocytes. When directed to adipogenesis, MSCs cultured on prism replicas are more amenable to differentiation than MSCs cultured on tissue culture polystyrene indicating a higher degree of plasticity in MSCs growing on calcite P. maxima prismatic topography. The study highlights the potential of the calcite topography of P. maxima as a biomimetic design for supporting expansion of MSC populations in vitro, which is of fundamental importance if it meets the demands for autologous MSCs for therapeutic use.
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| 13. |
- Andric, Fanny, et al.
(author)
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Immune Microenvironment in Sporadic Early-Onset versus Average-Onset Colorectal Cancer
- 2023
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In: Cancers. - : MDPI AG. - 2072-6694. ; 15:5
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Journal article (peer-reviewed)abstract
- Simple Summary The incidence of non-hereditary cancer in the left colon and rectum is increasing in young patients worldwide for unknown reasons. To understand this phenomenon, the biology of early-onset colorectal cancer needs to be established. Here, we investigated the immune response to tumors by selecting a highly representative group of patients younger than 45 years matched to those aged 70-75 years, excluding hereditary cases. Both T-cell distribution in tumors and expression of 770 immune-related genes were overall similar between the groups. The findings suggest that the immune response in cancer of the left colon and rectum is not dependent on age and that early-onset colorectal cancer is likely not related to immune response deficiencies. The incidence of left-sided colon and rectal cancer in young people are increasing worldwide, but its causes are poorly understood. It is not clear if the tumor microenvironment is dependent on age of onset, and little is known about the composition of tumor-infiltrating T cells in early-onset colorectal cancer (EOCRC). To address this, we investigated T-cell subsets and performed gene expression immune profiling in sporadic EOCRC tumors and matched average-onset colorectal cancer (AOCRC) tumors. Left-sided colon and rectal tumors from 40 cases were analyzed; 20 EOCRC (<45 years) patients were matched 1:1 to AOCRC (70-75 years) patients by gender, tumor location, and stage. Cases with germline pathogenic variants, inflammatory bowel disease or neoadjuvant-treated tumors were excluded. For T cells in tumors and stroma, a multiplex immunofluorescence assay combined with digital image analysis and machine learning algorithms was used. Immunological mediators in the tumor microenvironment were assessed by NanoString gene expression profiling of mRNA. Immunofluorescence revealed no significant difference between EOCRC and AOCRC with regard to infiltration of total T cells, conventional CD4(+) and CD8(+) T cells, regulatory T cells, or gamma delta T cells. Most T cells were located in the stroma in both EOCRC and AOCRC. Immune profiling by gene expression revealed higher expression in AOCRC of the immunoregulatory cytokine IL-10, the inhibitory NK cell receptors KIR3DL3 and KLRB1 (CD161), and IFN-a7 (IFNA7). In contrast, the interferon-induced gene IFIT2 was more highly expressed in EOCRC. However, in a global analysis of 770 tumor immunity genes, no significant differences could be detected. T-cell infiltration and expression of inflammatory mediators are similar in EOCRC and AOCRC. This may indicate that the immune response to cancer in left colon and rectum is not related to age of onset and that EOCRC is likely not driven by immune response deficiency.
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| 14. |
- Cusack, Daniela Francis, et al.
(author)
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Tradeoffs and Synergies in Tropical Forest Root Traits and Dynamics for Nutrient and Water Acquisition : Field and Modeling Advances
- 2021
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In: Frontiers in Forests and Global Change. - : Frontiers Media S.A.. - 2624-893X. ; 4
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Research review (peer-reviewed)abstract
- Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.
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| 15. |
- Cusack, Jeremy J., et al.
(author)
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Measuring the intensity of conflicts in conservation
- 2021
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In: Conservation Letters. - : John Wiley & Sons. - 1755-263X. ; 14:3
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Journal article (peer-reviewed)abstract
- Conflicts between the interests of biodiversity conservation and other human activities pose a major threat to natural ecosystems and human well-being, yet few methods exist to quantify their intensity and model their dynamics. We develop a categorization of conflict intensity based on the curve of conflict, a model originally used to track the escalation and deescalation of armed conflicts. Our categorization assigns six intensity levels reflecting the discourse and actions of stakeholders involved in a given conflict, from coexistence or collaboration to physical violence. Using a range of case studies, we demonstrate the value of our approach in quantifying conflict trends, estimating transition probabilities between conflict stages, and modeling conflict intensity as a function of relevant covariates. By taking an evidence-based approach to quantifying stakeholder behavior, the proposed framework allows for a better understanding of the drivers of conservation conflict development across a diverse range of socioecological scenarios.
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| 16. |
- Cusack, M., et al.
(author)
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Relic aragonite from Ordovician-Silurian brachiopods : Implications for the evolution of calcification
- 2011
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In: Geotechnique. - 0016-8505 .- 1751-7656. ; 39:10, s. 967-970
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Journal article (peer-reviewed)abstract
- Understanding the influence of aragonite/calcite sea conditions on the evolution of biocalcification relies strongly on the correct interpretation of the original composition of calcareous taxa. Aragonite dissolves or inverts into calcite over geological time, and its preservation is currently unknown to predate the Pennsylvanian. Here we present direct evidence for the common occurrence of relic aragonite in Ordovician and Silurian trimerellid brachiopods, thereby extending the known range of aragonite preservation by more than 130 million years. Together with associated hypercalcifying taxa of putatively original aragonite or high-magnesium calcite composition and considerations of the temperature dependence of aragonite and calcite precipitation, our results suggest that the evolution of aragonite biomineralization might have presented an adaptive advantage in shallow marine tropical waters of calcite seas. A targeted search for Paleozoic aragonite should both resolve the original composition of consistently recrystallized taxa and enable the reassessment of the aragonite/calcite sea paradigm in a paleoenvironmental context.
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| 17. |
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| 18. |
- Marklund, Olov, et al.
(author)
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Robust unwrapping algorithm for 3-D phase volumes of arbitrary shape containing knotted phase singularity loops
- 2005
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Reports (other academic/artistic)abstract
- The extension of path-independent 2-D phase unwrapping algorithms, based on placement of branch cut lines between phase singularities of opposite sign, was recently proposed for phase volumes in a recent paper by Huntley. In 3-D the singularities were shown to form closed loops and path-independence was achieved by placing branch cut surfaces across the loops. In the current paper we describe in detail an optimised and extended version of Huntley's algorithm. This deals in particular with two aspects which are essential for practical phase volumes: (1) how to close partial loops which pass through arbitrary boundaries separating valid and invalid phase data, and (2) how to select the set of loops having shortest length. The second algorithm is necessary to deal with the ambiguous cases that can arise when the singularities form knots, i.e. two loops pass through a single phase volume element. The perfomance of the algorithm is demonstrated on 3-D phase maps from two types of medical imaging data: MRI and x-ray interferometry.
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| 19. |
- Sukuru, Sai Chetan K, et al.
(author)
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Discovering new classes of Brugia malayi asparaginyl-tRNA synthetase inhibitors and relating specificity to conformational change.
- 2006
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In: Journal of computer-aided molecular design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 20:3, s. 159-78
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Journal article (peer-reviewed)abstract
- SLIDE software, which models the flexibility of protein and ligand side chains while docking, was used to screen several large databases to identify inhibitors of Brugia malayi asparaginyl-tRNA synthetase (AsnRS), a target for anti-parasitic drug design. Seven classes of compounds identified by SLIDE were confirmed as micromolar inhibitors of the enzyme. Analogs of one of these classes of inhibitors, the long side-chain variolins, cannot bind to the adenosyl pocket of the closed conformation of AsnRS due to steric clashes, though the short side-chain variolins identified by SLIDE apparently bind isosterically with adenosine. We hypothesized that an open conformation of the motif 2 loop also permits the long side-chain variolins to bind in the adenosine pocket and that their selectivity for Brugia relative to human AsnRS can be explained by differences in the sequence and conformation of this loop. Loop flexibility sampling using Rigidity Optimized Conformational Kinetics (ROCK) confirms this possibility, while scoring of the relative affinities of the different ligands by SLIDE correlates well with the compounds' ranks in inhibition assays. Combining ROCK and SLIDE provides a promising approach for exploiting conformational flexibility in structure-based screening and design of species selective inhibitors.
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