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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 4. |
- Fu, Keren, 1988, et al.
(författare)
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Adaptive Multi-Level Region Merging for Salient Object Detection
- 2014
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Ingår i: British Machine Vision Conference (BMVC) 2014. ; , s. 11 -
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Konferensbidrag (refereegranskat)abstract
- Most existing salient object detection algorithms face the problem of either under or over-segmenting an image. More recent methods address the problem via multi-level segmentation. However, the number of segmentation levels is manually predetermined and only works well on specific class of images. In this paper, a new salient object detection scheme is presented based on adaptive multi-level region merging. A graph based merging scheme is developed to reassemble regions based on their shared contourstrength. This merging process is adaptive to complete contours of salient objects that can then be used for global perceptual analysis, e.g., foreground/ground separation. Such contour completion is enhanced by graph-based spectral decomposition. We show that even though simple region saliency measurements are adopted for each region, encouraging performance can be obtained after across-level integration. Experiments by comparing with 13 existing methods on three benchmark datasets including MSRA-1000, SOD and SED show the proposed method results in uniform object enhancement and achieves state-of-the-art performance.
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| 5. |
- Lv, Zhong-Peng, et al.
(författare)
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Cation field-strength effects on ion irradiation-induced mechanical property changes of borosilicate glass structures
- 2023
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Ingår i: Journal of The American Ceramic Society. - 0002-7820 .- 1551-2916. ; 106:10, s. 5766-5780
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Tidskriftsartikel (refereegranskat)abstract
- We examine the impact of the glass network-modifier cation field strength (CFS) on ion irradiation-induced mechanical property changes in borosilicate (BS) glasses for the ternary M2O-B2O3-SiO2 systems with M = {Na, K, Rb} and the quaternary [0.5M((2))O-0.5Na(2)O]-B2O3-SiO2 systems with M = {Li, Na, K, Rb Mg, Ca, Sr, Ba}. B-11 nuclear magnetic resonance (NMR) experiments on the as-prepared BS glasses yielded the fractional population of four-coordinated B species (B-[4]) out of all {B-[3], B-[4]} groups in the glass network, along with the fraction of B-[4]-O-Si linkages out of all B-[4]-O-Si/B bonds. Both parameters correlated linearly with the (average) CFS of the M+ and/or {M(2)+, Na+} cations. Both the nanoindentation-derived hardness and Young's modulus values of the glasses reduced upon their irradiation by Si2+ ions, with the property deterioration decreasing linearly with increasing Mz+ CFS, that is, for higher Mz+center dot center dot center dot O interaction strength. The irradiation damage of the glass network also increased linearly with the fraction of B-[4]-O-Si linkages, which are the second weakest in the structure after the Mz+center dot center dot center dot O bonds. Our results underscore the advantages of employing BS glasses with high-CFS cations for enhancing the radiation resistance for nuclear waste storage.
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| 6. |
- Yang, Zhi Peng, et al.
(författare)
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Deterministic one-way logic gates on a cloud quantum computer
- 2022
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Ingår i: Physical Review A. - 2469-9934 .- 2469-9926. ; 105:4
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Tidskriftsartikel (refereegranskat)abstract
- One-way quantum computing is a promising candidate for fault-tolerant quantum computing. Here, we propose protocols to realize a deterministic one-way controlled-not (cnot) gate and one-way X rotations on current quantum-computing platforms. By applying a delayed-choice scheme, we overcome a limit of most currently available quantum computers, which are unable to implement further operations on measured qubits or operations conditioned on measurement results from other qubits. Moreover, we decrease the error rate of the one-way logic gates, compared to the original protocol using local operations and classical communication. In addition, we apply our deterministic one-way cnot gate in the Deutsch-Jozsa algorithm to show the feasibility of our proposal. We demonstrate all these one-way gates and algorithms by running experiments on the cloud quantum-computing platform IBM Quantum Experience.
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| 7. |
- Cao, Zhixing, et al.
(författare)
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Multi-scale data-driven engineering for biosynthetic titer improvement
- 2020
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Ingår i: Current Opinion in Biotechnology. - : Elsevier BV. - 0958-1669 .- 1879-0429. ; 65, s. 205-212
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Forskningsöversikt (refereegranskat)abstract
- Industrial biosynthesis is a very complex process which depends on a range of different factors, from intracellular genes and metabolites, to extracellular culturing conditions and bioreactor engineering. The identification of species that improve the titer of some reaction is akin to the task of finding a needle in a haystack. This review aims to summarize state-of-the-art biosynthesis titer improvement on different scales separately, particularly regarding the advancement of metabolic pathway rewiring and data-driven process optimization and control. By integrating multi-scale data and establishing a mathematical replica of a real biosynthesis, more refined quantitative insights can be gained for achieving a higher titer than ever.
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| 8. |
- Fu, Keren, 1988, et al.
(författare)
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Graph Construction for Salient Object Detection in Videos
- 2014
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Ingår i: Proceedings - International Conference on Pattern Recognition. - 1051-4651. - 9781479952083 ; , s. 2371-2376
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Konferensbidrag (refereegranskat)abstract
- Recently many graph-based salient region/object detection methods have been developed. They are rather effective for still images. However, little attention has been paid to salient region detection in videos. This paper addresses salient region detection in videos. A unified approach towards graph construction for salient object detection in videos is proposed. The proposed method combines static appearance and motion cues to construct graph, enabling a direct extension of original graph based salient region detection to video processing. To maintain coherence in both intra- and inter-frames, a spatial-temporal smoothing operation is proposed on a structured graph derived from consecutive frames. The effectiveness of the proposed method is tested and validated using seven videos from two video datasets.
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| 9. |
- Gao, Mingming, et al.
(författare)
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Engineered 2D MXene-based materials for advanced supercapacitors and micro-supercapacitors
- 2024
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Ingår i: Materials Today. - 1369-7021 .- 1873-4103. ; 72, s. 318-358
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Forskningsöversikt (refereegranskat)abstract
- The class of two-dimensional transition metal carbides/nitrides/oxycarbides (known as MXenes) has shown great potential in energy storage applications due to their intrinsic layered structure, outstanding electrical conductivity, tunable surface chemistry, and unique physicochemical properties. This review summarizes the latest progresses of MXene-based materials for supercapacitors and micro-supercapacitors. First, state-of-the-art structural engineering strategies for the construction of novel MXene-based electrodes are highlighted, as the electrochemical performance of MXenes is influenced by their structure, such as interlayer spacing and surface functional group density. Furthermore, the charge storage mechanisms of MXene-based electrodes in different electrolytes are discussed to stimulate further design and development of tailored materials for high-performance devices. Moreover, different device fabrication technologies are summarized and the achievements of specific device geometries (e.g., fiber-shape, planar-type, and three-dimensional devices) containing MXene-based materials are critically reviewed. Finally, perspectives and outlook for the development of high-performance MXene-based electrodes in terms of material engineering, performance improvement and device innovation are provided, clearly indicating research directions for next-generation advanced energy storage devices.
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| 10. |
- Guo, Hua, et al.
(författare)
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Quantitative phase analyses of biomedical pyrophosphate-bearing monetite and brushite cements by solid-state NMR and powder XRD
- 2020
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Ingår i: Ceramics International. - : Elsevier BV. - 0272-8842 .- 1873-3956. ; 46:8, s. 11000-11012
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Tidskriftsartikel (refereegranskat)abstract
- We present a comprehensive composition analysis of calcium phosphate cements (CPCs) incorporating increasing amounts of bioactive pyrophosphate species (up to 17 wt% P2O7). These cements comprise primarily poorly ordered monetite (CaHPO4) or brushite (CaHPO4 center dot 2H(2)O) and are investigated for enhanced osteoinductive bone/tooth implants. The specimens were characterized by magic-angle spinning (MAS) P-31 and H-1 nuclear magnetic resonance (NMR) spectroscopy along with powder X-ray diffraction (PXRD). P-31 MAS NMR was employed to quantify the major monetite/brushite constituents, the crystalline and amorphous pyrophosphates, as well as various minor orthophosphate by-products. The NMR-derived contents of the crystalline phases accorded well with those from Rietveld analyses of the corresponding PXRD data. The amounts of crystalline and amorphous pyrophosphate depended on the precise cement precursor mixture and preparation conditions, which together with their distinct structural roles may enable the design of cements with a tunable P2O74 - release into aqueous solutions.
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