| 1. |
- Machiela, Mitchell J., et al.
(författare)
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Characterization of Large Structural Genetic Mosaicism in Human Autosomes
- 2015
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 96:3, s. 487-497
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genome-wide association study (GWAS) data have revealed that detectable genetic mosaicism involving large (>2 Mb) structural autosomal alterations occurs in a fraction of individuals. We present results for a set of 24,849 genotyped individuals (total GWAS set II [TGSII]) in whom 341 large autosomal abnormalities were observed in 168 (0.68%) individuals. Merging data from the new TGSII set with data from two prior reports (the Gene-Environment Association Studies and the total GWAS set I) generated a large dataset of 127,179 individuals; we then conducted a meta-analysis to investigate the patterns of detectable autosomal mosaicism (n = 1,315 events in 925 [0.73%] individuals). Restricting to events >2 Mb in size, we observed an increase in event frequency as event size decreased. The combined results underscore that the rate of detectable mosaicism increases with age (p value = 5.5 x 3 10(-31)) and is higher in men (p value = 0.002) but lower in participants of African ancestry (p value = 0.003). In a subset of 47 individuals from whom serial samples were collected up to 6 years apart, complex changes were noted over time and showed an overall increase in the proportion of mosaic cells as age increased. Our large combined sample allowed for a unique ability to characterize detectable genetic mosaicism involving large structural events and strengthens the emerging evidence of non-random erosion of the genome in the aging population.
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| 2. |
- Machiela, Mitchell J, et al.
(författare)
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Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
- 2016
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
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| 3. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 4. |
- Chi, Xiaoming, et al.
(författare)
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Fractal superconducting nanowire single-photon detectors with reduced polarization sensitivity
- 2018
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Ingår i: Optics Letters. - : OPTICAL SOC AMER. - 0146-9592 .- 1539-4794. ; 43:20, s. 5017-5020
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate superconducting nanowire single-photon detectors (SNSPDs) based on a fractal design of the nanowires to reduce the polarization sensitivity of detection efficiency. We patterned niobium titanium nitride thin films into Peano curves with a linewidth of 100 nm and integrated the nanowires with optical microcavities to enhance their optical absorption. At a base temperature of 2.6 K, the fractal SNSPD exhibited a polarization-maximum device efficiency of 67% and a polarization-minimum device efficiency of 61% at a wavelength of 1550 nm. Therefore, the polarization sensitivity, defined as their ratio, was 1.1, lower than the polarization sensitivity of the SNSPDs in the meander design. The reduced polarization sensitivity of the detector could be maintained for higher-order spatial modes in multimode optical fibers and could tolerate misalignment between the optical mode and the detector. This fractal design is applicable to both amorphous and polycrystalline materials that are commonly used for making SNSPDs.
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| 5. |
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| 6. |
- Hu, Xiaolong, et al.
(författare)
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Superconducting nanowire single-photon detectors at the infrared spectrum range : detection efficiency and timing jitter
- 2019
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Ingår i: TERAHERTZ, RF, MILLIMETER, AND SUBMILLIMETER-WAVE TECHNOLOGY AND APPLICATIONS XII. - : SPIE. - 9781510624771
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Konferensbidrag (refereegranskat)abstract
- This paper reviews some recent research progress in superconducting nanowire single-photon detectors (SNSPDs) at the infrared spectrum range, with particular emphasis on detection efficiency and timing jitter. For detection efficiency, we present fractal SNSPDs with reduced polarization sensitivity; for timing jitter, we present two mechanisms of device timing jitter - vortex-crossing-induced timing jitter and spatial-inhomogeneity-induced timing jitter.
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| 7. |
- Hu, Xiaolong, et al.
(författare)
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Timing properties of superconducting nanowire single-photon detectors
- 2019
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Ingår i: Quantum Optics and Photon Counting 2019. - : SPIE - International Society for Optical Engineering. - 9781510627215
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Konferensbidrag (refereegranskat)abstract
- In this paper, we review theoretical and experimental research progress on timing properties of superconducting nanowire single-photon detectors, including six possible mechanisms that induce timing jitter and experiments towards ultra-low timing jitter.
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| 8. |
- Yu, Zheng Lin, et al.
(författare)
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Environmental water flow can boost foraging success of the juvenile rapa whelk Rapana venosa (Muricidae) in aquaculture tanks with still or flowing water : Indication of chemosensory foraging
- 2019
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 513
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Tidskriftsartikel (refereegranskat)abstract
- Artificial breeding of Rapana venosa has been attempted in China, but the high mortality rate of rapa whelk juveniles (10–40 mm) seriously restricts the breeding success of this species in artificial cultivation and the overall aquaculture industry, and thus the scale of industrialization is far from being realized. One main factor was found to contribute to this high mortality rate: the low predation efficiency of juveniles. We studied the foraging behavior of various sized R. venosa juveniles in still, flowing, and circulating water, with the juveniles being positioned either upstream or downstream from the prey in the flowing water experiments. Our findings demonstrated that the distance between juveniles and prey in still water significantly restricted the ability of juveniles to locate food, but water flow significantly enhanced this ability. In addition, the small-sized juveniles were found to be more active predators than the larger sized juveniles. Our findings demonstrated that circulating water flow is important to improve the survival and growth rate of juveniles in R. venosa cultures. Our results broaden the understanding of chemical orientation in gastropods and can be used to develop or improve commercial breeding strategies for R. venosa.
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| 9. |
- Chen, Gang, et al.
(författare)
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EDF-VD Scheduling of Flexible Mixed-Criticality System With Multiple-Shot Transitions
- 2018
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - 0278-0070 .- 1937-4151. ; 37:11, s. 2393-2403
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Tidskriftsartikel (refereegranskat)abstract
- The existing mixed-criticality (MC) real-time task models assume that once any high-criticality task overruns, all high-criticality jobs execute up to their most pessimistic WCET estimations simultaneously in a one-shot manner. This is very pessimistic in the sense of unnecessary resource overbooking. In this paper, we propose a more generalized mixed-critical real-time task model, called flexible MC model with multiple-shot transitions (FMC-MST), to address this problem. In FMC-MST, high-criticality tasks can transit multiple intermediate levels to handle less pessimistic overruns independently and to nonuni-formly scale the deadline on each level. We develop a run-time schedulability analysis for FMC-MST under EDF-VD scheduling, in which a better tradeoff between the penalties of low-criticality tasks and the overruns of high-criticality tasks is achieved to improve the service quality of low-criticality tasks. We also develop a resource optimization technique to find resource-efficient level-insertion configurations for FMC-MST task systems under MC timing constraints. Experiments demonstrate the effectiveness of FMC-MST compared with the state-of-the-art techniques.
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