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- Lawrenson, Kate, et al.
(författare)
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Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
- 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 locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.
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| 2. |
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| 3. |
- Amgad, M, et al.
(författare)
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Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group
- 2020
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Ingår i: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1, s. 16-
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Tidskriftsartikel (refereegranskat)abstract
- Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
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| 4. |
- Lazić, Predrag, 1975-, et al.
(författare)
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Low intensity conduction states in FeS2 : implications for absorption, open-circuit voltage and surface recombination
- 2013
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Ingår i: Journal of Physics. - : Institute of Physics (IOP). - 0953-8984 .- 1361-648X. ; 25:46, s. 465801-
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Tidskriftsartikel (refereegranskat)abstract
- Pyrite (FeS2), being a promising material for future solar technologies, has so far exhibited in experiments an open-circuit voltage (OCV) of around 0.2 V, which is much lower than the frequently quoted 'accepted' value for the fundamental bandgap of similar to 0.95 eV. Absorption experiments show large subgap absorption, commonly attributed to defects or structural disorder. However, computations using density functional theory with a semi-local functional predict that the bottom of the conduction band consists of a very low intensity sulfur p-band that may be easily overlooked in experiments because of the high intensity onset that appears 0.5 eV higher in energy. The intensity of absorption into the sulfur p-band is found to be of the same magnitude as contributions from defects and disorder. Our findings suggest the need to re-examine the value of the fundamental bandgap of pyrite presently in use in the literature. If the contribution from the p-band has so far been overlooked, the substantially lowered bandgap would partly explain the discrepancy with the OCV. Furthermore, we show that more states appear on the surface within the low energy sulfur p-band, which suggests a mechanism of thermalization into those states that would further prevent extracting electrons at higher energy levels through the surface. Finally, we speculate on whether misidentified states at the conduction band onset may be present in other materials.
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