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- van Bragt, JJMH, et al.
(författare)
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Characteristics and treatment regimens across ERS SHARP severe asthma registries
- 2020
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Ingår i: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 55:1
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the characteristics and treatments of patients with severe asthma across Europe, but both are likely to vary. This is the first study in the European Respiratory Society Severe Heterogeneous Asthma Research collaboration, Patient-centred (SHARP) Clinical Research Collaboration and it is designed to explore these variations. Therefore, we aimed to compare characteristics of patients in European severe asthma registries and treatments before starting biologicals.This was a cross-sectional retrospective analysis of aggregated data from 11 national severe asthma registries that joined SHARP with established patient databases.Analysis of data from 3236 patients showed many differences in characteristics and lifestyle factors. Current smokers ranged from 0% (Poland and Sweden) to 9.5% (Belgium), mean body mass index ranged from 26.2 (Italy) to 30.6 kg·m−2 (the UK) and the largest difference in mean pre-bronchodilator forced expiratory volume in 1 s % predicted was 20.9% (the Netherlands versus Hungary). Before starting biologicals patients were treated differently between countries: mean inhaled corticosteroid dose ranged from 700 to 1335 µg·day−1 between those from Slovenia versus Poland when starting anti-interleukin (IL)-5 antibody and from 772 to 1344 µg·day−1 in those starting anti-IgE (Slovenia versus Spain). Maintenance oral corticosteroid use ranged from 21.0% (Belgium) to 63.0% (Sweden) and from 9.1% (Denmark) to 56.1% (the UK) in patients starting anti-IL-5 and anti-IgE, respectively.The severe asthmatic population in Europe is heterogeneous and differs in both clinical characteristics and treatment, often appearing not to comply with the current European Respiratory Society/American Thoracic Society guidelines definition of severe asthma. Treatment regimens before starting biologicals were different from inclusion criteria in clinical trials and varied between countries.
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- 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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- Yakneen, S, et al.
(författare)
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Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
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Tidskriftsartikel (refereegranskat)abstract
- We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
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- Margaryan, Ashot, et al.
(författare)
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Population genomics of the Viking world
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 585:7825, s. 390-396
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Tidskriftsartikel (refereegranskat)abstract
- The maritime expansion of Scandinavian populations during the Viking Age (about ad750–1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci—including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response—in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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- Pinese, Mark, et al.
(författare)
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The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing. Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.
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- Guiglion, G., et al.
(författare)
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The RAdial Velocity Experiment (RAVE) : Parameterisation of RAVE spectra based on convolutional neural networks
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 644
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Tidskriftsartikel (refereegranskat)abstract
- Context Data-driven methods play an increasingly important role in the field of astrophysics In the context of large spectroscopic surveys of stars, data-driven methods are key in deducing physical parameters for millions of spectra in a short time. Convolutional neural networks (CNNs) enable us to connect observables (e.g. spectra, stellar magnitudes) to physical properties (atmospheric parameters, chemical abundances, or labels in general). Aims. We test whether it is possible to transfer the labels derived from a high-resolution stellar survey to intermediate-resolution spectra of another survey by using a CNN. Methods. We trained a CNN, adopting stellar atmospheric parameters and chemical abundances from APOGEE DR16 (resolution Ra22 500) data as training set labels. As input, we used parts of the intermediate-resolution RAVE DR6 spectra (R ∼ 7500) overlapping with the APOGEE DR16 data as well as broad-band ALLWISE and 2MASS photometry, together with Gaia DR2 photometry and parallaxes. Results. We derived precise atmospheric parameters Teff, log(g), and [M/H], along with the chemical abundances of [Fe/H], [α/M], [Mg/Fe], [Si/Fe], [Al/Fe], and [Ni/Fe] for 420 165 RAVE spectra. The precision typically amounts to 60 K in Teff, 0.06 in log(g) and 0.02-0.04 dex for individual chemical abundances. Incorporating photometry and astrometry as additional constraints substantially improves the results in terms of the accuracy and precision of the derived labels, as long as we operate in those parts of the parameter space that are well-covered by the training sample. Scientific validation confirms the robustness of the CNN results. We provide a catalogue of CNN-Trained atmospheric parameters and abundances along with their uncertainties for 420 165 stars in the RAVE survey. Conclusions. CNN-based methods provide a powerful way to combine spectroscopic, photometric, and astrometric data without the need to apply any priors in the form of stellar evolutionary models. The developed procedure can extend the scientific output of RAVE spectra beyond DR6 to ongoing and planned surveys such as Gaia RVS, 4MOST, and WEAVE. We call on the community to place a particular collective emphasis and on efforts to create unbiased training samples for such future spectroscopic surveys.
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| 9. |
- Yagoubov, P., et al.
(författare)
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Wideband 67-116 GHz receiver development for ALMA Band 2
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 634
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Tidskriftsartikel (refereegranskat)abstract
- Context. The Atacama Large Millimeter/submillimeter Array (ALMA) has been in operation since 2011, but it has not yet been populated with the full suite of its planned frequency bands. In particular, ALMA Band 2 (67-90 GHz) is the final band in the original ALMA band definition to be approved for production. Aims. We aim to produce a wideband, tuneable, sideband-separating receiver with 28 GHz of instantaneous bandwidth per polarisation operating in the sky frequency range of 67-116 GHz. Our design anticipates new ALMA requirements following the recommendations of the 2030 ALMA Development Roadmap. Methods. The cryogenic cartridge is designed to be compatible with the ALMA Band 2 cartridge slot, where the coldest components - the feedhorns, orthomode transducers, and cryogenic low noise amplifiers - operate at a temperature of 15 K. We use multiple simulation methods and tools to optimise our designs for both the passive optics and the active components. The cryogenic cartridge is interfaced with a room-temperature (warm) cartridge hosting the local oscillator and the downconverter module. This warm cartridge is largely based on GaAs semiconductor technology and is optimised to match the cryogenic receiver bandwidth with the required instantaneous local oscillator frequency tuning range. Results. Our collaboration has resulted in the design, fabrication, and testing of multiple technical solutions for each of the receiver components, producing a state-of-the-art receiver covering the full ALMA Band 2 and 3 atmospheric window. The receiver is suitable for deployment on ALMA in the coming years and it is capable of dual-polarisation, sideband-separating observations in intermediate frequency bands spanning 4-18 GHz for a total of 28 GHz on-sky bandwidth per polarisation channel. Conclusions. We conclude that the 67-116 GHz wideband implementation for ALMA Band 2 is now feasible and that this receiver provides a compelling instrumental upgrade for ALMA that will enhance observational capabilities and scientific reach.
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| 10. |
- Sundqvist, Martina, et al.
(författare)
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Anti-neutrophil cytoplasmic antibodies (ANCA): Antigen interactions and downstream effects.
- 2020
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Ingår i: Journal of leukocyte biology. - 1938-3673. ; 108:2, s. 617-626
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Forskningsöversikt (refereegranskat)abstract
- Neutrophils are the most abundant leukocytes in circulation and are key "first responders" in the immune response to infectious and non-infectious stimuli. Unlike other immune cells, neutrophils can mount a robust response (including a change in surface markers and the production of extracellular traps and reactive oxygen species) just minutes after sensing a disturbance. It has been speculated that, in some individuals, the activation of neutrophils inadvertently leads to the generation of anti-neutrophil cytoplasmic autoantibodies (ANCA) against particular neutrophil proteins (antigens) such as myeloperoxidase (MPO) and proteinase 3 (PR3). In these individuals, continuous ANCA-antigen interactions are thought to drive persistent activation of neutrophils, chronic immune activation, and disease, most notably, small vessel vasculitis. There are significant gaps however in our understanding of the underlying mechanisms and even the pathogenicity of ANCA given that vasculitis can develop in the absence of ANCA, and that ANCA have been found in circulation in other conditions with no apparent contribution to disease. These gaps are particularly evident in the context of human studies. Herein, we review knowledge on neutrophil-derived ANCA antigens PR3 and MPO, ANCA generation, and ANCA-antigen interaction(s) that may promote immune activation and disease.
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