| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Cha, Eunjung, 1985, et al.
(författare)
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Optimization of Channel Structures in InP HEMT Technology for Cryogenic Low-Noise and Low-Power Operation
- 2023
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Ingår i: IEEE Transactions on Electron Devices. - 1557-9646 .- 0018-9383. ; 70:5, s. 2431-2436
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Tidskriftsartikel (refereegranskat)abstract
- We report the impact from channel composition on the cryogenic low-noise performance at low dc power for a 100-nm gate-length InGaAs-InAlAs-InP high-electron mobility transistor (HEMT). Two indium (In) channel compositions, 65% and 80%, were studied by dc and RF characterization at 300 and 5 K. For the cryogenic low-noise optimization, it was important to increase the transconductance to gate–source capacitance ratio in the weak inversion region implying that a higher maximum cutoff frequency in the HEMT does not guarantee lower noise. The HEMT noise performance was obtained from noise measurements in a hybrid three-stage 4–8-GHz ( $\textit{C}$ -band) low-noise amplifier (LNA) down to 300- $\mu$ W dc power dissipation. While the HEMT LNA noise performance for both the channel compositions at 300 K was found to be comparable, the HEMT LNA at 5 K with 65% In channel showed a minimum noise temperature of 1.4 K, whereas the noise temperature in the HEMT LNA with 80% In channel HEMTs increased to 2.4 K. The difference in the noise became more pronounced at reduced dc power dissipation. The ultralow dc power of 300 $\mu$ W demonstrated for a cryogenic $\textit{C}$ -band LNA with an average noise temperature of 2.9 K and 24-dB gain is of interest for future qubit read-out electronics at 4 K.
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| 3. |
- Dekhtyar, Alex, et al.
(författare)
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From RE cares to SE cares: Software engineering for social good, one venue at a time
- 2020
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Ingår i: ICSE-SEIS '20: Proceedings of the ACM/IEEE 42nd International Conference on Software Engineering: Software Engineering in Society. - 0270-5257.
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Konferensbidrag (refereegranskat)abstract
- © 2020 Association for Computing Machinery. As software practitioners, we can help society by using our communities of experts to address a software need of a socially-conscious organization. Doing so can benefit society in the locale of a software engineering conference, and provides access to international experts for local organizations which may otherwise not have access. Furthermore, established Software Engineering (SE) researchers as well as practitioners and students have the opportunity for a unique learning experience. In this paper, we argue that the SE community should use SE conferences as the focal points for activities that benefit society at the locations of the conferences, and make such activities an integral, valued, and recognized part of the conference programs. The proposed series of events, termed SE Cares, can follow and learn from the model of Requirements Engineering (RE) Cares events that took place in 2018 and 2019, and can be a co-located event at all interested SE-related conferences.
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| 4. |
- Gerlee, Philip, 1980, et al.
(författare)
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Bridging scales in cancer progression: Mapping genotype to phenotype using neural networks
- 2015
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Ingår i: Seminars in Cancer Biology. - : Elsevier BV. - 1096-3650 .- 1044-579X. ; 30, s. 30-41
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Tidskriftsartikel (refereegranskat)abstract
- In this review we summarise our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to its phenotype. Our central premise is that cancer is an evolving system subject to mutation and selection, and the primary conduit for these processes to occur is the cancer cell whose behaviour is regulated on multiple biological scales. The selection pressure is mainly driven by the microenvironment that the tumour is growing in and this acts directly upon the cell phenotype. In turn, the phenotype is driven by the intracellular pathways that are regulated by the genotype. Integrating all of these processes is a massive undertaking and requires bridging many biological scales (i.e. genotype, pathway, phenotype and environment) that we will only scratch the surface of in this review. We will focus on models that use neural networks as a means of connecting these different biological scales, since they allow us to easily create heterogeneity for selection to act upon and importantly this heterogeneity can be implemented at different biological scales. More specifically, we consider three different neural networks that bridge different aspects of these scales and the dialogue with the micro-environment, (i) the impact of the micro-environment on evolutionary dynamics, (ii) the mapping from genotype to phenotype under drug-induced perturbations and (iii) pathway activity in both normal and cancer cells under different micro-environmental conditions.
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| 5. |
- Jumeaux, Coline, et al.
(författare)
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MicroRNA Detection by DNA-Mediated Liposome Fusion
- 2018
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Ingår i: ChemBioChem. - : Wiley. - 1439-7633 .- 1439-4227. ; 19:5, s. 434-438
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Tidskriftsartikel (refereegranskat)abstract
- Membrane fusion is a process of fundamental importance in biological systems that involves highly selective recognition mechanisms for the trafficking of molecular and ionic cargos. Mimicking natural membrane fusion mechanisms for the purpose of biosensor development holds great potential for amplified detection because relatively few highly discriminating targets lead to fusion and an accompanied engagement of a large payload of signal-generating molecules. In this work, sequence-specific DNA-mediated liposome fusion is used for the highly selective detection of microRNA. The detection of miR-29a, a known flu biomarker, is demonstrated down to 18 nm within 30 min with high specificity by using a standard laboratory microplate reader. Furthermore, one order of magnitude improvement in the limit of detection is demonstrated by using a novel imaging technique combined with an intensity fluctuation analysis, which is coined two-color fluorescence correlation microscopy.
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| 6. |
- 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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| 7. |
- Qian, Frank, et al.
(författare)
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Omega-3 Fatty Acid Biomarkers and Incident Atrial Fibrillation
- 2023
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Ingår i: Journal of the American College of Cardiology. - : Elsevier. - 0735-1097 .- 1558-3597. ; 82:4, s. 336-349
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The relationship between omega-3 fatty acids and atrial fibrillation (AF) remains controversial.OBJECTIVES: This study aimed to determine the prospective associations of blood or adipose tissue levels of eicosa-pentaenoic acid (EPA), docosapentaenoic acid (DPA), and docosahexaenoic acid (DHA) with incident AF.METHODS: We used participant-level data from a global consortium of 17 prospective cohort studies, each with baseline data on blood or adipose tissue omega-3 fatty acid levels and AF outcomes. Each participating study conducted a de novo analyses using a prespecified analytical plan with harmonized definitions for exposures, outcome, covariates, and sub-groups. Associations were pooled using inverse-variance weighted meta-analysis.RESULTS: Among 54,799 participants from 17 cohorts, 7,720 incident cases of AF were ascertained after a median 13.3 years of follow-up. In multivariable analysis, EPA levels were not associated with incident AF, HR per interquintile range (ie, the difference between the 90th and 10th percentiles) was 1.00 (95% CI: 0.95-1.05). HRs for higher levels of DPA, DHA, and EPA+DHA, were 0.89 (95% CI: 0.83-0.95), 0.90 (95% CI: 0.85-0.96), and 0.93 (95% CI: 0.87-0.99), respectively.CONCLUSIONS: In vivo levels of omega-3 fatty acids including EPA, DPA, DHA, and EPA+DHA were not associated with increased risk of incident AF. Our data suggest the safety of habitual dietary intakes of omega-3 fatty acids with respect to AF risk. Coupled with the known benefits of these fatty acids in the prevention of adverse coronary events, our study suggests that current dietary guidelines recommending fish/omega-3 fatty acid consumption can be maintained.
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