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- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 6. |
- Stormlund, S., et al.
(author)
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Freeze-all versus fresh blastocyst transfer strategy during in vitro fertilisation in women with regular menstrual cycles: multicentre randomised controlled trial
- 2020
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In: Bmj-British Medical Journal. - : BMJ. - 1756-1833. ; 370
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Journal article (peer-reviewed)abstract
- OBJECTIVE To compare the ongoing pregnancy rate between a freeze-all strategy and a fresh transfer strategy in assisted reproductive technology treatment. DESIGN Multicentre, randomised controlled superiority trial. SETTING Outpatient fertility clinics at eight public hospitals in Denmark, Sweden, and Spain. PARTICIPANTS 460 women aged 18-39 years with regular menstrual cycles starting their first, second, or third treatment cycle of in vitro fertilisation or intracytoplasmic sperm injection. INTERVENTIONS Women were randomised at baseline on cycle day 2 or 3 to one of two treatment groups: the freeze-all group (elective freezing of all embryos) who received gonadotropin releasing hormone agonist triggering and single frozen-thawed blastocyst transfer in a subsequent modified natural cycle; or the fresh transfer group who received human chorionic gonadotropin triggering and single blastocyst transfer in the fresh cycle. Women in the fresh transfer group with more than 18 follicles larger than 11 mm on the day of triggering had elective freezing of all embryos and postponement of transfer as a safety measure. MAIN OUTCOME MEASURES The primary outcome was the ongoing pregnancy rate defined as a detectable fetal heart beat after eight weeks of gestation. Secondary outcomes were live birth rate, positive human chorionic gonadotropin rate, time to pregnancy, and pregnancy related, obstetric, and neonatal complications. The primary analysis was performed according to the intention-to-treat principle. RESULTS Ongoing pregnancy rate did not differ significantly between the freeze-all and fresh transfer groups (27.8% (62/223) v 29.6% (68/230); risk ratio 0.98, 95% confidence interval 0.87 to 1.10, P=0.76). Additionally, no significant difference was found in the live birth rate (27.4% (61/223) for the freeze-all group and 28.7% (66/230) for the fresh transfer group; risk ratio 0.98, 95% confidence interval 0.87 to 1.10, P=0.83). No significant differences between groups were observed for positive human chorionic gonadotropin rate or pregnancy loss, and none of the women had severe ovarian hyperstimulation syndrome; only one hospital admission related to this condition occurred in the fresh transfer group. The risks of pregnancy related, obstetric, and neonatal complications did not differ between the two groups except for a higher mean birth weight after frozen blastocyst transfer and an increased risk of prematurity after fresh blastocyst transfer. Time to pregnancy was longer in the freeze-all group. CONCLUSIONS In women with regular menstrual cycles, a freeze-all strategy with gonadotropin releasing hormone agonist triggering for final oocyte maturation did not result in higher ongoing pregnancy and live birth rates than a fresh transfer strategy. The findings warrant caution in the indiscriminate application of a freeze-all strategy when no apparent risk of ovarian hyperstimulation syndrome is present.
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| 8. |
- Marçal, L. A.B., et al.
(author)
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Structural and chemical properties of anion exchanged CsPb(Br(1−x)Cl x )3 heterostructured perovskite nanowires imaged by nanofocused x-rays
- 2024
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In: Nanotechnology. - 0957-4484. ; 35:26
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Journal article (peer-reviewed)abstract
- Over the last years metal halide perovskites have demonstrated remarkable potential for integration in light emitting devices. Heterostructures allow for tunable bandgap depending on the local anion composition, crucial for optoelectronic devices, but local structural effects of anion exchange in single crystals is not fully understood. Here, we investigate how the anion exchange of CsPbBr3 nanowires fully and locally exposed to HCl vapor affects the local crystal structure, using nanofocused x-rays. We study the nanoscale composition and crystal structure as function of HCl exposure time and demonstrate the correlation of anion exchange with changes in the lattice parameter. The local composition was measured by x-ray fluorescence and x-ray diffraction, with general agreement of both methods but with much less variation using latter. The heterostructured nanowires exhibit unintentional gradients in composition, both axially and radially. Ferroelastic domains are observed for all HCl exposure times, and the magnitude of the lattice tilt at the domain walls scales with the Cl concentration.
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| 10. |
- A. B. Marçal, L., et al.
(author)
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Spatially resolved structural and chemical properties of the white layer in machined Inconel 718 super alloy
- 2024
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In: Materials and Design. - 0264-1275. ; 239
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Journal article (peer-reviewed)abstract
- Inconel 718 is one type of nickel-based alloy used for a large range of applications, including gas turbines and aeroengines components. Although mechanical and thermodynamic properties of this material have been deeply studied in the past years, a method able to investigate local properties of the thin white layer formed on the alloy surface after machining remains challenging. Here, a 90 nm X-ray beam is used to probe the local strain, crystal orientation, and chemical composition of grains in the white layer. Data reveals mosaicity induced by the tool during machining. The high spatial resolution, combined with crystal lattice sensitivity, shows that the average grain size is around 30 nm throughout the white layer, while the strain is anisotropic nearest to the surface. Results provide new insights on the basic properties of the white layer in super alloys, revealing important information about the impact of finish machining which might help to explain fatigue and cracking formation on these materials during their usage phase.
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