| 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. |
- Fuchsberger, Christian, et al.
(författare)
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The genetic architecture of type 2 diabetes
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 536:7614, s. 41-47
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Tidskriftsartikel (refereegranskat)abstract
- The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this disease. Here, to test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing in 12,940 individuals from five ancestry groups. To increase statistical power, we expanded the sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes.
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| 3. |
- Flannick, Jason, et al.
(författare)
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Data Descriptor : Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to ~82 K Europeans via the exome chip, and similar to ~90% of low-frequency non-coding variants in similar to ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
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| 4. |
- Björkman, Anne, 1981, et al.
(författare)
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Tundra Trait Team: A database of plant traits spanning the tundra biome
- 2018
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 27:12, s. 1402-1411
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Tidskriftsartikel (refereegranskat)abstract
- © 2018 The Authors Global Ecology and Biogeography Published by John Wiley & Sons Ltd Motivation: The Tundra Trait Team (TTT) database includes field-based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade-offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters. Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (>1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density. Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub-Antarctic Marion Island. More than 99% of observations are georeferenced. Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods. Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species. Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release.
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| 5. |
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| 6. |
- Green, Rasmus W., et al.
(författare)
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Endometrial cancer off-line staging using two-dimensional transvaginal ultrasound and three-dimensional volume contrast imaging : Intermethod agreement, interrater reliability and diagnostic accuracy
- 2018
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Ingår i: Gynecologic Oncology. - : Elsevier BV. - 0090-8258 .- 1095-6859. ; 150:3, s. 438-445
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The aim is to estimate agreement between two-dimensional transvaginal ultrasound (2D-TVS) and three-dimensional volume contrast imaging (3D-VCI) in diagnosing deep myometrial invasion (MI) and cervical stromal involvement (CSI) of endometrial cancer and to compare the two methods regarding inter-rater reliability and diagnostic accuracy. Methods: Fifteen ultrasound experts assessed off-line de-identified 3D-VCI volumes and 2D-TVU video clips from 58 patients with biopsy-confirmed endometrial cancer regarding the presence of deep (≥50%) MI and CSI. Video clips and 3D volumes were assessed independently. Interrater reliability was measured using kappa statistics. Histological diagnosis after hysterectomy served as gold standard. Accuracy measurements were correlated to rater experience using Spearman's rank correlation coefficient (ρ). Results: Agreement between 2D-TVU and 3D-VCI for diagnosing MI was median 76% (range 64–93%) and for CSI median 88% (range 79–97%). Interrater reliability was better for 2D-TVU than for 3D-VCI (Fleiss' kappa 0.41 vs. 0.31 for MI and 0.55 vs. 0.45 for CSI). Median accuracy for diagnosing deep MI was 76% (range 59–84%) with 2D-TVU and 69% (range 52–83%) for 3D-VCI; the corresponding figures for CSI were 88% (range 81–93%) and 86% (range 72–95%). Accuracy was significantly correlated to how many cases the raters assessed annually. Conclusions: Off-line assessment of MI and CSI in women with endometrial cancer using 3D-VCI has lower interrater reliability and lower accuracy than 2D-TVU video clip assessment. Since accuracy was correlated to the number of cases assessed annually it is advised to centralize these examinations to high-volume centres.
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| 7. |
- Green, Rasmus W
(författare)
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The value of new sonographic modalities, demographic, biometric and proliferative variables for the risk prediction in endometrial cancer
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: Endometrial cancer is the sixth most common type of cancer among women worldwide and constitutes 4.8% of all cancer in women. The incidence is highest in highincome countries, given how age and obesity are the two most important risk factors. The majority of cases present at an early stage, with a favourable prognosis. In those patients, added treatment after surgery does not improve survival rates. In advanced stages, the prognosis is generally poor, and treatment options are few with a modest effect at best. Therefore, correct staging and triaging of patients to low- and high-risk groups are the cornerstone of endometrial cancer treatment. Today, risk stratification is based on imaging with ultrasound and/or magnetic resonance imaging and histologic assessment. These are all based on human interpretation and coding and can thus be more or less reliable. Improving reliability and diagnostic accuracy of our instruments, or finding more objective risk factors to complement or replace the current standard, is thus necessary to further tailor treatment to each patient. This thesis aimed to assess DNA ploidy and S-phase fraction as prognostic markers, measure the degree of rater dependency in ultrasound staging, investigate the possible benefit of adding dynamic contrast-enhanced ultrasound and compare diagnostic performance in assessing local tumour extension with ultrasound as well as the prevalence of known high-risk ultrasound features. Methods: Study I used a population-based, consecutive cohort of 1140 women with FIGO stage I endometrioid endometrial cancer. Cox regression was used, including age, degree of differentiation, myometrial invasion, DNA ploidy, S-phase fraction and adjuvant treatment as covariates, with endometrial cancer death being the end-point. In study II, fifteen ultrasound experts assessed off-line 2D video clips and 3D volumes from 58 patients with endometrial cancer for deep myometrial invasion and cervical stromal involvement. Kappa statistics and diagnostic performance were calculated, and rater accuracy was correlated to rater experience measures. In study III, the added benefit to the routine ultrasound of dynamic contrastenhanced ultrasound in diagnosing local tumour extension of endometrial cancer was assessed by comparing the results in a prospectively enrolled study cohort (n=93) to a matched control cohort (n=279). In study IV, pre- and postmenopausal women from the prospective IETA-4 multicentre cohort (n=1538) were compared concerning the prevalence of high-risk sonographic features and the diagnostic performance in assessing local tumour extension with ultrasound. Results: A high S-phase fraction, but not DNA aneuploidy, was an independent prognostic factor for endometrial cancer death in FIGO stage I endometrioid cancer. Interrater reliability was higher with 2D video clips than with 3D volumes and diagnostic performance was also higher. Diagnostic performance was correlated to the number of cases each rater assessed annually. Dynamic contrast-enhanced ultrasound improved sensitivity in diagnosing deep myometrial invasion, without lowering specificity. Premenopausal women more often had low-risk cancer but still had high-risk sonographic features related to the vascularity of the endometrium, likely related to physiological features of a cycling endometrium. An intact endometrial-myometrial border suggested low-risk disease in both pre- and postmenopausal women. Local tumour extension was more accurately assessed in pre- compared to postmenopausal women. Conclusion: The utility and optimal cut-off value for S-phase fraction have to be sought in a new study before it can be introduced into clinical practice. Ultrasound is a reliable imaging modality but should be centralised to high-throughput centres to increase rater experience. Dynamic contrast-enhanced ultrasound is safe and does not require any special preparations and can thus be used as a complement in tricky cases to rule out myometrial invasion. Tumour vascularity in endometrial cancer assessment has to be interpreted in light of menopausal status.
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