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| 2. |
- 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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| 3. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 4. |
- Sinclair, Marlene, et al.
(författare)
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A systematic literature review of computer-based behavioural change interventions to inform the design of an online VBAC intervention for the OptiBIRTH European randomized trial.
- 2017
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Ingår i: Evidence Based Midwifery. - 1479-4489. ; 15:1, s. 5-13
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Tidskriftsartikel (refereegranskat)abstract
- Aim: The aim of this research was o systematically review computer-based, behavior change (BC) interventions during pregnancy and their design components in order to determine their best application within the context of the OptiBIRTH intervention. Design: A systematic literature review was undertaken using the Cochrane collaboration guidelines for systematic reviews of health promotion and public health interventions. Literature searches were conducted in; Ovid MEDLINE, PubMed, Cochrane Library, Embase, PsycINFO, from database inception to June 2015. Cochrane Risk of Bias criteria was applied to assess the methodological quality of the papers and a taxonomy of BC techniques was used to appraise the interventions. PICO. Participants included healthy pregnant women who were ≥18 years old. The types of intervention used were computer-based interventions designed to facilitate a BC approach in a sample of pregnant women. The comparison was routine antenatal care. The primary outcome included improved health behavior(s), as an indicator of the intention behind the intervention design. Results. A total of 343 papers were identified through database-searching and hand- searching methods; 80 duplicates were removed. From the remaining 263, 244 did not explicitly address the subject under review. Therefore, 19 full text articles were assessed for eligibility; 16 did not meet eligibility criteria and were excluded at this stage. This resulted in a total of three studies being selected for inclusion in this review (Jackson et al, 2011; Tzilos et al, 2011; Tsoh et al, 2010). The computer-based interventions were designed to bring about BC in relation to alcohol consumption, smoking or diet and exercise during pregnancy. Interventions delivered varied between two types; purely computer-delivered (Tzilos et al. 2011) or a combination of both computer plus face-to-face input (Jackson et al, 2011; Tsoh et al. 2010). Techniques used included motivational interviewing, problem solving cognitive dissonance and goal setting. Types of measurement outcomes varied but were all self-reported behavioral outcomes. Statistically significant improvements in behavioral outcomes were seen in the interventions by Jackson et al (2011) and Tsoh et al (2011), but not in the intervention by Tzilos et al (2011). The GRADE analysis identified that all studies combined lacked blinding and relied on self-reported data increasing risk of bias. Conclusion. This systematic review reports on the best available evidence and theory to design an online component of a complex intervention for use in an RCT to enhance women´s shared decision-making experience about vaginal births after caesarean (VBAC). The review reports the differences between the observed BC approach and that of a decision-making being focused on a more healthy option. As a result, techniques designed to create dissonance are considered appropriate. Shared decision-making, however, is conceptually different, in that the goal is to facilitate a woman in discovering the best direction of travel for her as person. Therefore, the authors argue that it is crucial for healthcare professionals designing complex healthcare interventions (either BC techniques or shared decision-making) to ensure that a person´s self-determination is respected through having access to relevant and understandable information and healthcare professionals who understand a woman´s motivation. However, it is not possible to draw firm conclusions from three studies and there is a requirement for further research.
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| 5. |
- Sung, Yun Ju, et al.
(författare)
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A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure
- 2019
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Ingår i: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 28:15, s. 2615-2633
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Tidskriftsartikel (refereegranskat)abstract
- Elevated blood pressure (BP), a leading cause of global morbidity and mortality, is influenced by both genetic and lifestyle factors. Cigarette smoking is one such lifestyle factor. Across five ancestries, we performed a genome-wide gene–smoking interaction study of mean arterial pressure (MAP) and pulse pressure (PP) in 129 913 individuals in stage 1 and follow-up analysis in 480 178 additional individuals in stage 2. We report here 136 loci significantly associated with MAP and/or PP. Of these, 61 were previously published through main-effect analysis of BP traits, 37 were recently reported by us for systolic BP and/or diastolic BP through gene–smoking interaction analysis and 38 were newly identified (P < 5 × 10−8, false discovery rate < 0.05). We also identified nine new signals near known loci. Of the 136 loci, 8 showed significant interaction with smoking status. They include CSMD1 previously reported for insulin resistance and BP in the spontaneously hypertensive rats. Many of the 38 new loci show biologic plausibility for a role in BP regulation. SLC26A7 encodes a chloride/bicarbonate exchanger expressed in the renal outer medullary collecting duct. AVPR1A is widely expressed, including in vascular smooth muscle cells, kidney, myocardium and brain. FHAD1 is a long non-coding RNA overexpressed in heart failure. TMEM51 was associated with contractile function in cardiomyocytes. CASP9 plays a central role in cardiomyocyte apoptosis. Identified only in African ancestry were 30 novel loci. Our findings highlight the value of multi-ancestry investigations, particularly in studies of interaction with lifestyle factors, where genomic and lifestyle differences may contribute to novel findings.
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| 6. |
- Tragante, Vinicius, et al.
(författare)
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Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci.
- 2014
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297. ; 94:3, s. 349-360
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Tidskriftsartikel (refereegranskat)abstract
- Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ∼50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
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| 7. |
- Brown, Christopher A., et al.
(författare)
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Multiscale analyses and characterizations of surface topographies
- 2018
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Ingår i: CIRP Annals - Manufacturing Technology. - : Elsevier BV. - 1726-0604 .- 0007-8506. ; 67:2, s. 839-862
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Tidskriftsartikel (refereegranskat)abstract
- This work studies multiscale analyses and characterizations of surface topographies from the engineering and scientific literature with an emphasis on production engineering research and design. It highlights methods that provide strong correlations between topographies and performance or topographies and processes, and methods that can confidently discriminate topographies that were processed or that perform differently. These methods have commonalities in geometric characterizations at certain scales, which are observable with statistics and measurements. It also develops a semantic and theoretical framework and proposes a new system for organizing and designating multiscale analyses. Finally, future possibilities for multiscale analyses are discussed.
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| 8. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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