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- Brinkman, Arie B., et al.
(författare)
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Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.
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- Cadenas-Sanchez, Cristina, et al.
(författare)
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Physical fitness reference standards for preschool children : The PREFIT project.
- 2019
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Ingår i: Journal of Science and Medicine in Sport. - : Elsevier. - 1440-2440 .- 1878-1861. ; 22:4, s. 430-437
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Reference values are necessary for classifying children, for health screening, and for early prevention as many non-communicable diseases aggravate during growth and development. While physical fitness reference standards are available in children aged 6 and older, such information is lacking in preschool children. Therefore, the purposes of this study were (1) to provide sex-and age-specific physical fitness reference standards for Spanish preschool children; and (2) to study sex differences across this age period and to characterise fitness performance throughout the preschool period.DESIGN: Cross-sectional.METHODS: A total of 3179 preschool children (1678 boys) aged 2.8-6.4 years old from Spain were included in the present study. Physical fitness was measured using the PREFIT battery.RESULTS: Age- and sex-specific percentiles for the physical fitness components are provided. Boys performed better than girls in the cardiorespiratory fitness, muscular strength, and speed-agility tests over the whole preschool period studied and for the different percentiles. In contrast, girls performed slightly better than boys in the balance test. Older children had better performance in all fitness tests than their younger counterparts.CONCLUSIONS: Our study provides age- and sex-specific physical fitness reference standards in preschool children allowing interpretation of fitness assessment. Sexual dimorphism in fitness tests exists already at preschool age, and these differences become larger with age. These findings will help health, sport, and school professionals to identify preschool children with a high/very low fitness level, to examine changes in fitness over time, and to analyse those changes obtained due to intervention effects.
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- Nik-Zainal, Serena, et al.
(författare)
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 534:7605, s. 47-54
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Tidskriftsartikel (refereegranskat)abstract
- We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.
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- Brunk, Elizabeth, et al.
(författare)
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Recon3D enables a three-dimensional view of gene variation in human metabolism
- 2018
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 36:3, s. 272-281
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Tidskriftsartikel (refereegranskat)abstract
- Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.
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| 7. |
- Carreira, B. M., et al.
(författare)
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Warm vegetarians? : Heat waves and diet shifts in tadpoles
- 2016
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 97:11, s. 2964-2974
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Tidskriftsartikel (refereegranskat)abstract
- Temperature can play an important role in determining the feeding preferences of ectotherms. In light of the warmer temperatures arising with the current climatic changes, omnivorous ectotherms may perform diet shifts toward higher herbivory to optimize energetic intake. Such diet shifts may also occur during heat waves, which are projected to become more frequent, intense, and longer lasting in the future. Here, we investigated how heat waves of different duration affect feeding preferences in omnivorous anuran tadpoles and how these choices affect larval life history. In laboratory experiments, we fed tadpoles of three species on animal, plant, or mixed diet and exposed them to short heat waves (similar to the heat waves these species experience currently) or long heat waves (predicted to increase under climate change). We estimated the dietary choices of tadpoles fed on the mixed diet using stable isotopes and recorded tadpole survival and growth, larval period, and mass at metamorphosis. Tadpole feeding preferences were associated with their thermal background, with herbivory increasing with breeding temperature in nature. Patterns in survival, growth, and development generally support decreased efficiency of carnivorous diets and increased efficiency or higher relative quality of herbivorous diets at higher temperatures. All three species increased herbivory in at least one of the heat wave treatments, but the responses varied among species. Diet shifts toward higher herbivory were maladaptive in one species, but beneficial in the other two. Higher herbivory in omnivorous ectotherms under warmer temperatures may impact species differently and further contribute to changes in the structure and function of freshwater environments.
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| 8. |
- G. Trainer, Melissa, et al.
(författare)
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Seasonal Variations in Atmospheric Composition as Measured in Gale Crater, Mars
- 2019
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Ingår i: Journal of Geophysical Research - Planets. - : John Wiley & Sons. - 2169-9097 .- 2169-9100. ; 124:11, s. 3000-3024
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Tidskriftsartikel (refereegranskat)abstract
- The Sample Analysis at Mars (SAM) instrument onboard the Mars Science Laboratory Curiosity rover measures the chemical composition of major atmospheric species (CO2, N2, 40Ar, O2, and CO) through a dedicated atmospheric inlet. We report here measurements of volume mixing ratios in Gale Crater using the SAM quadrupole mass spectrometer, obtained over a period of nearly 5 years (3 Mars years) from landing. The observation period spans the northern summer of MY 31 and solar longitude (LS) of 175° through spring of MY 34, LS = 12°. This work expands upon prior reports of the mixing ratios measured by SAM QMS in the first 105 sols of the mission. The SAM QMS atmospheric measurements were taken periodically, with a cumulative coverage of four or five experiments per season on Mars. Major observations include the seasonal cycle of CO2, N2, and Ar, which lags approximately 20–40° of LS behind the pressure cycle driven by CO2 condensation and sublimation from the winter poles. This seasonal cycle indicates that transport occurs on faster timescales than mixing. The mixing ratio of O2 shows significant seasonal and interannual variability, suggesting an unknown atmospheric or surface process at work. The O2 measurements are compared to several parameters, including dust optical depth and trace CH4 measurements by Curiosity. We derive annual mean volume mixing ratios for the atmosphere in Gale Crater: CO2 = 0.951 (±0.003), N2 = 0.0259 (±0.0006), 40Ar = 0.0194 (±0.0004), O2 = 1.61 (±0.09) x 10‐3, and CO = 5.8 (±0.8) x 10‐4.
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| 11. |
- Senkovskiy, Boris V., et al.
(författare)
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Semiconductor-to-Metal Transition and Quasiparticle Renormalization in Doped Graphene Nanoribbons
- 2017
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Ingår i: Advanced Electronic Materials. - : Wiley. - 2199-160X. ; 3:4
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Tidskriftsartikel (refereegranskat)abstract
- A semiconductor-to-metal transition in N = 7 armchair graphene nanoribbons causes drastic changes in its electron and phonon system. By using angle-resolved photoemission spectroscopy of lithium-doped graphene nanoribbons, a quasiparticle band gap renormalization from 2.4 to 2.1 eV is observed. Reaching high doping levels (0.05 electrons per atom), it is found that the effective mass of the conduction band carriers increases to a value equal to the free electron mass. This giant increase in the effective mass by doping is a means to enhance the density of states at the Fermi level which can have palpable impact on the transport and optical properties. Electron doping also reduces the Raman intensity by one order of magnitude, and results in relatively small (4 cm−1) hardening of the G phonon and softening of the D phonon. This suggests the importance of both lattice expansion and dynamic effects. The present work highlights that doping of a semiconducting 1D system is strikingly different from its 2D or 3D counterparts and introduces doped graphene nanoribbons as a new tunable quantum material with high potential for basic research and applications.
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| 12. |
- Smid, Marcel, et al.
(författare)
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Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.
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