| 1. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
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| 3. |
- Rhodes, Olin E., et al.
(author)
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Integration of ecosystem science into radioecology : A consensus perspective
- 2020
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 740
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Journal article (peer-reviewed)abstract
- In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.
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| 4. |
- Bastos, Carlos A.P., et al.
(author)
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Copper nanoparticles have negligible direct antibacterial impact
- 2020
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In: NanoImpact. - : Elsevier BV. - 2452-0748. ; 17
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Journal article (peer-reviewed)abstract
- Introduction: Soluble copper that can be acquired by bacteria is toxic and therefore antimicrobial. Whether nanostructured copper materials, in either disperse or agglomerated form, have antimicrobial impact, aside from that of their dissolution products, is not clear and was herein addressed. Methods: We took five nanostructured copper materials, two metallic, and three oxo-hydroxides with one of these being silicate-substituted. Four agglomerated in the bacterial growth media whilst the silicate-substituted material remained disperse and small (6.5 nm diameter). Antibacterial activity against E. coli was assessed with copper phase distribution measured over time. Using the dose of soluble copper, and benchmark dose non-linear regression modelling, we determined how well this phase predicted antimicrobial activity. Finally, we used Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) analysis to investigate whether membrane adhe- sion effects by copper were plausible or if intracellular uptake most likely explained the bacterial impact of copper. Results: Comparison over time of antimicrobial activity against particulate or soluble phases of the aquated materials clearly demonstrated that soluble copper but not particulate forms were associated with inhibition of bacterial growth. Indeed, the benchmark dose modelling showed the soluble dose required to cause a 50% reduction in E. coli growth was strongly clustered – for all particle formulations – at 14.5 mg/L (10–19 mg/L 90% confidence interval). By comparison, total copper levels associated with the same reduction in viability varied widely (45–549 mg/L). Finally, in favour of this soluble product dominance in terms of antimicrobial activity, copper had low association with bacterial membrane (something both soluble and particulate materials could do) but showed high intra-bacterial levels (something only soluble copper could do). Conclusion: Taken together our data show that it is the uptake of soluble but not particulate copper, and the intracellular loading not just contact and membrane association, that drives copper toxicity to bacteria. Therapeutic strategies for novel antimicrobial copper compounds should consider these findings.
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| 5. |
- Fedina, Tatiana, et al.
(author)
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A comparative study of water and gas atomized low alloy steel powders for additive manufacturing
- 2020
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In: Additive Manufacturing. - : Elsevier. - 2214-8604 .- 2214-7810. ; 36
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Journal article (peer-reviewed)abstract
- This work reports a study of the differences between laser processing of water and gas atomized low alloy steel powders with a focus on powder behavior and performance in additive manufacturing. Material packing densities were measured to establish a relationship between powder packing and track formation. The results showed that the track height when using water atomized powder was 15% lower than the value achieved for the gas atomized powder. High-speed imaging was utilized to observe the material behavior and analyze the powder particle movement under laser irradiation. It was found that water atomized powder has less particle entrainment due to its tendency towards mechanical interlocking. The occurrence of powder spattering and melt pool instabilities was also studied. More frequent spatter ejection is believed to be due to the higher amount of oxygen in the water atomized powder.
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| 6. |
- Olsson, Rickard, 1959-, et al.
(author)
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Normal vector distribution as a classification tool for convoluted rough surfaces with overhanging features
- 2020
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In: Journal of laser applications. - : Laser Institute of America. - 1042-346X .- 1938-1387. ; 32:2
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Journal article (peer-reviewed)abstract
- Convoluted rough surfaces involving overhanging features can be a natural consequence of laser additive manufacturing and other spray techniques or can be generated deliberately by laser surface texturing, e.g., to aid osseointegration. Overhanging features add an extra level of complexity to the topography of a rough surface and can have a substantial effect on wettability, etc. However, features of this type are invisible to traditional surface roughness measurement techniques. This work presents a computer-based surface analysis method that gives useful information about the presence and nature of overhanging features on rough technical surfaces. The technique uses micro-computer tomography to generate a typical cross section of the surface under investigation. The angles of the vectors normal to the surface can then be analyzed to reveal the presence of overhanging features, which can also be indicated by the standard deviation of the normal vector distribution. Titanium surfaces generated by six different techniques were compared. The characteristics of these surfaces varied strongly, as did the shapes of the overhangs involved. These variations are reflected by different statistical distributions of the normal vectors.
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| 7. |
- Pinese, Mark, et al.
(author)
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The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
- 2020
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing. Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.
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| 8. |
- Wills, John W., et al.
(author)
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Image-Based Cell Profiling Enables Quantitative Tissue Microscopy in Gastroenterology
- 2020
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In: Cytometry Part A. - : WILEY. - 1552-4922 .- 1552-4930. ; 97:12, s. 1222-1237
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Journal article (peer-reviewed)abstract
- Immunofluorescence microscopy is an essential tool for tissue-based research, yet data reporting is almost always qualitative. Quantification of images, at the per-cell level, enables "flow cytometry-type" analyses with intact locational data but achieving this is complex. Gastrointestinal tissue, for example, is highly diverse: from mixed-cell epithelial layers through to discrete lymphoid patches. Moreover, different species (e.g., rat, mouse, and humans) and tissue preparations (paraffin/frozen) are all commonly studied. Here, using field-relevant examples, we develop open, user-friendly methodology that can encompass these variables to provide quantitative tissue microscopy for the field. Antibody-independent cell labeling approaches, compatible across preparation types and species, were optimized. Per-cell data were extracted from routine confocal micrographs, with semantic machine learning employed to tackle densely packed lymphoid tissues. Data analysis was achieved by flow cytometry-type analyses alongside visualization and statistical definition of cell locations, interactions and established microenvironments. First, quantification of Escherichia coli passage into human small bowel tissue, following Ussing chamber incubations exemplified objective quantification of rare events in the context of lumen-tissue crosstalk. Second, in rat jejenum, precise histological context revealed distinct populations of intraepithelial lymphocytes between and directly below enterocytes enabling quantification in context of total epithelial cell numbers. Finally, mouse mononuclear phagocyte-T cell interactions, cell expression and significant spatial cell congregations were mapped to shed light on cell-cell communication in lymphoid Peyers patch. Accessible, quantitative tissue microscopy provides a new window-of-insight to diverse questions in gastroenterology. It can also help combat some of the data reproducibility crisis associated with antibody technologies and over-reliance on qualitative microscopy. (c) 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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