| 1. |
- Schael, S, et al.
(author)
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Precision electroweak measurements on the Z resonance
- 2006
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In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Research review (peer-reviewed)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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| 2. |
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| 3. |
- Aamodt, K., et al.
(author)
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The ALICE experiment at the CERN LHC
- 2008
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In: Journal of Instrumentation. - 1748-0221. ; 3:S08002
-
Research review (peer-reviewed)abstract
- ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries, Its overall dimensions are 16 x 16 x 26 m(3) with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008.
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| 4. |
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| 5. |
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| 6. |
- Clark, Andrew G., et al.
(author)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Journal article (peer-reviewed)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 7. |
- Wortman, J. R., et al.
(author)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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In: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
-
Journal article (peer-reviewed)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 8. |
- Ruperto, N., et al.
(author)
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PRINTO/PRES international website for families of children with rheumatic diseases: www.pediatric-rheumatology.printo.it
- 2005
-
In: Ann Rheum Dis. - : BMJ. - 0003-4967. ; 64:7, s. 1101-6
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Journal article (peer-reviewed)abstract
- OBJECTIVE: To prepare a website for families and health professionals containing up to date information about paediatric rheumatic diseases (PRD). METHODS: Firstly, paediatric rheumatology centres and family self help associations were surveyed to characterise current clinical practice of physicians providing care for children with PRD, research activities, and training facilities of each centre. Secondly, international consensus was reached on the content of the website. Finally, the website was developed and the texts translated. RESULTS: The web page contains three main sections: (a) description for families of the characteristics of 15 PRD; (b) list of paediatric rheumatology centres; (c) contact information for family self help associations. A version for 45 countries in 52 languages (with another three in progress) is now available on the web. 291 surveys from 171 centres and 102 family associations were received from 42 countries. The median proportion of time spent in paediatric practice in the centres examined was 100%, with 70% of this time dedicated to paediatric rheumatology. 90% of the centres were willing to perform clinical trials in the future. CONCLUSIONS: The PRINTO/PRES website provides a well defined and competent set of information about PRD, with appropriate multiple translated versions and easy web navigational direction.
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| 9. |
- Cavalieri, A L, et al.
(author)
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Clocking femtosecond X rays.
- 2005
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In: Phys Rev Lett. - 0031-9007. ; 94:11
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Journal article (peer-reviewed)abstract
- Linear-accelerator-based sources will revolutionize ultrafast x-ray science due to their unprecedented brightness and short pulse duration. However, time-resolved studies at the resolution of the x-ray pulse duration are hampered by the inability to precisely synchronize an external laser to the accelerator. At the Sub-Picosecond Pulse Source at the Stanford Linear-Accelerator Center we solved this problem by measuring the arrival time of each high energy electron bunch with electro-optic sampling. This measurement indirectly determined the arrival time of each x-ray pulse relative to an external pump laser pulse with a time resolution of better than 60 fs rms.
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| 10. |
- Gaffney, K J, et al.
(author)
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Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb
- 2005
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In: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 95:12
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Journal article (peer-reviewed)abstract
- The melting dynamics of laser excited InSb have been studied with femtosecond x-ray diffraction. These measurements observe the delayed onset of diffusive atomic motion, signaling the appearance of liquidlike dynamics. They also demonstrate that the root-mean-squared displacement in the [111] direction increases faster than in the [110] direction after the first 500 fs. This structural anisotropy indicates that the initially generated fluid differs significantly from the equilibrium liquid.
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| 11. |
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| 12. |
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| 13. |
- Manuguerra, M., et al.
(author)
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Multi-factor dimensionality reduction applied to a large prospective investigation on gene-gene and gene-environment interactions
- 2007
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In: Carcinogenesis. - : Oxford University Press (OUP). - 0143-3334 .- 1460-2180. ; 28:2, s. 414-422
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Journal article (peer-reviewed)abstract
- It is becoming increasingly evident that single-locus effects cannot explain complex multifactorial human diseases like cancer. We applied the multi-factor dimensionality reduction (MDR) method to a large cohort study on gene-environment and gene-gene interactions. The study (case-control nested in the EPIC cohort) was established to investigate molecular changes and genetic susceptibility in relation to air pollution and environmental tobacco smoke (ETS) in non-smokers. We have analyzed 757 controls and 409 cases with bladder cancer (n = 124), lung cancer (n = 116) and myeloid leukemia (n = 169). Thirty-six gene variants (DNA repair and metabolic genes) and three environmental exposure variables (measures of air pollution and ETS at home and at work) were analyzed. Interactions were assessed by prediction error percentage and cross-validation consistency (CVC) frequency. For lung cancer, the best model was given by a significant gene-environment association between the base excision repair (BER) XRCC1-Arg399Gln polymorphism, the double-strand break repair (DSBR) BRCA2-Asn372His polymorphism and the exposure variable 'distance from heavy traffic road', an indirect and robust indicator of air pollution (mean prediction error of 26%, P < 0.001, mean CVC of 6.60, P = 0.02). For bladder cancer, we found a significant 4-loci association between the BER APE1-Asp148Glu polymorphism, the DSBR RAD52-3'-untranslated region (3'-UTR) polymorphism and the metabolic gene polymorphisms COMT-Val158Met and MTHFR-677C > T (mean prediction error of 22%, P < 0.001, mean CVC consistency of 7.40, P < 0.037). For leukemia, a 3-loci model including RAD52-2259C > T, MnSOD-Ala9Val and CYP1A1-Ile462Val had a minimum prediction error of 31% (P < 0.001) and a maximum CVC of 4.40 (P = 0.086). The MDR method seems promising, because it provides a limited number of statistically stable interactions; however, the biological interpretation remains to be understood.
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| 14. |
- Mikkelsen, T N, et al.
(author)
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Experimental design of multifactor climate change experiments with elevated CO2, warming and drought: the CLIMAITE project
- 2008
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In: Functional Ecology. - : Wiley. - 1365-2435 .- 0269-8463. ; 22:1, s. 185-195
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Journal article (peer-reviewed)abstract
- Recent findings indicate that the interactions among CO2, temperature and water can be substantial, and that the combined effects on the biological systems of several factors may not be predicted from experiments with one or a few factors. Therefore realistic multifactorial experiments involving a larger set of main factors are needed. We describe a new Danish climate change-related field scale experiment, CLIMAITE, in a heath/grassland ecosystem. CLIMAITE is a full factorial combination of elevated CO2, elevated temperature and prolonged summer drought. The manipulations are intended to mimic anticipated major environmental changes at the site by year 2075 as closely as possible. The impacts on ecosystem processes and functioning (at ecophysiological levels, through responses by individuals and communities to ecosystem-level responses) are investigated simultaneously. The increase of [CO2] closely corresponds with the scenarios for year 2075, while the warming treatment is at the lower end of the predictions and seems to be the most difficult treatment to increase without unwanted side effects on the other variables. The drought treatment follows predictions of increased frequency of drought periods in summer. The combination of the treatments does not create new unwanted side effects on the treatments relative to the treatments alone.
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| 15. |
- Risgaard-Petersen, N., et al.
(author)
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Evidence for complete denitrification in a benthic foraminifer
- 2006
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 443:7107, s. 93-96
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Journal article (peer-reviewed)abstract
- Benthic foraminifera are unicellular eukaryotes found abundantly in many types of marine sediments. Many species survive and possibly reproduce in anoxic habitats(1), but sustainable anaerobic metabolism has not been previously described. Here we demonstrate that the foraminifer Globobulimina pseudospinescens accumulates intracellular nitrate stores and that these can be respired to dinitrogen gas. The amounts of nitrate detected are estimated to be sufficient to support respiration for over a month. In a Swedish fjord sediment where G. pseudospinescens is the dominant foraminifer, the intracellular nitrate pool in this species accounted for 20% of the large, cell-bound, nitrate pool present in an oxygen-free zone. Similarly high nitrate concentrations were also detected in foraminifera Nonionella cf. stella and a Stainforthia species, the two dominant benthic taxa occurring within the oxygen minimum zone of the continental shelf off Chile. Given the high abundance of foraminifera in anoxic marine environments(1-3), these new findings suggest that foraminifera may play an important role in global nitrogen cycling and indicate that our understanding of the complexity of the marine nitrogen cycle is far from complete.
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Bramsen, Jesper B., et al.
(author)
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A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity
- 2009
-
In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 37:9, s. 2867-2881
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Journal article (peer-reviewed)abstract
- The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3'-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Druker, Brian J., et al.
(author)
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Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia
- 2006
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In: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 355:23, s. 2408-2417
-
Journal article (peer-reviewed)abstract
- BACKGROUND: The cause of chronic myeloid leukemia (CML) is a constitutively active BCR-ABL tyrosine kinase. Imatinib inhibits this kinase, and in a short-term study was superior to interferon alfa plus cytarabine for newly diagnosed CML in the chronic phase. For 5 years, we followed patients with CML who received imatinib as initial therapy. METHODS: We randomly assigned 553 patients to receive imatinib and 553 to receive interferon alfa plus cytarabine and then evaluated them for overall and event-free survival; progression to accelerated-phase CML or blast crisis; hematologic, cytogenetic, and molecular responses; and adverse events. RESULTS: The median follow-up was 60 months. Kaplan-Meier estimates of cumulative best rates of complete cytogenetic response among patients receiving imatinib were 69% by 12 months and 87% by 60 months. An estimated 7% of patients progressed to accelerated-phase CML or blast crisis, and the estimated overall survival of patients who received imatinib as initial therapy was 89% at 60 months. Patients who had a complete cytogenetic response or in whom levels of BCR-ABL transcripts had fallen by at least 3 log had a significantly lower risk of disease progression than did patients without a complete cytogenetic response (P<0.001). Grade 3 or 4 adverse events diminished over time, and there was no clinically significant change in the profile of adverse events. CONCLUSIONS: After 5 years of follow-up, continuous treatment of chronic-phase CML with imatinib as initial therapy was found to induce durable responses in a high proportion of patients. (ClinicalTrials.gov number, NCT00006343 [ClinicalTrials.gov].)
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| 25. |
- Falconer, D., et al.
(author)
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New Air-interface Technologies and Deployment Concepts
- 2006
-
In: Technologies for the Wireless Future: Wireless World Research Forum (WWRF). - Chichester, UK : John Wiley & Sons. - 0470029056 - 9780470029053 ; , s. 131-226
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Book chapter (other academic/artistic)
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| 26. |
- Franks, P. W., et al.
(author)
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Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites
- 2008
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In: The FASEB Journal. - : Wiley. - 0892-6638 .- 1530-6860. ; 22:9, s. 3135-3145
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Journal article (peer-reviewed)abstract
- The purpose of this study was to characterize associations between PINK1 genotypes, PINK1 transcript levels, and metabolic phenotypes in healthy adults and those with type 2 diabetes (T2D). We measured PINK1 skeletal muscle transcript levels and 8 independent PINK1 single nucleotide polymorphisms (SNPs) in a cohort of 208 Danish whites and in a cohort of 1701 British whites (SNPs and metabolic phenotypes only). Furthermore, we assessed the effects of PINK1 transcript ablation in primary adipocytes using RNA interference (RNAi). Six PINK1 SNPs were associated with PINK1 transcript levels (P < 0.04 to P < 0.0001). Obesity modified the association between PINK1 transcript levels and T2D risk (interaction P=0.005); transcript levels were inversely related with T2D in obese (n=105) [odds ratio (OR) per SD increase in expression levels=0.44; 95% confidence interval (CI): 0.23, 0.84; P=0.013] but not in nonobese (n=103) (OR=1.20; 95% CI: 0.82, 1.76; P=0.34) individuals. In the British cohort, several PINK1 SNPs were associated with plasma nonesterified fatty acid concentrations. Nominal genotype associations were also observed for fasting glucose, 2-h glucose, and maximal oxygen consumption, although these were not statistically significant after correcting for multiple testing. In primary adipocytes, Pink1 knockdown affected fatty acid binding protein 4 (Fabp4) expression, indicating that PINK1 may influence substrate metabolism. We demonstrate that PINK1 polymorphisms are associated with PINK1 transcript levels and measures of fatty acid metabolism in a concordant manner, whereas our RNAi data imply that PINK1 may indirectly influence lipid metabolism.
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| 27. |
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| 28. |
- Gutierrez-Suarez, R., et al.
(author)
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Health-related quality of life of patients with juvenile idiopathic arthritis coming from 3 different geographic areas. The PRINTO multinational quality of life cohort study
- 2007
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In: Rheumatology (Oxford). - : Oxford University Press (OUP). - 1462-0324 .- 1462-0332. ; 46:2, s. 314-320
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Journal article (peer-reviewed)abstract
- OBJECTIVES: To compare health-related quality of life (HRQL) and to identify clinical determinants for poor HRQL of patients with juvenile idiopathic arthritis (JIA) coming from three geographic areas.METHODS: The HRQL was assessed through the Child Health Questionnaire (CHQ). A total of 30 countries were included grouped in three geographic areas: 16 countries in Western Europe; 10 in Eastern Europe; and four in Latin America. Potential determinants of poor HRQL included demographic data, physician's and parent's global assessments, measures of joint inflammation, disability as measured by Childhood Health Assessment Questionnaire (CHAQ) and erythrocyte sedimentation rate. Poor HRQL was defined as a CHQ physical summary score (PhS) or psychosocial summary score (PsS) <2 S.D. from that of healthy children.RESULTS: A total of 3167 patients with JIA, younger than 18 yrs, were included in this study. The most affected health concepts (<2 S.D. from healthy children) that differentiate the three geographic areas include physical functioning, bodily pain/discomfort, global health, general health perception, change in health with respect to the previous year, self-esteem and family cohesion. Determinants for poor HRQL were similar across geographic areas with physical well-being mostly affected by the level of disability while the psychosocial well-being by the intensity of pain.CONCLUSION: We found that patients with JIA have a significant impairment of their HRQL compared with healthy peers, particularly in the physical domain. Disability and pain are the most important determinants of physical and psychosocial well-being irrespective of the geographic area of origin.
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| 29. |
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| 30. |
- Home, P.D., et al.
(author)
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Rosiglitazone evaluated for cardiovascular outcomes in oral agent combination therapy for type 2 diabetes (RECORD): a multicentre, randomised, open-label trial
- 2009
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In: The Lancet. - : Elsevier: Lancet. - 0140-6736 .- 1474-547X. ; 373:9681, s. 2125-2135
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Journal article (peer-reviewed)abstract
- Background: Rosiglitazone is an insulin sensitiser used in combination with metformin, a sulfonylurea, or both, for lowering blood glucose in people with type 2 diabetes. We assessed cardiovascular outcomes after addition of rosiglitazone to either metformin or sulfonylurea compared with the combination of the two over 5-7 years of follow-up. We also assessed comparative safety. Methods: In a multicentre, open-label trial, 4447 patients with type 2 diabetes on metformin or sulfonylurea monotherapy with mean haemoglobin A 1c (HbA 1c) of 7·9% were randomly assigned to addition of rosiglitazone (n=2220) or to a combination of metformin and sulfonylurea (active control group, n=2227). The primary endpoint was cardiovascular hospitalisation or cardiovascular death, with a hazard ratio (HR) non-inferiority margin of 1·20. Analysis was by intention to treat. This study is registered with ClinicalTrials.gov, number NCT00379769. Findings: 321 people in the rosiglitazone group and 323 in the active control group experienced the primary outcome during a mean 5·5-year follow-up, meeting the criterion of non-inferiority (HR 0·99, 95% CI 0·85-1·16). HR was 0·84 (0·59-1·18) for cardiovascular death, 1·14 (0·80-1·63) for myocardial infarction, and 0·72 (0·49-1·06) for stroke. Heart failure causing admission to hospital or death occurred in 61 people in the rosiglitazone group and 29 in the active control group (HR 2·10, 1·35-3·27, risk difference per 1000 person-years 2·6, 1·1-4·1). Upper and distal lower limb fracture rates were increased mainly in women randomly assigned to rosiglitazone. Mean HbA 1c was lower in the rosiglitazone group than in the control group at 5 years. Interpretation: Addition of rosiglitazone to glucose-lowering therapy in people with type 2 diabetes is confirmed to increase the risk of heart failure and of some fractures, mainly in women. Although the data are inconclusive about any possible effect on myocardial infarction, rosiglitazone does not increase the risk of overall cardiovascular morbidity or mortality compared with standard glucose-lowering drugs. Funding: GlaxoSmithKline plc, UK. © 2009 Elsevier Ltd. All rights reserved.
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| 31. |
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| 32. |
- Knaapila, Matti, et al.
(author)
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A new small-angle X-ray scattering set-up on the crystallography beamline I711 at MAX-lab.
- 2009
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In: Journal of Synchrotron Radiation. - 1600-5775. ; 16:Pt 4, s. 498-504
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Journal article (peer-reviewed)abstract
- A small-angle X-ray scattering (SAXS) set-up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009-0.3 A(-1) for the standard set-up but depends on the sample-to-detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm x 0.37 mm (full width at half-maximum) at the sample position, with a flux of 4 x 10(10) photons s(-1) and lambda = 1.1 A. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead-throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro-fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost-effective SAXS station can be constructed on a multipurpose beamline.
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| 33. |
- Konstantinov, A., et al.
(author)
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Data management services of NorduGrid
- 2005
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In: CERN-2005-002. ; 2, s. 765-766
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Conference paper (peer-reviewed)abstract
- In common grid installations, services responsible for storing big data chunks, replication of those data and indexing their availability are usually completely decoupled. And a task of synchronizing data is passed to either user-level tools or separate services (like spiders) which are subject to failure and usually cannot perform properly if one of underlying services fails too. The NorduGrid Smart Storage Element (SSE) was designed to try to overcome those problems by combining the most desirable features into one service. It uses HTTPS/G for secure data transfer, Web Services for control (through same HTTPS/G channel) and can provide information to indexing services used in middlewares based on the Globus Toolkit (TM). At the moment, those are the Replica Catalog and the Replica Location Service. The modular internal design of the SSE and the power of C++ object programming allows to add support for other indexing services in an easy way. There are plans to complement it with a Smart Indexing Service capable of resolving inconsistencies hence creating a robust distributed data storage system.
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| 34. |
- Kozlowska, K., et al.
(author)
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Patterns of healthy lifestyle and positive health attitudes in older Europeans
- 2008
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In: The Journal of Nutrition, Health & Aging. - 1279-7707 .- 1760-4788. ; 12:10, s. 728-733
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Journal article (peer-reviewed)abstract
- Objectives: To determine (i) the extent to which recommended lifestyle healthy behaviors are adopted and the existence of positive attitudes to health; (ii) the relative influence of socio-demographic variables on multiple healthy lifestyle behaviors and positive attitudes to health; (iii) the association between healthy lifestyle behaviors and positive attitudes to health. Design: two distinct healthy behavioral measures were developed: (i) healthy lifestyles based on physical activity, no cigarette smoking, no/moderate alcohol drinking, maintaining a "healthy" weight and having no sleeping problems and (ii) positive health attitudes based on having positive emotional attitudes, such as: self-perceived good health status, being calm, peaceful and happy for most of the time, not expecting health to get worse and regular health check-ups. A composite healthy lifestyle index, ranging from 0 (none of behaviors met) to 5 (all behaviors met) was calculated by summing up the individual's scores for the five healthy lifestyle items. Afterwards, each individual's index was collapsed into three levels: 0-2 equivalent to 'level 1' (subjectively regarded as 'too low'), a score of 3 equivalent to 'level 2' ('fair') and 4-5 as 'level 3' satisfactory 'healthy lifestyle' practices. The same procedure was applied to the positive health attitudes index. Multinomial logistic regression analyses by a forward selection procedure were used to calculate the adjusted odds ratio (OR) with 95% confidence interval (95% CI). Participants: a multi-national sample consisting of 638 older Europeans from 8 countries, aged 65-74 and 75+, living alone or with others. Results and conclusions: maintaining a "healthy" weight was the most frequently cited factor in the healthy lifestyles index and therefore assumed to be the most important to the older Europeans in the study; positive attitudes to health were relatively low; participants achieved a 'satisfactory' level for healthy lifestyles index (level 3) more frequently than a satisfactory level for positive attitudes to health; having a satisfactory 'healthy lifestyle' was directly related to having a satisfactory level of positive attitudes to health based on the positive health attitudes index; income and geographical location in Europe appeared to be key predictors for meeting both the recommended healthy lifestyle factors in the index and having positive health attitudes however, the composition and nature of the study sample should be taken into consideration when considering the impact of the location on healthy lifestyles and attitudes to health across Europe.
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| 35. |
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| 36. |
- Langgard Nielsen, J., et al.
(author)
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Experiences with Data Indexing services supported by the NorduGrid middleware
- 2005
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In: CERN-2005-002. ; 2, s. 673-675
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Conference paper (peer-reviewed)abstract
- The NorduGrid middleware, ARC, has integrated support for querying and registering to Data Indexing services such as the Globus Replica Catalog and Globus Replica Location Server. This support allows one to use these indexing services for for example brokering during jobsubmission, automatic registration of files and many other things. This integrated support is complemented by a set of command-line tools for registering to and querying these Data Indexing services. In this article we will describe experiences with these indexing services both from a daily work point of view and in production environments such as the Atlas Data- Challenges 1 and 2. We will describe the advantages of such Data Indexing services as well as their shortcomings. Finally we will present a proposal for an extended Smart Indexing Service which should deal with the shortcomings described. Such an indexing service is being designed at the moment.
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| 37. |
- Lindenberg, AM, et al.
(author)
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Atomic-scale visualization of inertial dynamics
- 2005
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 308:5720, s. 392-395
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Journal article (peer-reviewed)abstract
- The motion of atoms on interatomic potential energy surfaces is fundamental to the dynamics of liquids and solids. An accelerator-based source of femtosecond x-ray pulses allowed us to follow directly atomic displacements on an optically modified energy landscape, leading eventually to the transition from crystalline solid to disordered liquid. We show that, to first order in time, the dynamics are inertial, and we place constraints on the shape and curvature of the transition-state potential energy surface. Our measurements point toward analogies between this nonequilibrium phase transition and the short-time dynamics intrinsic to equilibrium liquids.
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| 38. |
- Nejsum, Lene N., et al.
(author)
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Bidirectional regulation of AQP2 trafficking and recycling : involvement of AQP2-S256 phosphorylation
- 2005
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In: American Journal of Physiology: Renal Physiology. - : American Physiological Society. - 1931-857X .- 1522-1466. ; 288:5, s. F930-F938
-
Journal article (peer-reviewed)abstract
- The present study examined the role of PKA and serine256 (S256) phosphorylation for AQP2 trafficking and recycling using cells transfected with wild-type AQP2 (AQP2-WT) or mutant AQP2 and high-resolution confocal microscopic techniques. In transiently transfected MDCK-C7 cells, stimulation with forskolin induced translocation of AQP2-WT to the plasma membrane. Treatment of AQP2-WT cells with the PKA inhibitor H-89 following forskolin stimulation resulted in internalization of AQP2-WT. Moreover, H-89 treatment of AQP2-S256D (mimicking constitutively phosphorylated AQP2 and hence localized to the plasma membrane) resulted in redistribution of AQP2-S256D to intracellular vesicles, even in the presence of forskolin. Both PGE2 and dopamine stimulation induced endocytosis of AQP2-WT and AQP2-S256D, respectively, in forskolin-stimulated cells. Consistent with this, dopamine in the presence of vasopressin stimulated endocytosis of AQP2 in slices of rat kidney inner medulla without substantial dephosphorylation. In conclusion, these results strongly suggest that 1) S256 phosphorylation is necessary but not sufficient for AQP2 plasma membrane expression, 2) active PKA is required for AQP2 plasma membrane expression, 3) PGE2 and dopamine induce internalization of AQP2 independently of AQP2 dephosphorylation, and 4) preceding activation of cAMP production is necessary for PGE2 and dopamine to cause AQP2 internalization.
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| 39. |
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| 40. |
- Nielsen, Peter, et al.
(author)
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Multi-level Theoretical Framework – Meadow Background document no1
- 2009
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In: Meadow reports. ; 1, s. 1-59
-
Research review (peer-reviewed)abstract
- This report is one outcome of workpackage 2 in the EU funded MEADOW project. Its aim has been to establish an overview of theoretical literature in surveys on organisational change, innovation and work conditions. An international team of scholars have cooperated on this task. Scholars from Aalborg University (Denmark) have coordinated the workpackage and accepted responsibility for establishing a comprehensive multilevel framework regarding theories on organisational change, innovation and work conditions.
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| 41. |
- Nielsen, TR, et al.
(author)
-
Effects of infectious mononucleosis and HLA-DRB1*15 in multiple sclerosis
- 2009
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In: Multiple sclerosis (Houndmills, Basingstoke, England). - : SAGE Publications. - 1352-4585 .- 1477-0970. ; 15:4, s. 431-436
-
Journal article (peer-reviewed)abstract
- Background Both human leukocyte antigen (HLA)-DRB1*15 and Epstein-Barr virus infection presenting as infectious mononucleosis (IM) are recognized as risk factors for multiple sclerosis (MS). However, their combined effect and possible interaction on MS risk is not known. Objective To assess the association between HLA-DRB1*15 and risk of MS in persons with and without IM. Methods We compared the prevalence of DRB1*15 in MS patients with ( n = 76) and without ( n = 1,836) IM with the corresponding distributions in blood donors with ( n = 62) and without ( n = 484) IM histories. This allowed us to estimate the relative risk of MS associated with DRB1*15 in the presence and absence, respectively, of previous IM. We then estimated the interaction between DRB1*15 and IM as the ratio of the two individual odds ratios. Results In IM-naïve individuals, DRB1*15 carried a 2.4-fold (95% confidence interval [CI], 2.0–3.0) increased MS risk. In contrast, among persons with IM history, DRB1*15 was associated with a 7.0-fold (95% CI, 3.3–15.4) increased MS risk. Thus, the MS risk conferred by HLA-DRB1*15 was 2.9 (95% CI, 1.3–6.5)-fold stronger in the presence than in the absence of IM. Combined with previous results, this result indicates that DRB1*15-positive persons with a history of IM may be at a 10.0-fold (95% CI, 6.0–17.9) increased risk of MS compared with persons who are DRB1*15 and IM-naïve. Conclusion DRB1*15 and IM may act in synergy causing MS.
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| 42. |
- Pajchel, K., et al.
(author)
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Usage statistics and usage patterns on the NorduGrid: Analyzing the logging information collected on one of the largest production Grids of the world
- 2005
-
In: CERN-2005-002. ; 2, s. 711-714
-
Conference paper (peer-reviewed)abstract
- The Nordic Grid facility (NorduGrid [1]) came into operation during summer 2002 when the Scandinavian ATLAS HEP group started to use the Grid for the ATLAS Data Challenges (DC) and was thus the first Grid ever contributing to an ATLAS production. Since then, the Grid facility has been in continuous 24/7 operation. NorduGrid is being used by a growing set of active users from various scientific areas including physics, chemistry, biology and informatics. It has given major contributions to the ATLAS Data Challenge 1 [2] and the ongoing Data Challenge 2. · The increasing number of resources has made NorduGrid one of the largest production Grids in the world, continuously running on more than 30 sites more than 3000 CPUs. · The resources range from small test clusters at academic institutions to large farms at several supercomputer centers and the NorduGrid software runs on clusters with very different Linux distributions. This presentation gives a short overview of the design and implementation of the NorduGrid middleware, logging and monitoring facilities. It will be followed by a description of a typical job on NorduGrid and the information about its parameters which are monitored online and persistified in the logging service.
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| 43. |
- Pastene, Luis A., et al.
(author)
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Radiation and speciation of pelagic organisms during periods of global warming : the case of the common minke whale, Balaenoptera acutorostrata
- 2007
-
In: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 16:7, s. 1481-1495
-
Journal article (peer-reviewed)abstract
- How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean-surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control-region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re-establishment of the polar-equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.
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| 44. |
- Pastorello, A., et al.
(author)
-
A giant outburst two years before the core-collapse of a massive star
- 2007
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 829-832
-
Journal article (peer-reviewed)abstract
- The death of massive stars produces a variety of supernovae, which are linked to the structure of the exploding stars(1,2). The detection of several precursor stars of type II supernovae has been reported ( see, for example, ref. 3), but we do not yet have direct information on the progenitors of the hydrogen-deficient type Ib and Ic supernovae. Here we report that the peculiar type Ib supernova SN 2006jc is spatially coincident with a bright optical transient(4) that occurred in 2004. Spectroscopic and photometric monitoring of the supernova leads us to suggest that the progenitor was a carbon-oxygen Wolf - Rayet star embedded within a helium-rich circumstellar medium. There are different possible explanations for this pre-explosion transient. It appears similar to the giant outbursts of luminous blue variable stars (LBVs) of 60 - 100 solar masses(5), but the progenitor of SN 2006jc was helium- and hydrogen-deficient ( unlike LBVs). An LBV-like outburst of a Wolf - Rayet star could be invoked, but this would be the first observational evidence of such a phenomenon. Alternatively, a massive binary system composed of an LBV that erupted in 2004, and a Wolf - Rayet star exploding as SN 2006jc, could explain the observations.
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| 45. |
- Pham, M. K., et al.
(author)
-
Certified reference material for radionuclides in fish flesh sample IAEA-414 (mixed fish from the Irish Sea and North Sea)
- 2006
-
In: Proceedings of the 15th International Conference on Radionuclide Metrology and its Applications (Applied Radiation and Isotopes). - Amsterdam : Elsevier BV. - 0969-8043 .- 1872-9800. ; 64:10-11, s. 1253-1259
-
Conference paper (peer-reviewed)abstract
- A certified reference material (CRM) for radionuclides in fish sample IAEA-414 (mixed fish from the Irish Sea and North Seas) is described and the results of the certification process are presented. Nine radionuclides (K-40, Cs-137, Th-232, U-234, U-235, U-238, Pu-238, Pu239+240 and Am-241) were certified for this material. Information on massic activities with 95% confidence intervals is given for six other radionuclides (Sr-90, Pb-210(Po-210), Ra-226, Pu-239, Pu-240 Pu-241). Less frequently reported radionuclides (Tc-99, I-129, Th-228, Th-230 and Np-217) and information on some activity and mass ratios are also included. The CRM can be used for quality assurance/quality control of the analysis of radionuclides in fish sample, for the development and validation of analytical methods and for training purposes. The material is available from IAEA, Vienna, in 100 g units.
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| 46. |
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| 47. |
- Riisbro, R, et al.
(author)
-
Preoperative plasma soluble urokinase plasminogen activator receptor as a prognostic marker in rectal cancer patients. An EORTC-receptor and Biomarker Group collaboration
- 2005
-
In: International Journal of Biological Markers. - 0393-6155. ; 20:2, s. 93-102
-
Journal article (peer-reviewed)abstract
- Background and aims: Since approximately 30% of patients with Dukes' stage B colorectal cancer will experience disease recurrence within five years of primary treatment, current staging of patients with early colorectal cancer apparently fails to adequately predict patient outcome. It has previously been shown that the preoperative plasma concentration of soluble urokinase plasminogen activator receptor (suPAR) is associated with the survival of patients with early colorectal cancer. In this study we sought to confirm the independent prognostic value of suPAR in rectal cancer. Methods: suPAR was retrospectively determined by two different versions of a suPAR ELISA in preoperatively collected plasma samples from a Swedish (n=354) and a Danish (n=255) cohort of rectal cancer patients. Results: In both cohorts the suPAR concentration was significantly higher in Dukes' stage D patients than in Dukes' stage A-C patients (p < 0.0001). Among Dukes' stage A-C patients, no differences in median suPAR values were seen. In univariate analysis, continuous suPAR was found to be associated with survival (p < 0.0001 in both cohorts). Of particular interest was that similar results were obtained for Dukes' stage A and B patients when analyzed separately. In multivariate analysis, continuous suPAR was found in both cohorts to be independent of Dukes' stage. Conclusions: This study confirms that the preoperative concentration of plasma suPAR contains independent prognostic information on patients with rectal cancer. This result was independent of the two different versions of an in-house suPAR ELISA used to perform the analyses. The next step. in the evaluation of suPAR as a prognostic parameter in rectal cancer will be to launch an appropriately dimensioned prospective study where the benefit of applying preoperative plasma suPAR measurement to clinical decision-making regarding adjuvant therapy is assessed.
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| 48. |
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| 49. |
- Sollerman, J., et al.
(author)
-
Supernova 2006aj and the associated X-Ray Flash 060218
- 2006
-
In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 454, s. 503-509
-
Journal article (peer-reviewed)abstract
- We have studied the afterglow of the gamma-ray burst (GRB) of February 18, 2006. This is a nearby long GRB, with a very low peak energy, and is therefore classified as an X-ray Flash (XRF). XRF 060218 is clearly associated with a supernova - dubbed SN 2006aj. We present early spectra for SN 2006aj as well as optical lightcurves reaching out to 50 days past explosion. Our optical lightcurves define the rise times, the lightcurve shapes and the absolute magnitudes in the U, V and R bands, and we compare these data with data for other relevant supernovae. SN 2006aj evolved quite fast, somewhat similarly to SN 2002ap, but not as fast as SN 1994I. Our spectra show the evolution of the supernova over the peak, when the U-band portion of the spectrum rapidly fades due to extensive line blanketing. We compare to similar spectra of very energetic type Ic supernovae. Our first spectra are earlier than spectra for any other GRB-SN. The spectrum taken 12 days after burst in the rest frame is similar to somewhat later spectra of both SN 1998bw and SN 2003dh, implying a rapid early evolution. This is consistent with the fast lightcurve. From the narrow emission lines from the host galaxy we derive a redshift of z=0.0331±0.0007. This makes XRF 060218 the second closest gamma-ray burst detected. The flux of these emission lines indicate a high-excitation state, and a modest metallicity and star formation rate of the host galaxy.
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| 50. |
- Vineis, P., et al.
(author)
-
Genetic susceptibility according to three metabolic pathways in cancers of the lung and bladder and in myeloid leukemias in nonsmokers
- 2007
-
In: Annals of Oncology. - : Elsevier BV. - 1569-8041 .- 0923-7534. ; 18:7, s. 1230-1242
-
Journal article (peer-reviewed)abstract
- Background: We chose a set of candidate single nucleotide polymorphisms (SNPs) to investigate gene-environment interactions in three types of cancer that have been related to air pollution (lung, bladder and myeloid leukemia). Patients and methods: The study has been conducted as a nested case-control study within the European Prospective Investigation into Cancer and Nutrition cohort (409 cancer cases and 757 matched controls). We included never and ex-smokers. SNPs were in genes involved in oxidative stress, phase I metabolizing genes, phase 11 metabolizing genes and methylenetetrahydrofolate reductase (MTHFR). Results: The most notable findings are: GSTM1 deletion and bladder cancer risk [odds ratio (OR) = 1.60; 95% confidence interval 1.00-2.56]; CYP1A1 and leukemia (2.22, 1.33-3.70; heterozygotes); CYP1B1 and leukemia (0.47, 0.27-0.84; homozygotes); MnSOD and leukemia (1.91, 1.08-3.38; homozygotes) and NQO1 and lung cancer (8.03, 1.73-37.3; homozygotes). Other statistically significant associations were found in subgroups defined by smoking habits (never or ex-smokers), environmental tobacco smoke or gender, with no obvious pattern. When gene variants were organized according to the three main pathways, the emerging picture was of a strong involvement of combined phase I enzymes in leukemia, with an OR of 5 (1.63-15.4) for those having three or more variant alleles. The association was considerably stronger for leukemias arising before the age of 55.
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