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- Dunn, R. J. H., et al.
(författare)
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GLOBAL CLIMATE : State of the Climate in 2020
- 2021
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Ingår i: Bulletin of the American Meteorological Society. - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 102:8
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Tidskriftsartikel (refereegranskat)
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- Kang, E. Y., et al.
(författare)
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CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study
- 2023
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Ingår i: Cancer. - : Wiley. - 0008-543X .- 1097-0142. ; 129:5, s. 697-713
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Tidskriftsartikel (refereegranskat)abstract
- Background: Cyclin E1 (CCNE1) is a potential predictive marker and therapeutic target in tubo-ovarian high-grade serous carcinoma (HGSC). Smaller studies have revealed unfavorable associations for CCNE1 amplification and CCNE1 overexpression with survival, but to date no large-scale, histotype-specific validation has been performed. The hypothesis was that high-level amplification of CCNE1 and CCNE1 overexpression, as well as a combination of the two, are linked to shorter overall survival in HGSC. Methods: Within the Ovarian Tumor Tissue Analysis consortium, amplification status and protein level in 3029 HGSC cases and mRNA expression in 2419 samples were investigated. Results: High-level amplification (>8 copies by chromogenic in situ hybridization) was found in 8.6% of HGSC and overexpression (>60% with at least 5% demonstrating strong intensity by immunohistochemistry) was found in 22.4%. CCNE1 high-level amplification and overexpression both were linked to shorter overall survival in multivariate survival analysis adjusted for age and stage, with hazard stratification by study (hazard ratio [HR], 1.26; 95% CI, 1.08-1.47, p = .034, and HR, 1.18; 95% CI, 1.05-1.32, p = .015, respectively). This was also true for cases with combined high-level amplification/overexpression (HR, 1.26; 95% CI, 1.09-1.47, p = .033). CCNE1 mRNA expression was not associated with overall survival (HR, 1.00 per 1-SD increase; 95% CI, 0.94-1.06; p = .58). CCNE1 high-level amplification is mutually exclusive with the presence of germline BRCA1/2 pathogenic variants and shows an inverse association to RB1 loss. Conclusion: This study provides large-scale validation that CCNE1 high-level amplification is associated with shorter survival, supporting its utility as a prognostic biomarker in HGSC.
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- Kobel, M., et al.
(författare)
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p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study
- 2023
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Ingår i: Journal of Pathology Clinical Research. - : Wiley. - 2056-4538. ; 9:3, s. 208-222
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Tidskriftsartikel (refereegranskat)abstract
- Our objective was to test whether p53 expression status is associated with survival for women diagnosed with the most common ovarian carcinoma histotypes (high-grade serous carcinoma [HGSC], endometrioid carcinoma [EC], and clear cell carcinoma [CCC]) using a large multi-institutional cohort from the Ovarian Tumor Tissue Analysis (OTTA) consortium. p53 expression was assessed on 6,678 cases represented on tissue microarrays from 25 participating OTTA study sites using a previously validated immunohistochemical (IHC) assay as a surrogate for the presence and functional effect of TP53 mutations. Three abnormal expression patterns (overexpression, complete absence, and cytoplasmic) and the normal (wild type) pattern were recorded. Survival analyses were performed by histotype. The frequency of abnormal p53 expression was 93.4% (4,630/4,957) in HGSC compared to 11.9% (116/973) in EC and 11.5% (86/748) in CCC. In HGSC, there were no differences in overall survival across the abnormal p53 expression patterns. However, in EC and CCC, abnormal p53 expression was associated with an increased risk of death for women diagnosed with EC in multivariate analysis compared to normal p53 as the reference (hazard ratio [HR] = 2.18, 95% confidence interval [CI] 1.36-3.47, p = 0.0011) and with CCC (HR = 1.57, 95% CI 1.11-2.22, p = 0.012). Abnormal p53 was also associated with shorter overall survival in The International Federation of Gynecology and Obstetrics stage I/II EC and CCC. Our study provides further evidence that functional groups of TP53 mutations assessed by abnormal surrogate p53 IHC patterns are not associated with survival in HGSC. In contrast, we validate that abnormal p53 IHC is a strong independent prognostic marker for EC and demonstrate for the first time an independent prognostic association of abnormal p53 IHC with overall survival in patients with CCC.
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- Mueller, Stefanie H., et al.
(författare)
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Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
- 2023
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Ingår i: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 x 10(-6)) and AC058822.1 (P = 1.47 x 10(-4)), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 x 10(-5)), demonstrating the importance of diversifying study cohorts.
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- Heinze, Karolin, et al.
(författare)
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Validated biomarker assays confirm ARID1A loss is confounded with MMR deficiency, CD8 TIL infiltration, and provides no independent prognostic value in endometriosis-associated ovarian carcinomas.
- 2021
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Ingår i: The Journal of pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 256:4, s. 388-401
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Tidskriftsartikel (refereegranskat)abstract
- ARID1A (BAF250a) is a component of the SWI/SNF chromatin modifying complex, plays an important tumour suppressor role, and is considered prognostic in several malignancies. However, in ovarian carcinomas there are contradictory reports on its relationship to outcome, immune response, and correlation with clinicopathological features. We assembled a series of 1,623 endometriosis-associated ovarian carcinomas, including 1,078 endometrioid (ENOC) and 545 clear cell (CCOC) ovarian carcinomas through combining resources of the Ovarian Tumor Tissue Analysis (OTTA) Consortium, the Canadian Ovarian Unified Experimental Resource (COEUR), local, and collaborative networks. Validated immunohistochemical surrogate assays for ARID1A mutations were applied to all samples. We investigated associations between ARID1A loss/mutation, clinical features, outcome, CD8+ tumour-infiltrating lymphocytes (CD8+ TIL), and DNA mismatch repair deficiency (MMRd). ARID1A loss was observed in 42% of CCOC and 25% of ENOC. We found no associations between ARID1A loss and outcomes, stage, age, or CD8+ TIL status in CCOC. Similarly, we found no association with outcome or stage in endometrioid cases. In ENOC, ARID1A loss was more prevalent in younger patients (p=0.012), and associated with MMRd (p<0.001), and presence of CD8+ TIL (p=0.008). Consistent with MMRd being causative of ARID1A mutations, in a subset of ENOC we also observed an association between ARID1A loss-of-function mutation as a result of small indels (p=0.035, versus single nucleotide variants). In ENOC, the association between ARID1A loss, CD8+ TIL, and age, appears confounded by MMRd status. Although this observation does not explicitly rule out a role for ARID1A influence on CD8+ TIL infiltration in ENOC, given current knowledge regarding MMRd, it seems more likely that effects are dominated by the hypermutation phenotype. This large dataset with consistently applied biomarker assessment now provides a benchmark for the prevalence of ARID1A loss-of-function mutations in endometriosis-associated ovarian cancers and brings clarity to the prognostic significance. This article is protected by copyright. All rights reserved.
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- Zanti, Maria, et al.
(författare)
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A Likelihood Ratio Approach for Utilizing Case-Control Data in the Clinical Classification of Rare Sequence Variants : Application to BRCA1 and BRCA2
- 2023
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Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 2023
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Tidskriftsartikel (refereegranskat)abstract
- A large number of variants identified through clinical genetic testing in disease susceptibility genes are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion) can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analysis of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC) and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity-findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared with classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and preformatted Excel calculators for implementation of the method for rare variants in BRCA1, BRCA2, and other high-risk genes with known penetrance.
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- Zusin, Dmitriy, et al.
(författare)
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Ultrafast perturbation of magnetic domains by optical pumping in a ferromagnetic multilayer
- 2022
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 106:14
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast optical pumping of spatially nonuniform magnetic textures is known to induce far-from-equilibrium spin transport effects. Here, we use ultrafast x-ray diffraction with unprecedented dynamic range to study the laser-induced dynamics of labyrinth domain networks in ferromagnetic CoFe/Ni multilayers. We detected azimuthally isotropic, odd order, magnetic diffraction rings up to fifth order. The amplitudes of all three diffraction rings quench to different degrees within 1.6 ps. In addition, all three of the detected diffraction rings both broaden by 15% and radially contract by 6% during the quench process. We are able to rigorously quantify a 31% ultrafast broadening of the domain walls via Fourier analysis of the order-dependent quenching of the three detected diffraction rings. The broadening of the diffraction rings is interpreted as a reduction in the domain coherence length, but the shift in the ring radius, while unambiguous in its occurrence, remains unexplained. In particular, we demonstrate that a radial shift explained by domain-wall broadening can be ruled out. With the unprecedented dynamic range of our data, our results provide convincing evidence that labyrinth domain structures are spatially perturbed at ultrafast speeds under far-from-equilibrium conditions, albeit the mechanism inducing the perturbations remains yet to be clarified.
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- Partelow, Stefan, et al.
(författare)
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Aquaculture governance : five engagement arenas for sustainability transformation
- 2023
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Ingår i: Current Opinion in Environmental Sustainability. - 1877-3435 .- 1877-3443. ; 65
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Tidskriftsartikel (refereegranskat)abstract
- A greater focus on governance is needed to facilitate effective and substantive progress toward sustainability transformations in the aquaculture sector. Concerted governance efforts can help move the sector beyond fragmented technical questions associated with intensification and expansion, social and environmental impacts, and toward system-based approaches that address interconnected sustainability issues. Through a review and expert-elicitation process, we identify five engagement arenas to advance a governance agenda for aquaculture sustainability transformation: (1) setting sustainability transformation goals, (2) cross-sectoral linkages, (3) land–water–sea connectivity, (4) knowledge and innovation, and (5) value chains. We then outline the roles different actors and modes of governance can play in fostering sustainability transformations, and discuss action items for researchers, practitioners, and policymakers to operationalize activities within their engagement arenas.
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- Tengdin, Phoebe, et al.
(författare)
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Direct light–induced spin transfer between different elements in a spintronic Heusler material via femtosecond laser excitation
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science. - 2375-2548. ; 6:3
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Tidskriftsartikel (refereegranskat)abstract
- Heusler compounds are exciting materials for future spintronics applications because they display a wide range of tunable electronic and magnetic interactions. Here, we use a femtosecond laser to directly transfer spin polarization from one element to another in a half-metallic Heusler material, Co2MnGe. This spin transfer initiates as soon as light is incident on the material, demonstrating spatial transfer of angular momentum between neighboring atomic sites on time scales < 10 fs. Using ultrafast high harmonic pulses to simultaneously and independently probe the magnetic state of two elements during laser excitation, we find that the magnetization of Co is enhanced, while that of Mn rapidly quenches. Density functional theory calculations show that the optical excitation directly transfers spin from one magnetic sublattice to another through preferred spin-polarized excitation pathways. This direct manipulation of spins via light provides a path toward spintronic devices that can operate on few-femtosecond or faster time scales.
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- Westall, F., et al.
(författare)
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The Habitability of Venus
- 2023
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Ingår i: Space Science Reviews. - : Springer Nature. - 0038-6308 .- 1572-9672. ; 219:2
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Forskningsöversikt (refereegranskat)abstract
- Venus today is inhospitable at the surface, its average temperature of 750 K being incompatible to the existence of life as we know it. However, the potential for past surface habitability and upper atmosphere (cloud) habitability at the present day is hotly debated, as the ongoing discussion regarding a possible phosphine signature coming from the clouds shows. We review current understanding about the evolution of Venus with special attention to scenarios where the planet may have been capable of hosting microbial life. We compare the possibility of past habitability on Venus to the case of Earth by reviewing the various hypotheses put forth concerning the origin of habitable conditions and the emergence and evolution of plate tectonics on both planets. Life emerged on Earth during the Hadean when the planet was dominated by higher mantle temperatures (by about 200 ∘C), an uncertain tectonic regime that likely included squishy lid/plume-lid and plate tectonics, and proto continents. Despite the lack of well-preserved crust dating from the Hadean and Paleoarchean, we attempt to review current understanding of the environmental conditions during this critical period based on zircon crystals and geochemical signatures from this period, as well as studies of younger, relatively well-preserved rocks from the Paleoarchean. For these early, primitive life forms, the tectonic regime was not critical but it became an important means of nutrient recycling, with possible consequences on the global environment in the long-term, that was essential to the continuation of habitability and the evolution of life. For early Venus, the question of stable surface water is closely related to tectonics. We discuss potential transitions between stagnant lid and (episodic) tectonics with crustal recycling, as well as consequences for volatile cycling between Venus’ interior and atmosphere. In particular, we review insights into Venus’ early climate and examine critical questions about early rotation speed, reflective clouds, and silicate weathering, and summarize implications for Venus’ long-term habitability. Finally, the state of knowledge of the Venusian clouds and the proposed detection of phosphine is covered.
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