| 1. |
- Nie, Shuai, et al.
(författare)
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Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.
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| 2. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 3. |
- Du, Chenqiu, et al.
(författare)
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Home dampness/mold(D/M) improvement in children's residences over the past decade in China-a comparison of repeated surveys in 2010 and 2019
- 2021
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 205
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Tidskriftsartikel (refereegranskat)abstract
- There is mounting evidence that exposure to household dampness/mold (D/M) is the cause of respiratory, allergic diseases for children. While few research focuses on the effects caused by building environment changes, from a longitudinal investigation perspective, especially for China experiencing a rapid development in recent years. This study aimed to explore the changes of D/M in Chinese homes over the past 10 years and identify the impacts of climate, building energy efficiency and residents' behaviors. The cross-sectional surveys were repeatedly conducted in children' residences in 2010 (Period I) and 2019 (Period II), among Taiyuan, Urumqi in northern China, and Nanjing, Shanghai, Wuhan, Changsha, Chongqing in southern China. Finally, 23465 children in Period I and 34720 children in Period II were involved, with no changes of residences since birth. The results showed that the proportions for reported D/M indicators were significantly reduced in Period II: e.g., 93.8% and 84.1% residents respectively answered no visible mold spots and damp stains in current residences, compared to only 78.3% and 62.2% in Period I. Southern homes accounted for high proportions for D/M indicator occurrences; warm-humid climate, annual higher precipitation and lower sunshine hours, etc., exacerbated the indoor D/M exposure risks. While residents' behaviors like ventilation, airing quilt/beddings, regular cleaning ameliorated the reported D/M significantly. The findings, from a temporal and spacious dimension perspective, advance our understanding of indoor D/M changes, precisely improvement in children' homes over the past 10 years, benefiting to promote indoor air quality standards in China.
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| 4. |
- Du, Wei, et al.
(författare)
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Film Cooling in the Cutback for Trailing Edge With Different Incident Angles
- 2023
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Ingår i: Journal of Energy Resources Technology, Transactions of the ASME. - : ASME International. - 0195-0738. ; 145:5
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Tidskriftsartikel (refereegranskat)abstract
- The cutback film cooling was important to decrease the trailing edge temperature and prolong the working life of gas turbines. Many investigations concerning cutback film cooling have already been done. However, only a few papers involve the influence of incident angle on the film cooling effectiveness (η) at the trailing region. In this work, detached eddy simulation (DES) is applied to calculate the η near the cutback region for different incident angles. Five different incident angles (0 deg, 5 deg, 10 deg, 15 deg, and 20 deg) and three blowing ratios (0.2, 0.8, and 1.25) are considered. The flow structure, temperature distribution, and η characteristics are analyzed in detail. Results imply that the incident angle changes the flow structure notably. As the incident angle increases, the separation region is suppressed, but the η was changed nonlinearly. At the low blowing ratio, the incident angle mainly affects the η near the slot. However, the incident angle changes the η downstream of the slot exit under a high blowing ratio. When the blowing ratio becomes large, the η near the centerline becomes larger.
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| 5. |
- Du, Wei, et al.
(författare)
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Heat transfer in the trailing region of gas turbines – A state-of-the-art review
- 2021
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Ingår i: Applied Thermal Engineering. - : Elsevier BV. - 1359-4311. ; 199
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Tidskriftsartikel (refereegranskat)abstract
- Highly efficient gas turbines are beneficial for improving the energy structure, reducing carbon dioxide emissions and protecting the Earth's environment. A highly efficient gas turbine means a higher inlet temperature and requires a more efficient cooling structure. Due to the limitations of aerodynamics, structure and strength, cracks, fractures and ablation easily form at the trailing edge of gas turbines. Thus, it is vital to enhance the heat transfer in the trailing edge of gas turbines. In practical applications, internal cooling structures (pin fins, latticework ducts) and film cooling are used simultaneously. In addition, some innovative cooling structures have been proposed, such as dimples/protrusions, labyrinth channels and so on. Research progress on turbine trailing edge cooling structures is presented in this paper. For pin finned duct, the heat transfer and flow structure characteristics are introduced for single rows, multirows, static and rotating conditions. Investigations on latticework ducts are quite inadequate. Therefore, only the main flow and heat transfer characteristics are shown in this paper. For film cooling at the trailing edge, experimental results and numerical results are introduced. Finally, some suggestions for heat transfer research in the trailing edge region are proposed.
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| 6. |
- Jia, Kai-Hua, et al.
(författare)
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Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- 2021
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Ingår i: Horticulture Research. - : Oxford University Press (OUP). - 2052-7276 .- 2662-6810. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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| 7. |
- Jia, Kai-Hua, et al.
(författare)
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Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)
- 2020
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 13:4, s. 665-676
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Tidskriftsartikel (refereegranskat)abstract
- Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.
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| 8. |
- Jiao, Wei, et al.
(författare)
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A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
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| 9. |
- Jiao, Yingqi, et al.
(författare)
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Integration optimization of production and transportation of refined oil : A case study from China
- 2022
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Ingår i: Chemical engineering research & design. - : Institution of Chemical Engineers. - 0263-8762 .- 1744-3563. ; 188, s. 39-49
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Tidskriftsartikel (refereegranskat)abstract
- The logistics management of refined oil under a separation of production and transportation leads to high logistics costs and a mismatch between the supply and demand sides. This paper intends to develop a general framework to assess the impact of the integration of the production and transportation in terms of economic, environmental, and energy benefits. Firstly, this paper proposes a tactical-level mathematical model for optimizing the integration of production and transportation of refined oil to minimize the total cost. In the model, several factors, such as level of market demand, production capacity limits, transportation modes, and transportation capacity, are taken into consideration. Then, the energy, economy, and environment analysis method are applied to assess the impact of the integration on the field of refined oil logistics. Four scenarios are set up and a comparative analysis is carried out in detail in China. The optimal resource allocation scheme and production adjustment scheme for each scenario are obtained. The results show that after the integration, the logistics cost is reduced by 6.8 %− 11 %, the greenhouse gas emission is reduced by 7.3 %− 17.7 %, and the energy consumption per unit turnover is reduced by 4.4 %− 7.4 %. This proves that the integration of production and transportation guided by the proposed method performs positive economic, environmental, and energy benefits. Finally, policy implications are provided.
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| 10. |
- Li, Constance H., et al.
(författare)
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Sex differences in oncogenic mutational processes
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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