| 1. |
- Menden, MP, et al.
(författare)
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 2674-
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Tidskriftsartikel (refereegranskat)abstract
- The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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| 2. |
- Keskinen, H., et al.
(författare)
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Evolution of Nanoparticle Composition in CLOUD in Presence of Sulphuric Acid, Ammonia and Organics
- 2013
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Ingår i: NUCLEATION AND ATMOSPHERIC AEROSOLS. - : American Institute of Physics (AIP). - 9780735411524 ; , s. 291-294
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Konferensbidrag (refereegranskat)abstract
- In this study, we investigate the composition of nucleated nanoparticles formed from sulphuric acid, ammonia, amines, and oxidised organics in the CLOUD chamber experiments at CERN. The investigation is carried out via analysis of the particle hygroscopicity (size range of 15-63 nm), ethanol affinity (15-50nm), oxidation state (<50 nm), and ion composition (few nanometers). The organic volume fraction of particles increased with an increase in particle diameter in presence of the sulphuric acid, ammonia and organics. Vice versa, the sulphuric acid volume fraction decreased when the particle diameter increased. The results provide information on the size-dependent composition of nucleated aerosol particles.
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| 3. |
- Main, Chris J., et al.
(författare)
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Implementation Science and Employer Disability Practices : Embedding Implementation Factors in Research Designs
- 2016
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Ingår i: Journal of occupational rehabilitation. - : Springer-Verlag New York. - 1053-0487 .- 1573-3688. ; 26:4, s. 448-464
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: For work disability research to have an impact on employer policies and practices it is important for such research to acknowledge and incorporate relevant aspects of the workplace. The goal of this article is to summarize recent theoretical and methodological advances in the field of Implementation Science, relate these to research of employer disability management practices, and recommend future research priorities.Methods: The authors participated in a year-long collaboration culminating in an invited 3-day conference, “Improving Research of Employer Practices to Prevent Disability”, held October 14–16, 2015, in Hopkinton, MA, USA. The collaboration included a topical review of the literature, group conference calls to identify key areas and challenges, drafting of initial documents, review of industry publications, and a conference presentation that included feedback from peer researchers and a question/answer session with a special panel of knowledge experts with direct employer experience.Results: A 4-phase implementation model including both outer and inner contexts was adopted as the most appropriate conceptual framework, and aligned well with the set of process evaluation factors described in both the work disability prevention literature and the grey literature. Innovative interventions involving disability risk screening and psychologically-based interventions have been slow to gain traction among employers and insurers. Research recommendations to address this are : (1) to assess organizational culture and readiness for change in addition to individual factors; (2) to conduct process evaluations alongside controlled trials; (3) to analyze decision-making factors among stakeholders; and (4) to solicit input from employers and insurers during early phases of study design.Conclusions: Future research interventions involving workplace support and involvement to prevent disability may be more feasible for implementation if organizational decision-making factors are imbedded in research designs and interventions are developed to take account of these influences.
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| 4. |
- Aarons, G. A., et al.
(författare)
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Fostering international collaboration in implementation science and research : A concept mapping exploratory study
- 2019
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Ingår i: BMC Research Notes. - : BioMed Central Ltd.. - 1756-0500. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Objective: International collaboration in science has received increasing attention given emphases on relevance, generalizability, and impact of research. Implementation science (IS) is a growing discipline that aims to translate clinical research findings into health services. Research is needed to identify efficient and effective ways to foster international collaboration in IS. Concept-mapping (CM) was utilized with a targeted sample for preliminary exploration of fostering international collaboration. Concept-mapping is a mixed-method approach (qualitative/quantitative) particularly suited for identifying essential themes and action items to facilitate planning among diverse stakeholders. We sought to identify key factors likely to facilitate productive and rewarding international collaborations in implementation research. Results: We identified eleven dimensions: Strategic Planning; Practicality; Define Common Principles; Technological Tools for Collaboration; Funding; Disseminate Importance of Fostering International Collaboration in IS; Knowledge Sharing; Innovative & Adaptive Research; Training IS Researchers; Networking & Shared Identity; Facilitate Meetings. Strategic Planning and Funding were highest rated for importance and Strategic Planning and Networking and Shared Identity were rated most feasible to institute. Fostering international collaboration in IS can accelerate the efficiency, relevance, and generalizability of implementation research. Strategies should be developed and tested to improve international collaborations and engage junior and experienced investigators in collaborations advancing implementation science and practice.
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| 5. |
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| 6. |
- Kim, J., et al.
(författare)
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Hygroscopicity of nanoparticles produced from homogeneous nucleation in the CLOUD experiments
- 2016
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 16:1, s. 293-304
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Tidskriftsartikel (refereegranskat)abstract
- Sulfuric acid, amines and oxidized organics have been found to be important compounds in the nucleation and initial growth of atmospheric particles. Because of the challenges involved in determining the chemical composition of objects with very small mass, however, the properties of the freshly nucleated particles and the detailed pathways of their formation processes are still not clear. In this study,we focus on a challenging size range, i.e., particles that have grown to diameters of 10 and 15 nm following nucleation, and measure their water uptake. Water uptake is useful information for indirectly obtaining chemical composition of aerosol particles. We use a nanometer-hygroscopicity tandem differential mobility analyzer (nano-HTDMA) at sub-saturated conditions (ca. 90% relative humidity at 293 K) to measure the hygroscopicity of particles during the seventh Cosmics Leaving OUtdoor Droplets (CLOUD7) campaign performed at CERN in 2012. In CLOUD7, the hygroscopicity of nucleated nanoparticles was measured in the presence of sulfuric acid, sulfuric acid-dimethylamine, and sulfuric acid-organics derived from alpha-pinene oxidation. The hygroscopicity parameter kappa decreased with increasing particle size, indicating decreasing acidity of particles. No clear effect of the sulfuric acid concentration on the hygroscopicity of 10 nm particles produced from sulfuric acid and dimethylamine was observed, whereas the hygroscopicity of 15 nm particles sharply decreased with decreasing sulfuric acid concentrations. In particular, when the concentration of sulfuric acid was 5.1 x 10(6) molecules cm(-3) in the gas phase, and the dimethylamine mixing ratio was 11.8 ppt, the measured kappa of 15 nm particles was 0.31 +/- 0.01: close to the value reported for dimethylaminium sulfate (DMAS) (kappa(DMAS) similar to 0.28). Furthermore, the difference in kappa between sulfuric acid and sulfuric acid-dimethylamine experiments increased with increasing particle size. The kappa values of particles in the presence of sulfuric acid and organics were much smaller than those of particles in the presence of sulfuric acid and dimethylamine. This suggests that the organics produced from alpha-pinene ozonolysis play a significant role in particle growth even at 10 nm sizes.
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| 7. |
- Tröstl, Jasmin, et al.
(författare)
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The role of low-volatility organic compounds in initial particle growth in the atmosphere
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 533:7604, s. 527-531
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Tidskriftsartikel (refereegranskat)abstract
- About half of present-day cloud condensation nuclei originate from atmospheric nucleation, frequently appearing as a burst of new particles near midday(1). Atmospheric observations show that the growth rate of new particles often accelerates when the diameter of the particles is between one and ten nanometres(2,3). In this critical size range, new particles are most likely to be lost by coagulation with pre-existing particles(4), thereby failing to form new cloud condensation nuclei that are typically 50 to 100 nanometres across. Sulfuric acid vapour is often involved in nucleation but is too scarce to explain most subsequent growth(5,6), leaving organic vapours as the most plausible alternative, at least in the planetary boundary layer(7-10). Although recent studies(11-13) predict that low-volatility organic vapours contribute during initial growth, direct evidence has been lacking. The accelerating growth may result from increased photolytic production of condensable organic species in the afternoon(2), and the presence of a possible Kelvin (curvature) effect, which inhibits organic vapour condensation on the smallest particles (the nano-Kohler theory)(2,14), has so far remained ambiguous. Here we present experiments performed in a large chamber under atmospheric conditions that investigate the role of organic vapours in the initial growth of nucleated organic particles in the absence of inorganic acids and bases such as sulfuric acid or ammonia and amines, respectively. Using data from the same set of experiments, it has been shown(15) that organic vapours alone can drive nucleation. We focus on the growth of nucleated particles and find that the organic vapours that drive initial growth have extremely low volatilities (saturation concentration less than 10(-4.5) micrograms per cubic metre). As the particles increase in size and the Kelvin barrier falls, subsequent growth is primarily due to more abundant organic vapours of slightly higher volatility (saturation concentrations of 10(-4.5) to 10(-0.5) micrograms per cubic metre). We present a particle growth model that quantitatively reproduces our measurements. Furthermore, we implement a parameterization of the first steps of growth in a global aerosol model and find that concentrations of atmospheric cloud concentration nuclei can change substantially in response, that is, by up to 50 per cent in comparison with previously assumed growth rate parameterizations.
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| 8. |
- Almeida, Joao, et al.
(författare)
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Molecular understanding of sulphuric acid-amine particle nucleation in the atmosphere
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 502:7471, s. 359-
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Tidskriftsartikel (refereegranskat)abstract
- Nucleation of aerosol particles from trace atmospheric vapours is thought to provide up to half of global cloud condensation nuclei(1). Aerosols can cause a net cooling of climate by scattering sunlight and by leading to smaller but more numerous cloud droplets, which makes clouds brighter and extends their lifetimes(2). Atmospheric aerosols derived from human activities are thought to have compensated for a large fraction of the warming caused by greenhouse gases(2). However, despite its importance for climate, atmospheric nucleation is poorly understood. Recently, it has been shown that sulphuric acid and ammonia cannot explain particle formation rates observed in the lower atmosphere(3). It is thought that amines may enhance nucleation(4-16), but until now there has been no direct evidence for amine ternary nucleation under atmospheric conditions. Here we use the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN and find that dimethylamine above three parts per trillion by volume can enhance particle formation rates more than 1,000-fold compared with ammonia, sufficient to account for the particle formation rates observed in the atmosphere. Molecular analysis of the clusters reveals that the faster nucleation is explained by a base-stabilization mechanism involving acid-amine pairs, which strongly decrease evaporation. The ion-induced contribution is generally small, reflecting the high stability of sulphuric acid-dimethylamine clusters and indicating that galactic cosmic rays exert only a small influence on their formation, except at low overall formation rates. Our experimental measurements are well reproduced by a dynamical model based on quantum chemical calculations of binding energies of molecular clusters, without any fitted parameters. These results show that, in regions of the atmosphere near amine sources, both amines and sulphur dioxide should be considered when assessing the impact of anthropogenic activities on particle formation.
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| 9. |
- Kirkby, Jasper, et al.
(författare)
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Ion-induced nucleation of pure biogenic particles
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 533:7604, s. 521-526
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric aerosols and their effect on clouds are thought to be important for anthropogenic radiative forcing of the climate, yet remain poorly understood(1). Globally, around half of cloud condensation nuclei originate from nucleation of atmospheric vapours(2). It is thought that sulfuric acid is essential to initiate most particle formation in the atmosphere(3,4), and that ions have a relatively minor role(5). Some laboratory studies, however, have reported organic particle formation without the intentional addition of sulfuric acid, although contamination could not be excluded(6,7). Here we present evidence for the formation of aerosol particles from highly oxidized biogenic vapours in the absence of sulfuric acid in a large chamber under atmospheric conditions. The highly oxygenated molecules (HOMs) are produced by ozonolysis of a-pinene. We find that ions from Galactic cosmic rays increase the nucleation rate by one to two orders of magnitude compared with neutral nucleation. Our experimental findings are supported by quantum chemical calculations of the cluster binding energies of representative HOMs. Ion-induced nucleation of pure organic particles constitutes a potentially widespread source of aerosol particles in terrestrial environments with low sulfuric acid pollution.
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| 10. |
- Lehtipalo, Katrianne, et al.
(författare)
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The effect of acid-base clustering and ions on the growth of atmospheric nano-particles
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere.
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