| 1. |
- 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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| 2. |
- Chen, Xin, 1980, et al.
(författare)
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Improved resource allocation strategy in SU-CoMP network
- 2011
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Ingår i: The Journal of China Universities of Posts and Telecommunications. - 2210-5123. ; 18:4, s. 7-12
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Tidskriftsartikel (refereegranskat)abstract
- Coordinated Multi-Point transmission and reception (CoMP) for single user, named as SU-CoMP, is considered as an efficient approach tomitigate inter-cell interference in Orthogonal Frequency Division Multiple Access (OFDMA) systems. Two prevalent approaches in SU-CoMP areCoordinated Scheduling (CS) and Joint Processing (JP). Although JP in SU-CoMP has been proved to achieve a great link performanceimprovement for the cell-edge user, efficient Resource Allocation (RA) on the system level is quite needed. However, so far limited work has beendone considering JP, and most existing schemes achieved the improvement of cell-edge performance at cost of the cell-average performancedegradation compared to the single cell RA. In this paper, a two-phase strategy is proposed for SU-CoMP networks. CS and JP are combined toimprove both cell-edge and cell-average performance. Compared to the single cell RA, simulation results demonstrate that, the proposed strategyleads to both higher cell-average and cell-edge throughput.
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| 3. |
- Chen, Xin, 1980, et al.
(författare)
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Optimal and Efficient Power Allocation for OFDM Non-Coherent Cooperative Transmission
- 2012
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Ingår i: IEEE Wireless Communications and Networking Conference, WCNC. - 1525-3511. - 9781467304375 ; , s. 1584-1589
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Konferensbidrag (refereegranskat)abstract
- In this paper, we study the subchannel (SC) power allocation for orthogonal frequency division multiplexing (OFDM) multiple access points (APs) systems with non-coherent cooperative transmission. The objective is to maximize the total capacity under per-AP power constraints. It can be proved that the optimal solution can be obtained by the combination of an optimal SC partition search and the power allocation across SCs for each feasible partition. Existing work exhaustively searched the optimal SC partition and used Lagrange dual method to compute the power allocation across SCs. Since the entire complexity increases exponentially with the number of SCs, the existing method is unsuitable for practical implementation. In this paper, we propose a novel optimal power allocation algorithm for non-coherent cooperative transmission with a much lower complexity. Firstly, a concept of “cut-off SC” is proposed for searching the optimal SC partition. Then, an efficient optimal power allocation algorithm across SCs is proposed for any given cut-off SC. Simulation results demonstrate that the proposed algorithm is optimal with a polynomial complexity, and ends within an acceptable number of iterations.
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| 4. |
- Li, Jingya, 1986, et al.
(författare)
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A novel frequency reuse scheme for coordinated multi-point transmission.
- 2010
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Ingår i: IEEE Vehicular Technology Conference Spring, Taipei, Taiwan, May 2010. - 1550-2252. - 9781424425198 ; , s. 1-5
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Konferensbidrag (refereegranskat)abstract
- Coordinated Multi-Point (CoMP) transmission is considered in 3GPP LTE-Advanced as a key technique to improve the cell-edge performance. In order to support joint resource allocation among coordinate cells in CoMP systems, efficient frequency reuse schemes need to be designed. However, most of the existing frequency reuse schemes are not suitable for CoMP transmission due to not considering multi-cell joint transmission scenario in their frequency reuse rule. To solve this problem, a cooperative frequency reuse (CFR) scheme is proposed in this paper, which divides the cell-edge area of each cell into two types of zones, and defines a frequency reuse rule to support CoMP transmission for users in these zones. Compared with the conventional soft frequency reuse (SFR) scheme, simulation results demonstrate that the CFR scheme reduces the blocking probability by more than 50%, and improves the cell-edge throughput by 30~40%, with 5~9% additional cell-average throughput.
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| 5. |
- Li, Jingya, 1986, et al.
(författare)
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Downlink Radio Resource Allocation for Coordinated Cellular OFDMA Networks
- 2010
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Ingår i: IEICE Transactions on Communications. - 1745-1345. ; E93B:12, s. 3480-3488
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Tidskriftsartikel (refereegranskat)abstract
- Base station coordination is considered as a promising technique to mitigate inter-cell interference and improve the cell-edge performance in cellular orthogonal frequency division multiple-access (OFDMA) networks. The problem to design an efficient radio resource allocation scheme for coordinated cellular OFDMA networks incorporating base station coordination has been only partially investigated. In this contribution, a novel radio resource allocation algorithm with universal frequency reuse is proposed to support base station coordinated transmission. Firstly, with the assumption of global coordination between all base station sectors in the network, a coordinated subchannel assignment algorithm is proposed. Then, by dividing the entire network into a number of disjoint coordinated clusters of base station sectors, a reduced-feedback algorithm for subchannel assignment is proposed for practical use. The utility function based on the user average throughput is used to balance the efficiency and fairness of wireless resource allocation. System level simulation results demonstrate that the reduced-feedback subchannel assignment algorithm significantly improves the cell-edge average throughput and the fairness index of users in the network, with acceptable degradation of cell-average performance.
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| 6. |
- Li, Jingya, 1986, et al.
(författare)
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Multi-Beam Cooperative Frequency Reuse for Coordinated Multi-Point Systems
- 2010
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Ingår i: Journal of China Universities of Posts and Telecommunications. - 1005-8885. ; 17:6, s. 11-18
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Tidskriftsartikel (refereegranskat)abstract
- Coordinated Multi-Point (CoMP) transmission is considered in 3GPP LTE-Advanced as a key technique to mitigate inter-cell interference and improve the cell-edge performance. To apply CoMP joint transmission effectively, efficient frequency reuse schemes need to be designed to support resource management cooperation among coordinated cells. However, most of the existing frequency reuse schemes are not suitable for CoMP systems due to not considering multi-point cooperative transmission scenario in their frequency reuse rules. In addition, the restrictions of frequency resources in those schemes result in high blockingprobability. To solve the above two problems, a multi-beam cooperative frequency reuse (MBCFR) scheme is proposed in this paper, which reuses all the available frequency resources in each sector and supports multi-beam cooperative transmission for cell-edge users. Besides, the blocking probability is proved to be efficiently reduced. Then, a frequency-segment-sequence based MBCFR scheme is introduced to further reduce the inter-cell interference. System level simulations demonstrate that the proposedscheme results in higher cell-edge average throughput and cell-average throughput with lower blocking probability.
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| 7. |
- Li, Peng, et al.
(författare)
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Transcriptional reactivation of OTX2, RX1 and SIX3 during reprogramming contributes to the generation of RPE cells from human iPSCs
- 2016
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Ingår i: International Journal of Biological Sciences. - : Ivyspring International Publisher. - 1449-2288. ; 12:5, s. 505-517
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Tidskriftsartikel (refereegranskat)abstract
- Directed differentiation of human induced pluripotent stem cells (iPSCs) into retinal pigmented epithelium (RPE) holds great promise in cell replacement therapy for patients suffering from degenerative eye diseases, including age-related macular degeneration (AMD). In this study, we generated iPSCs from human dermal fibroblasts (HDFs) by electroporation with episomal plasmid vectors encoding OCT4, SOX2, KLF4, L-MYC together with p53 suppression. Intriguingly, cell reprogramming resulted in a metastable transcriptional activation and selective demethylation of neural and retinal specification-associated genes, such as OTX2, RX1 and SIX3. In contrast, RPE progenitor genes were transcriptionally silent in HDFs and descendant iPSCs. Overexpression of OCT4 and SOX2 directly stimulated the expression of OTX2, RX1 and SIX3 in HDFs and iPSCs. Luciferase and chromatin immunoprecipitation (ChIP) assays further identified an OCT4- and two SOX2-binding sites located in the proximal promoter of OTX2. Histone acetylation and methylation on the local promoter also participated in the reactivation of OTX2. The transcriptional conversion of RX1 and SIX3 genes partially attributed to DNA demethylation. Subsequently, iPSCs were induced into the RPE cells displaying the characteristics of polygonal shapes and pigments, and expressing typical RPE cell markers. Taken together, our results establish readily efficient and safe protocols to produce iPSCs and iPSC-derived RPE cells, and underline that the reactivation of anterior neural transcription factor OTX2, eye field transcription factor RX1 and SIX3 in iPSCs is a feature of pluripotency acquisition and predetermines the potential of RPE differentiation.
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| 8. |
- Luo, Yiqi, et al.
(författare)
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Toward more realistic projections of soil carbon dynamics by Earth system models
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236. ; 30:1, s. 40-56
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Tidskriftsartikel (refereegranskat)abstract
- Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.
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| 9. |
- Rothfels, Carl J., et al.
(författare)
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The evolutionary history of ferns inferred from 25 low-copy nuclear genes
- 2015
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Ingår i: American Journal of Botany. - : Wiley. - 0002-9122 .- 1537-2197. ; 102:7, s. 1089-1107
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Tidskriftsartikel (refereegranskat)abstract
- PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35 877 bp), along with rigorous alignment, orthology inference and model selection. KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to similar to 200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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| 10. |
- Shi, Furong, et al.
(författare)
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A Nitroxide Radical Conjugated Polymer as an Additive to Reduce Nonradiative Energy Loss in Organic Solar Cells
- 2023
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Ingår i: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 35:23
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Tidskriftsartikel (refereegranskat)abstract
- Nonfullerene-acceptor-based organic solar cells (NFA-OSCs) are now set off to the 20% power conversion efficiency milestone. To achieve this, minimizing all loss channels, including nonradiative photovoltage losses, seems a necessity. Nonradiative recombination, to a great extent, is known to be an inherent material property due to vibrationally induced decay of charge-transfer (CT) states or their back electron transfer to the triplet excitons. Herein, it is shown that the use of a new conjugated nitroxide radical polymer with 2,2,6,6-tetramethyl piperidine-1-oxyl side groups (GDTA) as an additive results in an improvement of the photovoltaic performance of NFA-OSCs based on different active layer materials. Upon the addition of GDTA, the open-circuit voltage (VOC), fill factor (FF), and short-circuit current density (JSC) improve simultaneously. This approach is applied to several material systems including state-of-the-art donor/acceptor pairs showing improvement from 15.8% to 17.6% (in the case of PM6:Y6) and from 17.5% to 18.3% (for PM6:BTP-eC9). Then, the possible reasons behind the observed improvements are discussed. The results point toward the suppression of the CT state to triplet excitons loss channel. This work presents a facile, promising, and generic approach to further improve the performance of NFA-OSCs.
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