| 1. |
- Kattge, Jens, et al.
(författare)
-
TRY plant trait database - enhanced coverage and open access
- 2020
-
Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
-
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.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
|
|
| 5. |
- Kaasinen, E, et al.
(författare)
-
Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans
- 2019
-
Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 1252-
-
Tidskriftsartikel (refereegranskat)abstract
- Clonal hematopoiesis driven by somatic heterozygous TET2 loss is linked to malignant degeneration via consequent aberrant DNA methylation, and possibly to cardiovascular disease via increased cytokine and chemokine expression as reported in mice. Here, we discover a germline TET2 mutation in a lymphoma family. We observe neither unusual predisposition to atherosclerosis nor abnormal pro-inflammatory cytokine or chemokine expression. The latter finding is confirmed in cells from three additional unrelated TET2 germline mutation carriers. The TET2 defect elevates blood DNA methylation levels, especially at active enhancers and cell-type specific regulatory regions with binding sequences of master transcription factors involved in hematopoiesis. The regions display reduced methylation relative to all open chromatin regions in four DNMT3A germline mutation carriers, potentially due to TET2-mediated oxidation. Our findings provide insight into the interplay between epigenetic modulators and transcription factor activity in hematological neoplasia, but do not confirm the putative role of TET2 in atherosclerosis.
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
- Sandholm, Niina, et al.
(författare)
-
New susceptibility loci associated with kidney disease in type 1 diabetes
- 2012
-
Ingår i: PLOS Genetics. - San Francisco, USA : Public Library of Science, PLOS. - 1553-7390 .- 1553-7404. ; 8:9, s. e1002921-
-
Tidskriftsartikel (refereegranskat)abstract
- Diabetic kidney disease, or diabetic nephropathy (DN), is a major complication of diabetes and the leading cause of end-stage renal disease (ESRD) that requires dialysis treatment or kidney transplantation. In addition to the decrease in the quality of life, DN accounts for a large proportion of the excess mortality associated with type 1 diabetes (T1D). Whereas the degree of glycemia plays a pivotal role in DN, a subset of individuals with poorly controlled T1D do not develop DN. Furthermore, strong familial aggregation supports genetic susceptibility to DN. However, the genes and the molecular mechanisms behind the disease remain poorly understood, and current therapeutic strategies rarely result in reversal of DN. In the GEnetics of Nephropathy: an International Effort (GENIE) consortium, we have undertaken a meta-analysis of genomewide association studies (GWAS) of T1D DN comprising similar to 2.4 million single nucleotide polymorphisms (SNPs) imputed in 6,691 individuals. After additional genotyping of 41 top ranked SNPs representing 24 independent signals in 5,873 individuals, combined meta-analysis revealed association of two SNPs with ESRD: rs7583877 in the AFF3 gene (P = 1.2 x 10(-8)) and an intergenic SNP on chromosome 15q26 between the genes RGMA and MCTP2, rs12437854 (P = 2.0 x 10(-9)). Functional data suggest that AFF3 influences renal tubule fibrosis via the transforming growth factor-beta (TGF-beta 1) pathway. The strongest association with DN as a primary phenotype was seen for an intronic SNP in the ERBB4 gene (rs7588550, P = 2.1 x 10(-7)), a gene with type 2 diabetes DN differential expression and in the same intron as a variant with cis-eQTL expression of ERBB4. All these detected associations represent new signals in the pathogenesis of DN.
|
|
| 9. |
|
|
| 10. |
|
|
| 11. |
|
|
| 12. |
|
|
| 13. |
- Naranjo, A., et al.
(författare)
-
Smokers and non-smokers with rheumatoid arthritis have similar clinical status : data from the multinational QUEST-RA database
- 2010
-
Ingår i: Clinical and Experimental Rheumatology. - 0392-856X .- 1593-098X. ; 28:6, s. 820-827
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives To analyse clinical severity/activity of rheumatoid arthritis (RA) according to smoking status. Methods The QUEST-RA multinational database reviews patients for Core Data Set measures including 28 swollen and tender joint count, physician global estimate, erythrocyte sedimentation rate (ESR), HAQ-function, pain, and patient global estimate, as well as DAS28, rheumatoid factor (RE), nodules, erosions and number of DMARDs were recorded. Smoking status was assessed by self-report as "never smoked", "currently smoking" and "former smokers". Patient groups with different smoking status were compared for demographic and RA measures. Results Among the 7,307 patients with smoking data available, status as "never smoked," "current smoker" and "former smoker" were reported by 65%, 15% and 20%. Ever smokers were more likely to be RF-positive (OR 1.32; 1.17-1.48, p<0.001). Rheumatoid nodules were more frequent in ever smokers (OR 1.41; 1.24-1.59, p<0.001). The percentage of patients with erosive arthritis and extra-articular disease was similar in all smoking categories. Mean DAS28 was 4.4 (SD 1.6) in non-smokers vs. 4.0 (SD 1.6) in those who had ever smoked. However, when adjusted by age, sex, disease duration, and country gross domestic product, only ESR remained significantly different among Core Data Set measures (mean 31.7mm in non-smokers vs. 26.8mm in ever smoked category). Conclusion RA patients who had ever smoked were more likely to have RF and nodules, hut values for other clinical status measures were similar in all smoking categories (never smoked, current smokers and former smokers).
|
|
| 14. |
|
|
| 15. |
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
|
|
| 20. |
|
|
| 21. |
- Makinen, M, et al.
(författare)
-
Trainers' Attitudes towards Cardiopulmonary Resuscitation, Current Care Guidelines, and Training
- 2016
-
Ingår i: Emergency medicine international. - : Hindawi Limited. - 2090-2840 .- 2090-2859. ; 2016, s. 3701468-
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives. Studies have shown that healthcare personnel hesitate to perform defibrillation due to individual or organisational attitudes. We aimed to assess trainers’ attitudes towards cardiopulmonary resuscitation and defibrillation (CPR-D), Current Care Guidelines, and associated training.Methods. A questionnaire was distributed to CPR trainers attending seminars in Finland (N=185) focusing on the updated national Current Care Guidelines 2011. The questions were answered using Likert scale (1 = totally disagree, 7 = totally agree). Factor loading of the questionnaire was made using maximum likelihood analysis and varimax rotation. Seven scales were constructed (Hesitation,Nurse’s Role,Nontechnical Skill,Usefulness,Restrictions,Personal, andOrganisation). Cronbach’s alphas were 0.92–0.51. Statistics were Student’st-test, ANOVA, stepwise regression analysis, and Pearson Correlation.Results. The questionnaire was returned by 124/185, 67% CPR trainers, of whom two-thirds felt that their undergraduate training in CPR-D had not been adequate. Satisfaction with undergraduate defibrillation training correlated with theNontechnical Skillsscale (p<0.01). Participants scoring high onHesitationscale (p<0.01) were less confident about theirNurse’s Role(p<0.01) andNontechnical Skills(p<0.01).Conclusion. Quality of undergraduate education affects the work of CPR trainers and some feel uncertain of defibrillation. The train-the-trainers courses and undergraduate medical education should focus more on practical scenarios with defibrillators and nontechnical skills.
|
|
| 22. |
|
|
| 23. |
- Marschall, Tobias, et al.
(författare)
-
Computational pan-genomics : status, promises and challenges
- 2018
-
Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 19:1, s. 118-135
-
Tidskriftsartikel (refereegranskat)abstract
- Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
|
|
| 24. |
- Oksa, L, et al.
(författare)
-
Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia
- 2022
-
Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:9
-
Tidskriftsartikel (refereegranskat)abstract
- T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with no well-established prognostic biomarkers. We examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. The genetic deletion of PRMT7 by CRISPR-Cas9 reduced the colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with the RNA and DNA processing and the T-ALL pathogenesis. Among them was RUNX1, whose target gene expression was consequently deregulated. These results suggest that PRMT7 plays an active role in the pathogenesis of T-ALL.
|
|
| 25. |
|
|
