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| 3. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 6. |
- Kraus, Stefan, et al.
(författare)
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Planet Formation Imager (PFI) : Science vision and key requirements
- 2016
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Ingår i: Optical and Infrared Interferometry and Imaging V. - : SPIE. - 9781510601932 ; 9907
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Konferensbidrag (refereegranskat)abstract
- The Planet Formation Imager (PFI) project aims to provide a strong scientific vision for ground-based optical astronomy beyond the upcoming generation of Extremely Large Telescopes. We make the case that a breakthrough in angular resolution imaging capabilities is required in order to unravel the processes involved in planet formation. PFI will be optimised to provide a complete census of the protoplanet population at all stellocentric radii and over the age range from 0.1 to ∼100 Myr. Within this age period, planetary systems undergo dramatic changes and the final architecture of planetary systems is determined. Our goal is to study the planetary birth on the natural spatial scale where the material is assembled, which is the "Hill Sphere" of the forming planet, and to characterise the protoplanetary cores by measuring their masses and physical properties. Our science working group has investigated the observational characteristics of these young protoplanets as well as the migration mechanisms that might alter the system architecture. We simulated the imprints that the planets leave in the disk and study how PFI could revolutionise areas ranging from exoplanet to extragalactic science. In this contribution we outline the key science drivers of PFI and discuss the requirements that will guide the technology choices, the site selection, and potential science/technology tradeoffs.
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| 7. |
- Boyajian, T., et al.
(författare)
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Stellar diameters and temperatures - VI. High angular resolution measurements of the transiting exoplanet host stars HD 189733 and HD 209458 and implications for models of cool dwarfs
- 2015
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 447:1, s. 846-857
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Tidskriftsartikel (refereegranskat)abstract
- We present direct radii measurements of the well-known transiting exoplanet host stars HD 189733 and HD 209458 using the CHARA Array interferometer. We find the limb-darkened angular diameters to be thetaLD = 0.3848 +/- 0.0055 and 0.2254 +/- 0.0072 milliarcsec for HD 189733 and HD 209458, respectively. HD 189733 and HD 209458 are currently the only two transiting exoplanet systems where detection of the respective planetary companion's orbital motion from high resolution spectroscopy has revealed absolute masses for both star and planet. We use our new measurements together with the orbital information from radial velocity and photometric time series data, Hipparcos distances, and newly measured bolometric fluxes to determine the stellar effective temperatures (Teff = 4875 +/- 43, 6093 +/- 103 K), stellar linear radii (R* = 0.805 +/- 0.016, 1.203 +/- 0.061 Rsun), mean stellar densities (rho* = 1.62 +/- 0.11, 0.58 +/- 0.14 rhosun), planetary radii (Rp = 1.216 +/- 0.024, 1.451 +/- 0.074 RJup), and mean planetary densities (rhop = 0.605 +/- 0.029, 0.196 +/- 0.033 rhoJup) for HD 189733 b and HD 209458 b, respectively. The stellar parameters for HD 209458, a F9 dwarf, are consistent with indirect estimates derived from spectroscopic and evolutionary modeling. However, we find that models are unable to reproduce the observational results for the K2 dwarf, HD 189733. We show that, for stellar evolutionary models to match the observed stellar properties of HD 189733, adjustments lowering the solar-calibrated mixing length parameter from 1.83 to 1.34 need to be employed.
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| 11. |
- Demenais, F, et al.
(författare)
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Association of MC1R Variants and Host Phenotypes With Melanoma Risk in CDKN2A Mutation Carriers: A GenoMEL Study.
- 2010
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 102, s. 1568-1583
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Tidskriftsartikel (refereegranskat)abstract
- Background Carrying the cyclin-dependent kinase inhibitor 2A (CDKN2A) germline mutations is associated with a high risk for melanoma. Penetrance of CDKN2A mutations is modified by pigmentation characteristics, nevus phenotypes, and some variants of the melanocortin-1 receptor gene (MC1R), which is known to have a role in the pigmentation process. However, investigation of the associations of both MC1R variants and host phenotypes with melanoma risk has been limited. Methods We included 815 CDKN2A mutation carriers (473 affected, and 342 unaffected, with melanoma) from 186 families from 15 centers in Europe, North America, and Australia who participated in the Melanoma Genetics Consortium. In this family-based study, we assessed the associations of the four most frequent MC1R variants (V60L, V92M, R151C, and R160W) and the number of variants (1, ≥2 variants), alone or jointly with the host phenotypes (hair color, propensity to sunburn, and number of nevi), with melanoma risk in CDKN2A mutation carriers. These associations were estimated and tested using generalized estimating equations. All statistical tests were two-sided. Results Carrying any one of the four most frequent MC1R variants (V60L, V92M, R151C, R160W) in CDKN2A mutation carriers was associated with a statistically significantly increased risk for melanoma across all continents (1.24 × 10(-6) ≤ P ≤ .0007). A consistent pattern of increase in melanoma risk was also associated with increase in number of MC1R variants. The risk of melanoma associated with at least two MC1R variants was 2.6-fold higher than the risk associated with only one variant (odds ratio = 5.83 [95% confidence interval = 3.60 to 9.46] vs 2.25 [95% confidence interval = 1.44 to 3.52]; P(trend) = 1.86 × 10(-8)). The joint analysis of MC1R variants and host phenotypes showed statistically significant associations of melanoma risk, together with MC1R variants (.0001 ≤ P ≤ .04), hair color (.006 ≤ P ≤ .06), and number of nevi (6.9 × 10(-6) ≤ P ≤ .02). Conclusion Results show that MC1R variants, hair color, and number of nevi were jointly associated with melanoma risk in CDKN2A mutation carriers. This joint association may have important consequences for risk assessments in familial settings.
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| 13. |
- Komajda, M, et al.
(författare)
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The chronic ischaemic cardiovascular disease ESC Pilot Registry: Results of the six-month follow-up
- 2018
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Ingår i: European journal of preventive cardiology. - : Oxford University Press (OUP). - 2047-4881 .- 2047-4873. ; 25:4, s. 377-387
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Tidskriftsartikel (refereegranskat)abstract
- Chronic ischaemic cardiovascular disease (CICD) remains a leading cause of morbidity and mortality worldwide. The CICD Pilot Registry enrolled 2420 patients across 10 European Society of Cardiology countries prospectively to describe characteristics, management strategies and clinical outcomes in this setting. We report here the six-month outcomes. Methods and results From the overall population, 2203 patients were analysed at six months. Fifty-eight patients (2.6%) died after inclusion; 522 patients (23.7%) experienced all-cause hospitalisation or death. The rate of prescription of angiotensin-converting enzyme inhibitors, beta-blockers and aspirin was mildly decreased at six months (all P < 0.02). Patients who experienced all-cause hospitalisation or death were older, more often had a history of non-ST-segment elevation myocardial infarction, of chronic kidney disease, peripheral revascularisation and/or chronic obstructive pulmonary disease than those without events. Independent predictors of all-cause mortality/hospitalisation were age (hazard ratio (HR) 1.17, 95% confidence interval (CI) 1.07–1.27) per 10 years, and a history of previous peripheral revascularisation (HR 1.45, 95% CI 1.03–2.03), chronic kidney disease (HR 1.31, 95% CI 1.0–1.68) or chronic obstructive pulmonary disease (HR 1.42, 95% CI 1.06–1.91, all P < 0.05). We observed a higher rate of events in eastern, western and northern countries compared to southern countries and in cohort 1. Conclusion In this contemporary European registry of CICD patients, the rate of severe clinical outcomes at six months was high and was influenced by age, heart rate and comorbidities. The medical management of this condition remains suboptimal, emphasising the need for larger registries with long-term follow-up. Ad-hoc programmes aimed at implementing guidelines adherence and follow-up procedures are necessary, in order to improve quality of care and patient outcomes.
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| 14. |
- Barrett-Lee, Peter J., et al.
(författare)
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Independent risk factors for anemia in cancer patients receiving chemotherapy : results from the European Cancer Anaemia Survey
- 2006
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Ingår i: Oncology. - : S. Karger AG. - 0030-2414 .- 1423-0232. ; 70:1, s. 34-48
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: To develop a hitherto unavailable risk factor model for accurately predicting anemia development in cancer patients before chemotherapy (CT) administration. METHODS: 2,070 nonanemic patients from the European Cancer Anaemia Survey (ECAS) with hemoglobin (Hb) > or =12 g/dl at enrollment who received their first CT during ECAS and underwent at least two CT cycles were divided randomly into split half (SH) 1 and SH2 (n = 1,035 each). The model was developed on SH1 using logistic regression to simultaneously evaluate predictive factors, and was validated using SH2 and an additional similar subpopulation of 5,901 ECAS patients. Anemia risk values were assigned to the predictive factors and the sum of the predictive factors gave the total anemia risk score; lower-, higher-, and highest-risk cutoff points of the total anemia risk score were determined. RESULTS: Variables ultimately identified as significant predictive factors for anemia were: lower initial Hb (< or =12.9 g/dl in females, and < or =13.4 g/dl in males); having lung or gynecologic cancer versus gastrointestinal (GI)/colorectal cancer; cancer at any other site versus GI/colorectal cancer; treatment with platinum CT, and female gender. CONCLUSION: Using this evidence-based risk model, nonanemic patients who are at the highest risk of developing anemia prior to receiving CT can be identified clinically, allowing appropriate anemia management to be planned.
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| 15. |
- Bengtsson, Johan, 1985, et al.
(författare)
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Metaxa: Automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts
- 2011
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Ingår i: SocBiN Bioinformatics Conference, Helsinki, Finland, 2011.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. However, the gene is not only present in the nuclear genome of eukaryotes and the core genome of prokaryotes, but also in the mitochondria and chloroplasts of eukaryotes. The SSU genes in the core genome, mitochondria and chloroplast are conceptually paralogous and should in most situations not be aligned and analyzed jointly, e.g. when estimating species diversity. Identifying the origin of SSU sequences in complex sequence datasets is a time-consuming and largely manual undertaking. To ease this situation, we have created Metaxa, an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacte- rial, nuclear eukaryote, mitochondrial, or chloroplast origin. Metaxa very efficiently detects SSU sequences from fragments as short as 200 base pairs, and correctly classifies 97% of the identified genes at read lengths typically obtained from pyrosequencing. In addition, Metaxa shows a false positive rate of 0.00012% when run on random DNA fragments, showing the robustness of the method. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 16. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
- 2011
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Ingår i: Antonie van Leeuwenhoek: international journal of general and molecular microbiology. - : Springer Science and Business Media LLC. - 0003-6072 .- 1572-9699. ; 100:3, s. 471-475
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Tidskriftsartikel (refereegranskat)abstract
- The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.
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| 17. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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| 18. |
- Creevey, O. L., et al.
(författare)
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Fundamental properties of the Population II fiducial stars HD 122563 and Gmb 1830 from CHARA interferometric observations
- 2012
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 545, s. A17-
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Tidskriftsartikel (refereegranskat)abstract
- We have determined the angular diameters of two metal-poor stars, HD 122563 and Gmb 1830, using CHARA and Palomar Testbed Interferometer observations. For the giant star HD 122563, we derive an angular diameter theta(3D) = 0.940 +/- 0.011 milliarcseconds (mas) using limb-darkening from 3D convection simulations and for the dwarf star Gmb 1830 (HD 103095) we obtain a 1D limb-darkened angular diameter theta(1D) = 0.679 +/- 0.007 mas. Coupling the angular diameters with photometry yields effective temperatures with precisions better than 55 K (T-eff = 4598 +/- 41 K and 4818 +/- 54 K - for the giant and the dwarf star, respectively). Including their distances results in very well-determined luminosities and radii (L = 230 +/- 7 L-circle dot, R = 24.1 +/- 1.1 R-circle dot and L = 0.213 +/- 0.002 L-circle dot, R = 0.665 +/- 0.014 R-circle dot, respectively). We used the CESAM2k stellar structure and evolution code in order to produce models that fit the observational data. We found values of the mixing-length parameter alpha (which describes 1D convection) that depend on the mass of the star. The masses were determined from the models with precisions of < 3% and with the well-measured radii excellent constraints on the surface gravity are obtained (log g = 1.60 +/- 0.04, 4.59 +/- 0.02 dex, respectively). The very small errors on both log g and T-eff provide stringent constraints for spectroscopic analyses given the sensitivity of abundances to both of these values. The precise determination of T-eff for the two stars brings into question the photometric scales for metal-poor stars.
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| 19. |
- Escaned, Javier, et al.
(författare)
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Applied coronary physiology for planning and guidance of percutaneous coronary interventions. A clinical consensus statement from the European Association of Percutaneous Cardiovascular Interventions (EAPCI) of the European Society of Cardiology
- 2023
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Ingår i: EuroIntervention. - : Europa Digital & Publishing. - 1774-024X .- 1969-6213. ; 19:6, s. 464-
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Tidskriftsartikel (refereegranskat)abstract
- The clinical value of fractional flow reserve and non-hyperaemic pressure ratios are well established in determining an indication for percutaneous coronary intervention (PCI) in patients with coronary artery disease (CAD). In addition, over the last 5 years we have witnessed a shift towards the use of physio-logy to enhance procedural planning, assess post-PCI functional results, and guide PCI optimisation. In this regard, clinical studies have reported compelling data supporting the use of longitudinal vessel analysis, obtained with pressure guidewire pullbacks, to better understand how obstructive CAD contributes to myocardial ischaemia, to establish the likelihood of functionally successful PCI, to identify the presence and location of residual flow-limiting stenoses and to predict long-term outcomes. The introduction of new functional coronary angiography tools, which merge angiographic information with fluid dynamic equations to deliver information equivalent to intracoronary pressure measurements, are now available and potentially also applicable to these endeavours. Furthermore, the ability of longitudinal vessel analysis to predict the functional results of stenting has played an integral role in the evolving field of simulated PCI. Nevertheless, it is important to have an awareness of the value and challenges of physiology-guided PCI in specific clinical and anatomical contexts. The main aim of this European Association of Percutaneous Cardiovascular Interventions clinical consensus statement is to offer up-to-date evidence and expert opin-ion on the use of applied coronary physiology for procedural PCI planning, disease pattern recognition and post-PCI optimisation.
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| 20. |
- Escaned, Javier, et al.
(författare)
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Safety of the Deferral of Coronary Revascularization on the Basis of Instantaneous Wave-Free Ratio and Fractional Flow Reserve Measurements in Stable Coronary Artery Disease and Acute Coronary Syndromes
- 2018
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Ingår i: JACC. - : Elsevier. - 1936-8798 .- 1876-7605. ; 11:15, s. 1437-1449
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES The aim of this study was to investigate the clinical outcomes of patients deferred from coronary revascularization on the basis of instantaneous wave-free ratio (iFR) or fractional flow reserve (FFR) measurements in stable angina pectoris (SAP) and acute coronary syndromes (ACS). BACKGROUND Assessment of coronary stenosis severity with pressure guidewires is recommended to determine the need for myocardial revascularization. METHODS The safety of deferral of coronary revascularization in the pooled per-protocol population (n = 4,486) of the DEFINE-FLAIR (Functional Lesion Assessment of Intermediate Stenosis to Guide Revascularisation) and iFR-SWEDEHEART (Instantaneous Wave-Free Ratio Versus Fractional Flow Reserve in Patients With Stable Angina Pectoris or Acute Coronary Syndrome) randomized clinical trials was investigated. Patients were stratified according to revascularization decision making on the basis of iFR or FFR and to clinical presentation (SAP or ACS). The primary endpoint was major adverse cardiac events (MACE), defined as the composite of all-cause death, nonfatal myocardial infarction, or unplanned revascularization at 1 year. RESULTS Coronary revascularization was deferred in 2,130 patients. Deferral was performed in 1,117 patients (50%) in the iFR group and 1,013 patients (45%) in the FFR group (p < 0.01). At 1 year, the MACE rate in the deferred population was similar between the iFR and FFR groups (4.12% vs. 4.05%; fully adjusted hazard ratio: 1.13; 95% confidence interval: 0.72 to 1.79; p = 0.60). A clinical presentation with ACS was associated with a higher MACE rate compared with SAP in deferred patients (5.91% vs. 3.64% in ACS and SAP, respectively; fully adjusted hazard ratio: 0.61 in favor of SAP; 95% confidence interval: 0.38 to 0.99; p = 0.04). CONCLUSIONS Overall, deferral of revascularization is equally safe with both iFR and FFR, with a low MACE rate of about 4%. Lesions were more frequently deferred when iFR was used to assess physiological significance. In deferred patients presenting with ACS, the event rate was significantly increased compared with SAP at 1 year. (C) 2018 The Authors. Published by Elsevier on behalf of the American College of Cardiology Foundation.
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| 21. |
- Iles, Mark M., et al.
(författare)
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A variant in FTO shows association with melanoma risk not due to BMI
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:4, s. 428-432
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Tidskriftsartikel (refereegranskat)abstract
- We report the results of an association study of melanoma that is based on the genome-wide imputation of the genotypes of 1,353 cases and 3,566 controls of European origin conducted by the GenoMEL consortium. This revealed an association between several SNPs in intron 8 of the FTO gene, including rs16953002, which replicated using 12,313 cases and 55,667 controls of European ancestry from Europe, the USA and Australia (combined P = 3.6 x 10(-12), per-allele odds ratio for allele A = 1.16). In addition to identifying a new melanomasusceptibility locus, this is to our knowledge the first study to identify and replicate an association with SNPs in FTO not related to body mass index (BMI). These SNPs are not in intron 1 (the BMI-related region) and exhibit no association with BMI. This suggests FTO's function may be broader than the existing paradigm that FTO variants influence multiple traits only through their associations with BMI and obesity.
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