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| 2. |
- Gaulton, Kyle J, et al.
(author)
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Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
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Journal article (peer-reviewed)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
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| 3. |
- Tedersoo, L., et al.
(author)
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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
- 2021
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 111, s. 573-588
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Journal article (peer-reviewed)abstract
- Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
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| 4. |
- Scott, Robert A., et al.
(author)
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An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans
- 2017
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In: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 66:11, s. 2888-2902
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Journal article (peer-reviewed)abstract
- To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 x 10(-8)), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.
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| 5. |
- Laukkanen, P., et al.
(author)
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Anomalous bismuth-stabilized (2x1) reconstructions on GaAs(100) and InP(100) surfaces
- 2008
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 100, s. 086101-
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Journal article (peer-reviewed)abstract
- First-principles phase diagrams of bismuth-stabilized GaAs- and InP(100) surfaces demonstrate for the first time the presence of anomalous (2 x 1) reconstructions, which disobey the common electron counting principle. Combining these theoretical results with our scanning-tunneling-microscopy and photoemission measurements, we identify novel (2 x 1) surface structures, which are composed of symmetric Bi-Bi and asymmetric mixed Bi-As and Bi-P dimers, and find that they are stabilized by stress relief and pseudogap formation.
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| 6. |
- Punkkinen, M. P. J., et al.
(author)
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Bismuth-stabilized (2x1) and (2x4) reconstructions on GaAs(100) surfaces : Combined first-principles, photoemission, and scanning tunneling microscopy study
- 2008
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In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 78, s. 195304-
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Journal article (peer-reviewed)abstract
- Bismuth adsorbate-stabilized (2x1) and (2x4) reconstructions of the GaAs(100) surfaces have been studied by first-principles calculations, valence-band and core-level photoelectron spectroscopies, and scanning tunneling microscopy. It is demonstrated that large Bi atom size leads to the formation of the pseudogap at the Fermi energy and to the lower energy of an adsorbate-derived surface band, which contributes to the stabilization of the exceptional Bi/GaAs(100)(2x1) reconstruction. It is proposed that the Bi/GaAs(100)(2x4) reconstructions include asymmetric mixed Bi-As dimers, in addition to the Bi-Bi dimers. Based on the calculations, we solve the atomic origins of the surface core-level shifts (SCLSs) of the Bi 5d photoemission spectra from the Bi/GaAs(100)(2x4) surfaces. This allows for resolving the puzzle related to the identification of two SCLS components often found in the measurements of the Bi 5d and Sb 4d core-level emissions of the Bi/III-V and Sb/III-V(100)(2x4) surfaces. Finally, the reason for the absence of the common (2x4)-beta 2 structure and additional support for the stability of the (2x1) structure on the Bi/III-V(100) surfaces are discussed in terms of Bi atom size and subsurface stress.
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| 7. |
- Punkkinen, M. P. J., et al.
(author)
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Surface core-level shifts of GaAs(100)(2x4) from first principles
- 2007
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In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 76:11
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Journal article (peer-reviewed)abstract
- First-principles calculations show that measured surface core-level shifts (SCLSs) of the GaAs(100)(2x4) surfaces can be described within the initial state effects. The calculated As 3d and Ga 3d SCLSs for the beta 2 and alpha 2 reconstructions of the GaAs(100)(2x4) surfaces are in reasonable agreement with recent measurements. In particular, the results confirm that both the lower and the higher binding energy SCLSs, relative to the bulk emission in the As 3d photoelectron spectra, are intrinsic properties of the GaAs(100)(2x4) surfaces. The most positive and most negative As shifts are attributed to the third layer As atoms, which differs from the previous intuitive suggestions. In general, calculations show that significant SCLSs arise from deep layers, and that there are more than two SCLSs. Our previously measured As 3d spectra are fitted afresh using the calculated SCLSs. The intensity ratios of the SCLSs, obtained from the fits, show that as the heating temperature of the GaAs(100)(2x4) surface is increased gradually, the area of the alpha 2 reconstruction increases on the surface, but the beta 2 phase remains within the whole temperature range, in agreement with previous experimental findings. Our results show that the combination of the experimental and theoretical results is a prerequisite for the accurate analysis of the SCLSs of the complex reconstructed surfaces.
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| 8. |
- Tedersoo, Leho, et al.
(author)
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Global patterns in endemicity and vulnerability of soil fungi.
- 2022
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In: Global change biology. - : Wiley. - 1365-2486 .- 1354-1013. ; 28:22, s. 6696-6710
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Journal article (peer-reviewed)abstract
- Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
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| 9. |
- Shefferson, Richard P., et al.
(author)
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Drivers of vegetative dormancy across herbaceous perennial plant species
- 2018
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In: Ecology Letters. - : WILEY. - 1461-023X .- 1461-0248. ; 21:5, s. 724-733
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Journal article (peer-reviewed)abstract
- Vegetative dormancy, that is the temporary absence of aboveground growth for 1year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life-history costs of sprouting, and of dormancy. Short-lived and mycoheterotrophic species have higher proportions of dormant plants than long-lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.
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| 10. |
- Soininen, E.M., et al.
(author)
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Location of studies and evidence of effects of herbivory on Arctic vegetation: a systematic map
- 2021
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In: Environmental Evidence. - : BioMed Central (BMC). - 2047-2382. ; 10:1
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Journal article (peer-reviewed)abstract
- Background: Herbivores modify the structure and function of tundra ecosystems. Understanding their impacts is necessary to assess the responses of these ecosystems to ongoing environmental changes. However, the effects of herbivores on plants and ecosystem structure and function vary across the Arctic. Strong spatial variation in herbivore effects implies that the results of individual studies on herbivory depend on local conditions, i.e., their ecological context. An important first step in assessing whether generalizable conclusions can be produced is to identify the existing studies and assess how well they cover the underlying environmental conditions across the Arctic. This systematic map aims to identify the ecological contexts in which herbivore impacts on vegetation have been studied in the Arctic. Specifically, the primary question of the systematic map was: “What evidence exists on the effects of herbivores on Arctic vegetation?”.Methods: We used a published systematic map protocol to identify studies addressing the effects of herbivores on Arctic vegetation. We conducted searches for relevant literature in online databases, search engines and specialist websites. Literature was screened to identify eligible studies, defined as reporting primary data on herbivore impacts on Arctic plants and plant communities. We extracted information on variables that describe the ecological context of the studies, from the studies themselves and from geospatial data. We synthesized the findings narratively and created a Shiny App where the coded data are searchable and variables can be visually explored.Review findings: We identified 309 relevant articles with 662 studies (representing different ecological contexts or datasets within the same article). These studies addressed vertebrate herbivory seven times more often than invertebrate herbivory. Geographically, the largest cluster of studies was in Northern Fennoscandia. Warmer and wetter parts of the Arctic had the largest representation, as did coastal areas and areas where the increase in temperature has been moderate. In contrast, studies spanned the full range of ecological context variables describing Arctic vertebrate herbivore diversity and human population density and impact.Conclusions: The current evidence base might not be sufficient to understand the effects of herbivores on Arctic vegetation throughout the region, as we identified clear biases in the distribution of herbivore studies in the Arctic and a limited evidence base on invertebrate herbivory. In particular, the overrepresentation of studies in areas with moderate increases in temperature prevents robust generalizations about the effects of herbivores under different climatic scenarios.
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