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- 2019
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Tidskriftsartikel (refereegranskat)
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- Loza, M. J., et al.
(författare)
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Validated and longitudinally stable asthma phenotypes based on cluster analysis of the ADEPT study
- 2016
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Ingår i: Respiratory Research. - : Springer Nature. - 1465-9921 .- 1465-993X. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Asthma is a disease of varying severity and differing disease mechanisms. To date, studies aimed at stratifying asthma into clinically useful phenotypes have produced a number of phenotypes that have yet to be assessed for stability and to be validated in independent cohorts. The aim of this study was to define and validate, for the first time ever, clinically driven asthma phenotypes using two independent, severe asthma cohorts: ADEPT and U-BIOPRED. Methods: Fuzzy partition-around-medoid clustering was performed on pre-specified data from the ADEPT participants (n = 156) and independently on data from a subset of U-BIOPRED asthma participants (n = 82) for whom the same variables were available. Models for cluster classification probabilities were derived and applied to the 12-month longitudinal ADEPT data and to a larger subset of the U-BIOPRED asthma dataset (n = 397). High and low type-2 inflammation phenotypes were defined as high or low Th2 activity, indicated by endobronchial biopsies gene expression changes downstream of IL-4 or IL-13. Results: Four phenotypes were identified in the ADEPT (training) cohort, with distinct clinical and biomarker profiles. Phenotype 1 was "mild, good lung function, early onset", with a low-inflammatory, predominantly Type-2, phenotype. Phenotype 2 had a "moderate, hyper-responsive, eosinophilic" phenotype, with moderate asthma control, mild airflow obstruction and predominant Type-2 inflammation. Phenotype 3 had a "mixed severity, predominantly fixed obstructive, non-eosinophilic and neutrophilic" phenotype, with moderate asthma control and low Type-2 inflammation. Phenotype 4 had a "severe uncontrolled, severe reversible obstruction, mixed granulocytic" phenotype, with moderate Type-2 inflammation. These phenotypes had good longitudinal stability in the ADEPT cohort. They were reproduced and demonstrated high classification probability in two subsets of the U-BIOPRED asthma cohort. Conclusions: Focusing on the biology of the four clinical independently-validated easy-to-assess ADEPT asthma phenotypes will help understanding the unmet need and will aid in developing tailored therapies. Trial registration:NCT01274507(ADEPT), registered October 28, 2010 and NCT01982162(U-BIOPRED), registered October 30, 2013.
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- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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- Beye, Martin, et al.
(författare)
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Chemical Bond Activation Observed with an X-ray Laser
- 2016
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185 .- 1948-7185. ; 7:18, s. 3647-3651
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Tidskriftsartikel (refereegranskat)abstract
- The concept of bonding and antibonding orbitals is fundamental in chemistry. The population of those orbitals and the energetic difference between the two reflect the strength of the bonding interaction. Weakening the bond is expected to reduce this energetic splitting, but the transient character of bond-activation has so far prohibited direct experimental access. Here we apply time-resolved soft X-ray spectroscopy at a free electron laser to directly observe the decreased bonding antibonding splitting following bond-activation using an ultrashort optical laser pulse.
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| 7. |
- Lempart, Michael, et al.
(författare)
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Pelvic U-Net : multi-label semantic segmentation of pelvic organs at risk for radiation therapy anal cancer patients using a deeply supervised shuffle attention convolutional neural network
- 2022
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Ingår i: Radiation Oncology. - : Springer Science and Business Media LLC. - 1748-717X. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Delineation of organs at risk (OAR) for anal cancer radiation therapy treatment planning is a manual and time-consuming process. Deep learning-based methods can accelerate and partially automate this task. The aim of this study was to develop and evaluate a deep learning model for automated and improved segmentations of OAR in the pelvic region. Methods: A 3D, deeply supervised U-Net architecture with shuffle attention, referred to as Pelvic U-Net, was trained on 143 computed tomography (CT) volumes, to segment OAR in the pelvic region, such as total bone marrow, rectum, bladder, and bowel structures. Model predictions were evaluated on an independent test dataset (n = 15) using the Dice similarity coefficient (DSC), the 95th percentile of the Hausdorff distance (HD95), and the mean surface distance (MSD). In addition, three experienced radiation oncologists rated model predictions on a scale between 1–4 (excellent, good, acceptable, not acceptable). Model performance was also evaluated with respect to segmentation time, by comparing complete manual delineation time against model prediction time without and with manual correction of the predictions. Furthermore, dosimetric implications to treatment plans were evaluated using different dose-volume histogram (DVH) indices. Results: Without any manual corrections, mean DSC values of 97%, 87% and 94% were found for total bone marrow, rectum, and bladder. Mean DSC values for bowel cavity, all bowel, small bowel, and large bowel were 95%, 91%, 87% and 81%, respectively. Total bone marrow, bladder, and bowel cavity segmentations derived from our model were rated excellent (89%, 93%, 42%), good (9%, 5%, 42%), or acceptable (2%, 2%, 16%) on average. For almost all the evaluated DVH indices, no significant difference between model predictions and manual delineations was found. Delineation time per patient could be reduced from 40 to 12 min, including manual corrections of model predictions, and to 4 min without corrections. Conclusions: Our Pelvic U-Net led to credible and clinically applicable OAR segmentations and showed improved performance compared to previous studies. Even though manual adjustments were needed for some predicted structures, segmentation time could be reduced by 70% on average. This allows for an accelerated radiation therapy treatment planning workflow for anal cancer patients.
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- Bender, P., et al.
(författare)
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Structural and magnetic properties of multi-core nanoparticles analysed using a generalised numerical inversion method
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The structural and magnetic properties of magnetic multi-core particles were determined by numerical inversion of small angle scattering and isothermal magnetisation data. The investigated particles consist of iron oxide nanoparticle cores (9 nm) embedded in poly(styrene) spheres (160 nm). A thorough physical characterisation of the particles included transmission electron microscopy, X-ray diffraction and asymmetrical flow field-flow fractionation. Their structure was ultimately disclosed by an indirect Fourier transform of static light scattering, small angle X-ray scattering and small angle neutron scattering data of the colloidal dispersion. The extracted pair distance distribution functions clearly indicated that the cores were mostly accumulated in the outer surface layers of the poly(styrene) spheres. To investigate the magnetic properties, the isothermal magnetisation curves of the multicore particles (immobilised and dispersed in water) were analysed. The study stands out by applying the same numerical approach to extract the apparent moment distributions of the particles as for the indirect Fourier transform. It could be shown that the main peak of the apparent moment distributions correlated to the expected intrinsic moment distribution of the cores. Additional peaks were observed which signaled deviations of the isothermal magnetisation behavior from the non-interacting case, indicating weak dipolar interactions.
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| 9. |
- Dalby, Lars, et al.
(författare)
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The status of the Nordic populations of the Mallard (Anas platyrhynchos) in a changing world
- 2013
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Ingår i: Ornis Fennica. - : University of Helsinki. - 0030-5685. ; 90:1, s. 2-15
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Tidskriftsartikel (refereegranskat)abstract
- Dabbling ducks (Anas spp.) are important migratory quarry species, protected as a shared resource under international legislation. However, there is a lack of sufficient high-quality data on vital demographic rates and long-term trends in numbers to judge the conservation status of many duck populations at the flyway level. In response to reported declines in the North-West European flyway population of the Mallard, we compiled available data on this species in the Nordic countries up to 2010. Generally, national breeding numbers showed increasing trends, wintering abundance showed variable trends, and productivity measures indicated stable or increasing trends. Major knowledge gaps were identified, namely the size of hunting bags, the influence of the released Mallards and the role of short-stopping in explaining changing patterns of wintering abundance across the North-West European flyway. Numerically the Nordic breeding population appears in "good condition", and the wintering numbers have been either stable or increasing in the last two decades. The annual number of releases needs to be determined in order to judge the sustainability of the current levels of exploitation. Overall, none of the indicators showed alarming signs for the Mallard population in the Nordic countries when considered in isolation. However, the widespread decline in wintering numbers elsewhere across North-western Europe requires urgent pan-European action.
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| 10. |
- Engdar, Ulf, et al.
(författare)
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Investigation of turbulence models applied to premixed combustion using a level-set flamelet library approach
- 2004
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Ingår i: Journal of Engineering for Gas Turbines and Power. - : ASME International. - 1528-8919 .- 0742-4795. ; 126:4, s. 701-707
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Tidskriftsartikel (refereegranskat)abstract
- Most of the common modeling approaches to premixed combustion in engineering applications are either based on the assumption of infinitely fast chemistry or the flamelet assumption with simple chemistry. The level-set flamelet library approach (FLA) has shown great potential in predicting major species and heat release, as well as intermediate and minor species, where more simple models often fail. In this approach, the mean flame surface is tracked by a level-set equation. The flamelet libraries are generated by all external code, which employs a detailed chemical mechanism. However a model for the turbulent flame speed is required, which, among other considerations, depends on the turbulence intensity, i.e., these models may show sensitivity to turbulence modeling. In this paper, the FLA model was implemented in the commercial CFD program Star-Cd, and applied to a lean premixed flame stabilized by a triangular prism (bluff body). The objective of this paper has been to investigate the impact on the mean flame position, and hence on the temperature and species distribution, using three different turbulent flame speed models in combination with four different turbulence models. The turbulence models investigated are: the standard k-epsilon model, a cubic nonlinear k-e model, the standard k-omega model and the shear stress transport (SST) k-omega model. In general, the computed results agree well with experimental data for all computed cases, although the turbulence intensity is strongly underestimated at the downstream position. The use of the nonlinear k-epsilon model offers no advantage over the standard model, regardless of flame speed model. The k-omega based turbulence models predict the highest turbulence intensity with the shortest flame lengths as a consequence. The Muller flame speed model shows the least sensitivity to the choice of turbulence model.
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