| 1. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 2. |
- Alexandrov, Ludmil B., et al.
(författare)
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Signatures of mutational processes in human cancer
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 500:7463, s. 415-421
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Tidskriftsartikel (refereegranskat)abstract
- All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, 'kataegis', is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy.
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| 3. |
- Read, Randy J., et al.
(författare)
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A New Generation of Crystallographic Validation Tools for the Protein Data Bank
- 2011
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 19:10, s. 1395-1412
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Tidskriftsartikel (refereegranskat)abstract
- This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a now assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.
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| 4. |
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| 5. |
- Caplat, Paul, et al.
(författare)
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Sophia Title
- 2013
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Ingår i: Oikos. - : Wiley. - 1600-0706 .- 0030-1299. ; 122:9, s. 1265-1274
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Tidskriftsartikel (refereegranskat)abstract
- Synthesis Prediction and management of species responses to climate change is an urgent but relatively young research field. Therefore, climate change ecology must by necessity borrow from other fields. Invasion ecology is particularly well-suited to informing climate change ecology because both invasion ecology and climate change ecology address the trajectories of rapidly changing novel systems. Here we outline the broad range of active research questions in climate change ecology where research from invasion ecology can stimulate advances. We present ideas for how concepts, case-studies and methodology from invasion ecology can be adapted to improve prediction and management of species responses to climate change. A major challenge in this era of rapid climate change is to predict changes in species distributions and their impacts on ecosystems, and, if necessary, to recommend management strategies for maintenance of biodiversity or ecosystem services. Biological invasions, studied in most biomes of the world, can provide useful analogs for some of the ecological consequences of species distribution shifts in response to climate change. Invasions illustrate the adaptive and interactive responses that can occur when species are confronted with new environmental conditions. Invasion ecology complements climate change research and provides insights into the following questions: 1) how will species distributions respond to climate change? 2) how will species movement affect recipient ecosystems? And 3) should we, and if so how can we, manage species and ecosystems in the face of climate change? Invasion ecology demonstrates that a trait-based approach can help to predict spread speeds and impacts on ecosystems, and has the potential to predict climate change impacts on species ranges and recipient ecosystems. However, there is a need to analyse traits in the context of life-history and demography, the stage in the colonisation process (e.g. spread, establishment or impact), the distribution of suitable habitats in the landscape, and the novel abiotic and biotic conditions under which those traits are expressed. As is the case with climate change, invasion ecology is embedded within complex societal goals. Both disciplines converge on similar questions of when to intervene? and what to do? which call for a better understanding of the ecological processes and social values associated with changing ecosystems.
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| 6. |
- Lasslop, Gitta, et al.
(författare)
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Separation of net ecosystem exchange into assimilation and respiration using a light response curve approach: critical issues and global evaluation
- 2010
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 16:1, s. 187-208
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Forskningsöversikt (refereegranskat)abstract
- The measured net ecosystem exchange (NEE) of CO2 between the ecosystem and the atmosphere reflects the balance between gross CO2 assimilation [gross primary production (GPP)] and ecosystem respiration (R-eco). For understanding the mechanistic responses of ecosystem processes to environmental change it is important to separate these two flux components. Two approaches are conventionally used: (1) respiration measurements made at night are extrapolated to the daytime or (2) light-response curves are fit to daytime NEE measurements and respiration is estimated from the intercept of the ordinate, which avoids the use of potentially problematic nighttime data. We demonstrate that this approach is subject to biases if the effect of vapor pressure deficit (VPD) modifying the light response is not included. We introduce an algorithm for NEE partitioning that uses a hyperbolic light response curve fit to daytime NEE, modified to account for the temperature sensitivity of respiration and the VPD limitation of photosynthesis. Including the VPD dependency strongly improved the model's ability to reproduce the asymmetric diurnal cycle during periods with high VPD, and enhances the reliability of R-eco estimates given that the reduction of GPP by VPD may be otherwise incorrectly attributed to higher R-eco. Results from this improved algorithm are compared against estimates based on the conventional nighttime approach. The comparison demonstrates that the uncertainty arising from systematic errors dominates the overall uncertainty of annual sums (median absolute deviation of GPP: 47 g C m(-2) yr(-1)), while errors arising from the random error (median absolute deviation: similar to 2 g C m(-2) yr(-1)) are negligible. Despite site-specific differences between the methods, overall patterns remain robust, adding confidence to statistical studies based on the FLUXNET database. In particular, we show that the strong correlation between GPP and R-eco is not spurious but holds true when quasi-independent, i.e. daytime and nighttime based estimates are compared.
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| 7. |
- Sorensen, Julie A, et al.
(författare)
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The social marketing of safety behaviors : a quasi-randomized controlled trial of tractor retrofitting incentives
- 2011
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Ingår i: American Journal of Public Health. - 0090-0036 .- 1541-0048. ; 101:4, s. 678-684
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Tidskriftsartikel (refereegranskat)abstract
- Objectives. We assessed the effect of social marketing incentives on dispositions toward retrofitting and retrofitting behavior among farmers whose tractors lacked rollover protective structures. Methods. From 2006 to 2007, we conducted a quasi-randomized controlled trial with 391 farm owners in New York and Pennsylvania surveyed before and after exposure to 1 of 3 tractor retrofitting incentive combinations. These combinations were offered in 3 trial regions; region 1 received rebates; region 2 received rebates, messages, and promotion and was considered the social marketing region; and region 3 received messages and promotion. A fourth region served as a control. Results. The social marketing region generated the greatest increases in readiness to retrofit, intentions to retrofit, and message recall. In addition, postintervention stage of change, intentions, attitudes, subjective norms, and perceived behavioral control levels were higher among farmers who had retrofitted tractors. Conclusions. Our results showed that a social marketing approach (financial incentives, tailored messages, and promotion) had the greatest influence on message recall, readiness to retrofit tractors, and intentions to retrofit tractors and that behavioral measures were fairly good predictors of tractor retrofitting behaviors.
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