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- Sherratt, K., et al.
(författare)
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Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations
- 2023
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance.Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models.Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.
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| 2. |
- Teixeira, J., et al.
(författare)
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Tropical and Subtropical Cloud Transitions in Weather and Climate Prediction Models : The GCSS/WGNE Pacific Cross-Section Intercomparison (GPCI)
- 2011
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Ingår i: Journal of Climate. - 0894-8755 .- 1520-0442. ; 24:20, s. 5223-5256
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Tidskriftsartikel (refereegranskat)abstract
- A model evaluation approach is proposed in which weather and climate prediction models are analyzed along a Pacific Ocean cross section, from the stratocumulus regions off the coast of California, across the shallow convection dominated trade winds, to the deep convection regions of the ITCZ-the Global Energy and Water Cycle Experiment Cloud System Study/Working Group on Numerical Experimentation (GCSS/WGNE) Pacific Cross-Section Intercomparison (GPCI). The main goal of GPCI is to evaluate and help understand and improve the representation of tropical and subtropical cloud processes in weather and climate prediction models. In this paper, a detailed analysis of cloud regime transitions along the cross section from the subtropics to the tropics for the season June-July-August of 1998 is presented. This GPCI study confirms many of the typical weather and climate prediction model problems in the representation of clouds: underestimation of clouds in the stratocumulus regime by most models with the corresponding consequences in terms of shortwave radiation biases; overestimation of clouds by the 40-yr ECMWF Re-Analysis (ERA-40) in the deep tropics (in particular) with the corresponding impact in the outgoing longwave radiation; large spread between the different models in terms of cloud cover, liquid water path and shortwave radiation; significant differences between the models in terms of vertical cross sections of cloud properties (in particular), vertical velocity, and relative humidity. An alternative analysis of cloud cover mean statistics is proposed where sharp gradients in cloud cover along the GPCI transect are taken into account. This analysis shows that the negative cloud bias of some models and ERA-40 in the stratocumulus regions [as compared to the first International Satellite Cloud Climatology Project (ISCCP)] is associated not only with lower values of cloud cover in these regimes, but also with a stratocumulus-to-cumulus transition that occurs too early along the trade wind Lagrangian trajectory. Histograms of cloud cover along the cross section differ significantly between models. Some models exhibit a quasi-bimodal structure with cloud cover being either very large (close to 100%) or very small, while other models show a more continuous transition. The ISCCP observations suggest that reality is in-between these two extreme examples. These different patterns reflect the diverse nature of the cloud, boundary layer, and convection parameterizations in the participating weather and climate prediction models.
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- Knudsen, N. P. H., et al.
(författare)
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Different human vaccine adjuvants promote distinct antigenin-dependent immunological signatures tailored to different pathogens
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The majority of vaccine candidates in clinical development are highly purified proteins and peptides relying on adjuvants to enhance and/or direct immune responses. Despite the acknowledged need for novel adjuvants, there are still very few adjuvants in licensed human vaccines. A vast number of adjuvants have been tested pre-clinically using different experimental conditions, rendering it impossible to directly compare their activity. We performed a head-to-head comparison of five different adjuvants Alum, MF59 (R), GLA-SE, IC31 (R) and CAF01 in mice and combined these with antigens from M. tuberculosis, influenza, and chlamydia to test immune-profiles and efficacy in infection models using standardized protocols. Regardless of antigen, each adjuvant had a unique immunological signature suggesting that the adjuvants have potential for different disease targets. Alum increased antibody titers; MF59 (R) induced strong antibody and IL-5 responses; GLA-SE induced antibodies and Th1; CAF01 showed a mixed Th1/Th17 profile and IC31 (R) induced strong Th1 responses. MF59 (R) and GLA-SE were strong inducers of influenza HI titers while CAF01, GLA-SE and IC31 (R) enhanced protection to TB and chlamydia. Importantly, this is the first extensive attempt to categorize clinical-grade adjuvants based on their immune profiles and protective efficacy to inform a rational development of next generation vaccines for human use.
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| 21. |
- Luu, TT, et al.
(författare)
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Independent control of natural killer cell responsiveness and homeostasis at steady-state by CD11c+ dendritic cells
- 2016
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6, s. 37996-
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Tidskriftsartikel (refereegranskat)abstract
- During infection and inflammation, dendritic cells (DC) provide priming signals for natural killer (NK) cells via mechanisms distinct from their antigen processing and presentation functions. The influence of DC on resting NK cells, i.e. at steady-state, is less well studied. We here demonstrate that as early as 1 day after DC depletion, NK cells in naïve mice downregulated the NKG2D receptor and showed decreased constitutive phosphorylation of AKT and mTOR. Subsequently, apoptotic NK cells appeared in the spleen concomitant with reduced NK cell numbers. At 4 days after the onset of DC depletion, increased NK cell proliferation was seen in the spleen resulting in an accumulation of Ly49 receptor-negative NK cells. In parallel, NK cell responsiveness to ITAM-mediated triggering and cytokine stimulation dropped across maturation stages, suggestive of a functional deficiency independent from the homeostatic effect. A role for IL-15 in maintaining NK cell function was supported by a gene signature analysis of NK cell from DC-depleted mice as well as by in vivo DC transfer experiments. We propose that DC, by means of IL-15 transpresentation, are required to maintain not only homeostasis, but also function, at steady-state. These processes appear to be regulated independently from each other.
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| 23. |
- Luu, TT, et al.
(författare)
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Short-term IL-15 priming leaves a long-lasting signalling imprint in mouse NK cells independently of a metabolic switch
- 2021
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Ingår i: Life science alliance. - : Life Science Alliance, LLC. - 2575-1077. ; 4:4
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Tidskriftsartikel (refereegranskat)abstract
- IL-15 priming of NK cells is a broadly accepted concept, but the dynamics and underlying molecular mechanisms remain poorly understood. We show that as little as 5 min of IL-15 treatment in vitro, followed by removal of excess cytokines, results in a long-lasting, but reversible, augmentation of NK cell responsiveness upon activating receptor cross-linking. In contrast to long-term stimulation, improved NK cell function after short-term IL-15 priming was not associated with enhanced metabolism but was based on the increased steady-state phosphorylation level of signalling molecules downstream of activating receptors. Inhibition of JAK3 eliminated this priming effect, suggesting a cross talk between the IL-15 receptor and ITAM-dependent activating receptors. Increased signalling molecule phosphorylation levels, calcium flux, and IFN-γ secretion lasted for up to 3 h after IL-15 stimulation before returning to baseline. We conclude that IL-15 rapidly and reversibly primes NK cell function by modulating activating receptor signalling. Our findings suggest a mechanism by which NK cell reactivity can potentially be maintained in vivo based on only brief encounters with IL-15 trans-presenting cells.
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| 27. |
- Pind, A. A. A., et al.
(författare)
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Adjuvants Enhance the Induction of Germinal Center and Antibody Secreting Cells in Spleen and Their Persistence in Bone Marrow of Neonatal Mice
- 2019
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Immaturity of the immune system contributes to poor vaccine responses in early life. Germinal center (GC) activation is limited due to poorly developed follicular dendritic cells (FDC), causing generation of few antibody-secreting cells (ASCs) with limited survival and transient antibody responses. Herein, we compared the potential of five adjuvants, namely LT-K63, mmCT, MF59, IC31, and alum to overcome limitations of the neonatal immune system and to enhance and prolong responses of neonatal mice to a pneumococcal conjugate vaccine Pnc1-TT. The adjuvants LT-K63, mmCT, MF59, and IC31 significantly enhanced GC formation and FDC maturation in neonatal mice when co-administered with Pnc1-TT. This enhanced GC induction correlated with significantly enhanced vaccine-specific ASCs by LT-K63, mmCT, and MF59 in spleen 14 days after immunization. Furthermore, mmCT, MF59, and IC31 prolonged the induction of vaccine-specific ASCs in spleen and increased their persistence in bone marrow up to 9 weeks after immunization, as previously shown for LT-K63. Accordingly, serum Abs persisted above protective levels against pneumococcal bacteremia and pneumonia. In contrast, alum only enhanced the primary induction of vaccine-specific IgG Abs, which was transient. Our comparative study demonstrated that, in contrast to alum, LT-K63, mmCT, MF59, and IC31 can overcome limitations of the neonatal immune system and enhance both induction and persistence of protective immune response when administered with Pnc1-TT. These adjuvants are promising candidates for early life vaccination.
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| 31. |
- Sarkar, Anjana, 1978-, et al.
(författare)
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Photocatalytic activity of TiO2 nanoparticles : effect of thermal annealing under various gaseous atmospheres
- 2012
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Ingår i: Nanotechnology. - : Institute of Physics Publishing (IOPP). - 0957-4484 .- 1361-6528. ; 23:47, s. 475711-475719
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Tidskriftsartikel (refereegranskat)abstract
- The structure, composition and photocatalytic activity of TiO2 nanoparticles annealed in various gas atmospheres (N2, NH3 and H2) were studied in this work. The effect of treatment on crystal structure, particle size, chemical composition and optical absorbance were assessed by means of x-ray diffraction, transmission electron microscopy, x-ray photoelectron spectroscopy and diffuse optical reflectance/transmittance measurements, respectively. Photocatalytic properties of the materials were evaluated by three different methods: degradation of methyl orange in water, killing of Staphylococcus aureus bacteria and photogeneration of radicals in the presence of 3-carboxy-2,2,5,5-tetramethyl pyrrolidine-1-oxyl (PCA) marker molecules. The results indicate that the correlation between pretreatment and the photocatalytic performance depends on the photocatalytic processes and cannot be generalized.
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| 32. |
- Schmied, L, et al.
(författare)
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Platelet-Mediated Protection of Cancer Cells From Immune Surveillance - Possible Implications for Cancer Immunotherapy
- 2021
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Ingår i: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 12, s. 640578-
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Tidskriftsartikel (refereegranskat)abstract
- The growing insights in the complex interactions between metastatic cancer-cells and platelets have revealed that platelet tumor cell interactions in the blood stream are an important factor supporting tumor metastasis. An increased coagulability of platelets facilitates the vascular evasion and establishment of solid tumor metastasis. Furthermore, platelets can support an immunosuppressive tumor microenvironment or shield tumor cells directly from engagement of cytotoxic lymphocytes as e.g., natural killer (NK) cells. Platelets are both in the tumor microenvironment and systemically the quantitatively most important source of TGF-β, which is a key cytokine for immunosuppression in the tumor microenvironment. If similar platelet-tumor interactions are of physiological relevance in hematological malignancies remains less well-studied. This might be important, as T- and NK cell mediated graft vs. leukemia effects (GvL) are well-documented and malignant hematological cells have a high exposure to platelets compared to solid tumors. As NK cell-based immunotherapies gain increasing attention as a therapeutic option for patients suffering from hematological and other malignancies, we review the known interactions between platelets and NK cells in the solid tumor setting and discuss how these could also apply to hematological cancers. We furthermore explore the possible implications for NK cell therapy in patients with solid tumors and patients who depend on frequent platelet transfusions. As platelets have a protective and supportive effect on cancer cells, the impact of platelet transfusion on immunotherapy and the combination of immunotherapy with platelet inhibitors needs to be evaluated.
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| 36. |
- Trunina, Natalia A., et al.
(författare)
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Monitoring of TiO2 and ZnO Nanoparticle Penetration Into Fnamel and Dentine of Human Tooth IN VITRO and Assessment of Their Photocatalytic Ability
- 2014
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Ingår i: IEEE Journal of Selected Topics in Quantum Electronics. - 1077-260X .- 1558-4542. ; 20:3, s. Article Number: UNSP 7300108-
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Tidskriftsartikel (refereegranskat)abstract
- Penetration of nanoparticles into tooth enamel and dentine is of significant interest upon solving problems related to reduction of tooth sensitivity, enamel strengthening, disinfection, restoration as well as cosmetic bleaching. This paper aims at studying the process of nanoparticle penetration into tooth enamel and dentine samples using nonlinear optical microscopy and at investigating the influence of the same nanoparticles on the generation of free radicals using the electronic paramagnetic resonance technique. We presented in vitro measurements demonstrating that nonlinear optical microscopy, namely, two-photon-excited autfluorescence, second harmonic generation, and hyper-Rayleigh scattering-based microscopy can be used for monitoring and imaging TiO2 and ZnO nanoparticle penetration into tooth tissues. The results indicate that ZnO nanoparticles penetrated into the human tooth enamel and dentine up to a depth of 12 and 45 mu m, respectively, and TiO2 nanoparticles penetrated into dentine to a depth of 5 mu m. The penetration mainly- occurs along either enamel rods or dentinal tubules. Permeability of the dentine was found to be higher than that of enamel (for ZnO particles) by one order of magnitude and the diffusion rate was affected by the particle size being higher for smaller, submicron particles (ZnO) than for micronsized aggregates (TiO2 I. Nitrogen-doped TiO2 nanoparticles generate more radicals in the UV-VIS spectral range in comparison to pristine TiO2 (anatase) and ZnO nanoparticles, therefore, they can potentially be used for disinfection purposes of superficial tooth areas (up to 5-mu m deep).
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| 37. |
- White, Christopher J., et al.
(författare)
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Potential applications of subseasonal-to-seasonal (S2S) predictions
- 2017
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Ingår i: Meteorological Applications. - : John Wiley & Sons. - 1350-4827 .- 1469-8080. ; 24:3, s. 315-325
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Tidskriftsartikel (refereegranskat)abstract
- While seasonal outlooks have been operational for many years, until recently the extended-range timescale referred to as subseasonal-to-seasonal (S2S) has received little attention. S2S prediction fills the gap between short-range weather prediction and long-range seasonal outlooks. Decisions in a range of sectors are made in this extended-range lead time; therefore, there is a strong demand for this new generation of forecasts. International efforts are under way to identify key sources of predictability, improve forecast skill and operationalize aspects of S2S forecasts; however, challenges remain in advancing this new frontier. If S2S predictions are to be used effectively, it is important that, along with science advances, an effort is made to develop, communicate and apply these forecasts appropriately. In this study, the emerging operational S2S forecasts are presented to the wider weather and climate applications community by undertaking the first comprehensive review of sectoral applications of S2S predictions, including public health, disaster preparedness, water management, energy and agriculture. The value of applications-relevant S2S predictions is explored, and the opportunities and challenges facing their uptake are highlighted. It is shown how social sciences can be integrated with S2S development, from communication to decision-making and valuation of forecasts, to enhance the benefits of ‘climate services’ approaches for extended-range forecasting. While S2S forecasting is at a relatively early stage of development, it is concluded that it presents a significant new window of opportunity that can be explored for application-ready capabilities that could allow many sectors the opportunity to systematically plan on a new time horizon.
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| 38. |
- Zomer, Aldert, et al.
(författare)
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Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage
- 2012
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Ingår i: Journal of Bacteriology. - 0021-9193. ; 194:24, s. 6969-6969
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Tidskriftsartikel (refereegranskat)abstract
- Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical M. catarrhalis isolates and will facilitate study of M. catarrhalis pathogenesis.
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