| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)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. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Sumaila, U. Rashid, et al.
(författare)
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WTO must ban harmful fisheries subsidies
- 2021
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Belorizky, Elie, et al.
(författare)
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Comparison of different methods for calculating the paramagnetic relaxation enhancement of nuclear spins as a function of the magnetic field
- 2008
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 128:5
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Tidskriftsartikel (refereegranskat)abstract
- The enhancement of the spin-lattice relaxation rate for nuclear spins in a ligand bound to a paramagnetic metal ion [known as the paramagnetic relaxation enhancement (PRE)] arises primarily through the dipole-dipole (DD) interaction between the nuclear spins and the electron spins. In solution, the DD interaction is modulated mostly by reorientation of the nuclear spin-electron spin axis and by electron spin relaxation. Calculations of the PRE are in general complicated, mainly because the electron spin interacts so strongly with the other degrees of freedom that its relaxation cannot be described by second-order perturbation theory or the Redfield theory. Three approaches to resolve this problem exist in the literature: The so-called slow-motion theory, originating from Swedish groups [Benetis et al., Mol. Phys. 48, 329 (1983); Kowalewski et al., Adv. Inorg. Chem. 57, (2005); Larsson et al., J. Chem. Phys. 101, 1116 (1994); T. Nilsson et al., J. Magn. Reson. 154, 269 (2002)] and two different methods based on simulations of the dynamics of electron spin in time domain, developed in Grenoble [Fries and Belorizky, J. Chem. Phys. 126, 204503 (2007); Rast et al., ibid. 115, 7554 (2001)] and Ann Arbor [Abernathy and Sharp, J. Chem. Phys. 106, 9032 (1997); Schaefle and Sharp, ibid. 121, 5387 (2004); Schaefle and Sharp, J. Magn. Reson. 176, 160 (2005)], respectively. In this paper, we report a numerical comparison of the three methods for a large variety of parameter sets, meant to correspond to large and small complexes of gadolinium(III) and of nickel(II). It is found that the agreement between the Swedish and the Grenoble approaches is very good for practically all parameter sets, while the predictions of the Ann Arbor model are similar in a number of the calculations but deviate significantly in others, reflecting in part differences in the treatment of electron spin relaxation. The origins of the discrepancies are discussed briefly.
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| 5. |
- Burgers, Leonie E., et al.
(författare)
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Validation of the EULAR definition of arthralgia suspicious for progression to rheumatoid arthritis
- 2017
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Ingår i: Rheumatology. - : OXFORD UNIV PRESS. - 1462-0324 .- 1462-0332. ; 56:12, s. 2123-2128
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Tidskriftsartikel (refereegranskat)abstract
- Objectives. Recently a EULAR-taskforce defined arthralgia suspicious for progression to RA, in order to allow inclusion of homogeneous sets of arthralgia patients in clinical studies. This longitudinal study aimed (i) to validate this definition in arthralgia patients in whom rheumatologists felt that imminent RA was more likely than other arthralgias [clinically suspect arthralgia (CSA)], that is, the target population fulfilling the entry criterion, and (ii) to explore the performance in arthralgia patients who were referred to secondary care prior to rheumatological evaluation, hence ignoring the entry criterion. Methods. The definition was assessed in 241 Dutch patients identified with CSA by rheumatologists and 113 patients referred to the Umea university hospital with recent-onset arthralgia in small joints. The external reference was arthritis development < 2 years' follow-up. Results. CSA patients with a positive definition (>= 3/7 parameters present) had an increased risk for developing arthritis compared with definition-negative CSA patients (hazard ratio = 2.1, 95% CI: 0.9, 4.7). The sensitivity was 84% and the positive predictive value 30%. In arthralgia patients in whom the definition was applied before rheumatological evaluation, a positive definition was neither sensitive (10%) nor predictive (positive predictive value 3%). Conclusion. The EULAR definition of arthralgia suspicious for progression to RA is sensitive when used to support the rheumatologist's opinion on imminent RA. This validation study shows that the definition, when used as designed, further homogenizes patients that rheumatologists consider at risk for RA. To arrive at a high specificity, the clinical definition needs to be combined with biomarkers.
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| 6. |
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| 7. |
- Franke, Lude, et al.
(författare)
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Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes
- 2016
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Ingår i: European Journal of Human Genetics. - : Nature Publishing Group. - 1018-4813 .- 1476-5438. ; 24:2, s. 263-270
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Tidskriftsartikel (refereegranskat)abstract
- Segmental duplications (SDs) comprise about 5% of the human genome and are enriched for immune genes. SD loci often show copy numbers variations (CNV), which are difficult to tag with genotyping methods. CNV in the Fc gamma receptor region (FCGR) has been suggested to be associated with rheumatic diseases. The objective of this study was to delineate association of FCGR-CNV with rheumatoid arthritis (RA), coeliac disease and Inflammatory bowel disease incidence. We developed a method to accurately quantify CNV in SD loci based on the intensity values from the Immunochip platform and applied it to the FCGR locus. We determined the method's validity using three independent assays: segregation analysis in families, arrayCGH, and whole genome sequencing. Our data showed the presence of two separate CNVs in the FCGR locus. The first region encodes FCGR2A, FCGR3A and part of FCGR2C gene, the second encodes another part of FCGR2C, FCGR3B and FCGR2B. Analysis of CNV status in 4578 individuals with RA and 5457 controls indicated association of duplications in the FCGR3B gene in antibody-negative RA (P = 0.002, OR = 1.43). Deletion in FCGR3B was associated with increased risk of antibody-positive RA, consistently with previous reports (P = 0.023, OR = 1.23). A clear genotype-phenotype relationship was observed: CNV polymorphisms of the FCGR3A gene correlated to CD16A expression (encoded by FCGR3A) on CD8 T-cells. In conclusion, our method allows determining the CNV status of the FCGR locus, we identified association of CNV in FCGR3B to RA and showed a functional relationship between CNV in the FCGR3A gene and CD16A expression.
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| 8. |
- Kowalewski, Jozef, et al.
(författare)
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Comparison of different methods for calculating the paramagnetic relaxation enhancement of nuclear spins as a function of the magnetic field
- 2008
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Ingår i: Journal of Chemical Physics. ; 128, s. 052315-
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Tidskriftsartikel (refereegranskat)abstract
- The enhancement of the spin-lattice relaxation rate for nuclear spins in a ligand bound to a paramagnetic metal ion (known as the paramagnetic relaxation enhancement, PRE) arises primarily through the dipole-dipole (DD) interaction between the nuclear spins and the electron spins. In solution, the DD interaction is modulated mostly by reorientation of the nuclear spin-electron spin axis and by electron spin relaxation. Calculations of the PRE are in a general complicated, mainly because the electron spin interacts so strongly with the other degrees of freedom that its relaxation cannot be described by second-order perturbation theory, or the Redfield theory. Three approaches to resolve this problem exist in the literature: the so-called slow-motion theory, originating from Swedish groups, and two different methods based on simulations of the dynamics of electron spin in time domain, developed in Grenoble and Ann Arbor, respectively. In this paper, we report a numerical comparison of the three methods for a large variety of parameter sets, meant to correspond to large and small complexes of gadolinium(III) and of nickel(II). It is found that the agreement between the Swedish and the Grenoble approaches is very good for practically all parameter sets, while the predictions of the Ann Arbor model are similar in a number of the calculations but deviate significantly in others, reflecting in part differences in the treatment of electron spin relaxation. The origins of the discrepancies are discussed briefly.
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| 9. |
- Källberg, Henrik, et al.
(författare)
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Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking in two subsets of rheumatoid arthritis
- 2007
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 80:5, s. 867-875
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Tidskriftsartikel (refereegranskat)abstract
- Gene-gene and gene-environment interactions are key features in the development of rheumatoid arthritis (RA) and other complex diseases. The aim of this study was to use and compare three different definitions of interaction between the two major genetic risk factors of RA—the HLA-DRB1 shared epitope (SE) alleles and the PTPN22 R620W allele—in three large case-control studies: the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA) study, the North American RA Consortium (NARAC) study, and the Dutch Leiden Early Arthritis Clinic study (in total, 1,977 cases and 2,405 controls). The EIRA study was also used to analyze interactions between smoking and the two genes. “Interaction” was defined either as a departure from additivity, as interaction in a multiplicative model, or in terms of linkage disequilibrium—for example, deviation from independence of penetrance of two unlinked loci. Consistent interaction, defined as departure from additivity, between HLA-DRB1 SE alleles and the A allele of PTPN22 R620W was seen in all three studies regarding anti-CCP–positive RA. Testing for multiplicative interactions demonstrated an interaction between the two genes only when the three studies were pooled. The linkage disequilibrium approach indicated a gene-gene interaction in EIRA and NARAC, as well as in the pooled analysis. No interaction was seen between smoking and PTPN22 R620W. A new pattern of interactions is described between the two major known genetic risk factors and the major environmental risk factor concerning the risk of developing anti-CCP–positive RA. The data extend the basis for a pathogenetic hypothesis for RA involving genetic and environmental factors. The study also raises and illustrates principal questions concerning ways to define interactions in complex diseases.
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| 10. |
- Munoz-Gama, Jorge, et al.
(författare)
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Process mining for healthcare : Characteristics and challenges
- 2022
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Ingår i: Journal of Biomedical Informatics. - : Elsevier BV. - 1532-0464 .- 1532-0480. ; 127
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Tidskriftsartikel (refereegranskat)abstract
- Process mining techniques can be used to analyse business processes using the data logged during their execution. These techniques are leveraged in a wide range of domains, including healthcare, where it focuses mainly on the analysis of diagnostic, treatment, and organisational processes. Despite the huge amount of data generated in hospitals by staff and machinery involved in healthcare processes, there is no evidence of a systematic uptake of process mining beyond targeted case studies in a research context. When developing and using process mining in healthcare, distinguishing characteristics of healthcare processes such as their variability and patient-centred focus require targeted attention. Against this background, the Process-Oriented Data Science in Healthcare Alliance has been established to propagate the research and application of techniques targeting the data-driven improvement of healthcare processes. This paper, an initiative of the alliance, presents the distinguishing characteristics of the healthcare domain that need to be considered to successfully use process mining, as well as open challenges that need to be addressed by the community in the future.
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