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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Robinson, Andreas, 1975-, et al.
(author)
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Discriminative Learning and Target Attention for the 2019 DAVIS Challenge onVideo Object Segmentation
- 2019
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In: CVPR 2019 workshops.
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Conference paper (peer-reviewed)abstract
- In this work, we address the problem of semi-supervised video object segmentation, where the task is to segment a target object in every image of the video sequence, given a ground truth only in the first frame. To be successful it is crucial to robustly handle unpredictable target appearance changes and distracting objects in the background. In this work we obtain a robust and efficient representation of the target by integrating a fast and light-weight discriminative target model into a deep segmentation network. Trained during inference, the target model learns to discriminate between the local appearances of target and background image regions. Its predictions are enhanced to accurate segmentation masks in a subsequent refinement stage.To further improve the segmentation performance, we add a new module trained to generate global target attention vectors, given the input mask and image feature maps. The attention vectors add semantic information about thetarget from a previous frame to the refinement stage, complementing the predictions provided by the target appearance model. Our method is fast and requires no network fine-tuning. We achieve a combined J and F-score of 70.6 on the DAVIS 2019 test-challenge data
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| 3. |
- Sterner, Thomas, 1952, et al.
(author)
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Policy design for the Anthropocene
- 2019
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In: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2, s. 14-21
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Journal article (peer-reviewed)abstract
- © 2019, Springer Nature Limited. Today, more than ever, ‘Spaceship Earth’ is an apt metaphor as we chart the boundaries for a safe planet1. Social scientists both analyse why society courts disaster by approaching or even overstepping these boundaries and try to design suitable policies to avoid these perils. Because the threats of transgressing planetary boundaries are global, long-run, uncertain and interconnected, they must be analysed together to avoid conflicts and take advantage of synergies. To obtain policies that are effective at both international and local levels requires careful analysis of the underlying mechanisms across scientific disciplines and approaches, and must take politics into account. In this Perspective, we examine the complexities of designing policies that can keep Earth within the biophysical limits favourable to human life.
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| 4. |
- Tiegs, Scott D., et al.
(author)
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Global patterns and drivers of ecosystem functioning in rivers and riparian zones
- 2019
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In: Science Advances. - Washington : American Association of Advancement in Science. - 2375-2548. ; 5:1
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Journal article (peer-reviewed)abstract
- River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.
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- Uhlén, Mathias, et al.
(author)
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The human secretome
- 2019
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In: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 12:609
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Journal article (peer-reviewed)abstract
- The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immuno-assays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.
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| 6. |
- Wallberg, Andreas, et al.
(author)
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A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
- 2019
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In: BMC Genomics. - : BMC. - 1471-2164. ; 20
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Journal article (peer-reviewed)abstract
- BackgroundThe ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.ResultsEach of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.ConclusionsThe improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.
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