A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals

The importance of groundwater-derived carbon dioxide in the restoration of small Sphagnum bogs

Essential for successful bog restoration is the reestablishment of Sphagnum mosses. High carbon dioxide availability has been shown to be of great importance for the growth of Sphagnum mosses. In well-developed Sphagnum bogs large amounts of carbon dioxide are produced by (an)aerobic decomposition of the peat layer. In cut-over Sphagnum bogs this carbon source is often greatly reduced. In this study the importance of groundwater-derived carbon dioxide is demonstrated in aquatic environments, where Sphagnum species have started to form floating mats after former cutover activities by farmers. We discuss the results of measures taken to restore one of the largest wet heathland reserves in western Europe. After rewetting, some bogs developed markedly well, whereas others did not. The developmental success of 10 small bogs was quantified by analysing aerial photographs and sampling of surface and groundwater. The analysis of the ground- and surface water samples revealed that in the well-developed bogs there were significantly higher TIC/CO2 concentrations than in poorly developed bogs. It is concluded that in the early stages of bog formation the growth of Sphagnum is better in bog systems that are fed by an inflow of carbonrich groundwater from outside the bog. The present findings suggest that high carbon dioxide availability is a prerequisite for the successful reestablishment of Sphagnum mosses in peat-bog restoration projects and that carbon-rich groundwater can substitute for the carbon dioxide from decomposing peat

A comparative study of image retargeting

Example of retargeting the butterfly image shown in Figure 2 to half its size. In this study we evaluate 8 different image retargeting methods, asking users to compare their results and examine what qualities in retargeted images mattered to them. We also correlate the users ’ preferences with automatic image similarity measures. Our findings provide insights on the retargeting problem, and present a clear benchmark for future research in the field. The numerous works on media retargeting call for a methodological approach for evaluating retargeting results. We present the first comprehensive perceptual study and analysis of image retargeting. First, we create a benchmark of images and conduct a large scale user study to compare a representative number of state-of-the-art retargeting methods. Second, we present analysis of the users ’ responses, where we find that humans in general agree on the evaluation of the results and show that some retargeting methods are consistently more favorable than others. Third, we examine whether computational image distance metrics can predict human retargeting perception. We show that current measures used in this context are not necessarily consistent with human rankings, and demonstrate that better results can be achieved using image features that were not previously considered for this task. We also reveal specific qualities in retargeted media that are more important for viewers. The importance of our work lies in promoting better measures to assess and guide retargeting algorithms in the future. The full benchmark we collected, including all images, retargeted results, and the collected user data, are available to the research community for further investigation a