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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Bixby, H., et al.
(författare)
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Rising rural body-mass index is the main driver of the global obesity epidemic in adults
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 569:7755, s. 260-4
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Tidskriftsartikel (refereegranskat)abstract
- Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities(.)(1,2) This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity(3-6). Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017-and more than 80% in some low- and middle-income regions-was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing-and in some countries reversal-of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.
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| 4. |
- Cao, Hong Min, et al.
(författare)
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The loud and the quiet: Searching for radio counterparts of two radio-weak BL Lac candidates with VLBI
- 2019
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Ingår i: Monthly Notices of the Royal Astronomical Society: Letters. - : Oxford University Press (OUP). - 1745-3925 .- 1745-3933. ; 482:1, s. L34-L39
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Tidskriftsartikel (refereegranskat)abstract
- BL Lac objects are known to have compact jets inclined to our line of sight at a small angle, showing prominent radio emission. Two radio-weak BL Lac candidates with no counterparts in current radio surveys were recently reported by Massaro et al. Both sources were selected as candidate low-energy counterparts of unassociated Fermi γ -ray sources. We carried out very long baseline interferometry (VLBI) observations with the European VLBI Network (EVN) at 5 GHz to explore their radio properties at the milliarcsecond (mas) scale. One target, J1410+7405, is clearly detected with the EVN. Its measured 5-GHz flux density, 2.4 mJy, is consistent with recent interferometricmeasurementswith theKarlG. JanskyVery LargeArray, suggesting that the radio emission is confined to the inner ≲10-mas region. J1410+7405 is therefore identified as a radio-loud jetted active galactic nucleus, and its brightness temperature exceeds ~109 K. Its properties are similar to those of other γ -ray-detected BL Lac objects. On the other hand, the second target, J0644+6031, remains undetected with the EVN with a 6s brightness upper limit of 0.12 mJy beam-1. This source is thus radio-quiet, confirming its peculiarity, or possibly questioning its BL Lac nature.
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| 5. |
- Chen, Dan, et al.
(författare)
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Analysis of the genetic architecture of susceptibility to cervical cancer indicates that common SNPs explain a large proportion of the heritability
- 2015
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Ingår i: Carcinogenesis. - : Oxford University Press (OUP). - 0143-3334 .- 1460-2180. ; 36:9, s. 992-998
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Tidskriftsartikel (refereegranskat)abstract
- The genetic architecture of susceptibility to cervical cancer is not well-understood. By using a genome-wide association study (GWAS) of 1034 cervical cancer patients and 3948 controls with 632 668 single-nucleotide polymorphisms (SNPs), we estimated that 24.0% [standard error (SE) = 5.9%, P = 3.19 x 10(-6)] of variation in liability to cervical cancer is captured by autosomal SNPs, a bit lower than the heritability estimated from family study (27.0%), suggesting that a substantial proportion of the heritability is tagged by common SNPs. The remaining missing heritability most probably reflects incomplete linkage disequilibrium between causal variants and the genotyped SNPs. The variance explained by each chromosome is not related to its length (R-2 = 0.020, P = 0.516). Published genome-wide significant variants only explain 2.1% (SE = 1.5%, P = 0) of phenotypic variance, which reveals that most of the heritability has not been detected, presumably due to small individual effects. Another 2.1% (SE = 1.1%, P = 0.013) of variation is attributable to biological pathways associated with risk of cervical cancer, supporting that pathway analysis can identify part of the hidden heritability. Except for human leukocyte antigen genes and MHC class I polypeptide-related sequence A (MICA), none of the 82 candidate genes/regions reported in other association studies contributes to the heritability of cervical cancer in our dataset. This study shows that risk of cervical cancer is influenced by many common germline genetic variants of small effects. The findings are important for further study design to identify the hiding heritability that has not yet been revealed. More susceptibility loci are yet to be found in GWASs with higher power.
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| 6. |
- Chen, XÍ, et al.
(författare)
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TDHQ Enabling Fine-granularity Adaptive Loading for SSB-DMT Systems
- 2018
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Ingår i: IEEE Photonics Technology Letters. - : Institute of Electrical and Electronics Engineers Inc.. - 1041-1135 .- 1941-0174. ; 30:19, s. 1687-1690
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Tidskriftsartikel (refereegranskat)abstract
- In this letter, we introduce time domain hybrid quadrature amplitude modulation (TDHQ) for the single sideband (SSB) discrete multi-tone (DMT) systems. Experimental results reveal that with a single precoding set and the proposed adaptive loading algorithm, the TDHQ scheme can achieve finer granularity and therefore smoother continuous growth of data rate than that with the conventional quadrature amplitude modulation (QAM). Besides, thanks to the frame construction and the tailored mapping rule, the scheme with TDHQ has an obviously better peak to average power ratio (PAPR).
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| 7. |
- Cui, Tao, 1982-, et al.
(författare)
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Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology
- 2019
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Ingår i: Carcinogenesis. - : Oxford University Press (OUP). - 0143-3334 .- 1460-2180. ; 40:2, s. 269-278
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Tidskriftsartikel (refereegranskat)abstract
- Invasive cervical cancer (ICC) with very low titer of high-risk human papillomavirus (HPV) has worse clinical outcome than cases with high titer, indicating a difference in molecular etiology. Fresh-frozen ICC tumors (n = 49) were classified into high- and low-HPV-titer cases using real-time PCR-based HPV genotyping. The mutation spectra were studied using the AmpliSeq Comprehensive Cancer Panel and the expression profiles using total RNA sequencing, and the results were validated using the AmpliSeq Transcriptome assay. HPV DNA genotyping and RNA sequencing showed that 16.6% of ICC tumors contained very low levels of HPV DNA and HPV transcripts. Tumors with low HPV levels had more mutations with a high allele frequency and fewer mutations with low allele frequency relative to tumors with high HPV titer. A number of genes showed significant expression differences between HPV titer groups, including genes with somatic mutations. Gene ontology and pathway analyses implicated the enrichment of genes involved in DNA replication, cell cycle control and extracellular matrix in tumors with low HPV titer. The results indicate that in low titer tumors, HPVs act as trigger of cancer development whereas somatic mutations are clonally selected and become drivers of the tumor development process. In contrast, in tumors with high HPV titer the expression of HPV oncoproteins plays a major role in tumor development and the many low frequency somatic mutations represent passengers. This putative subdivision of invasive cervical tumors may explain the higher radiosensitivity of ICC tumors with high HPV titer and thereby have consequences for clinical management.
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| 8. |
- Cui, Yong, et al.
(författare)
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Over 16% efficiency organic photovoltaic cells enabled by a chlorinated acceptor with increased open-circuit voltages
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Broadening the optical absorption of organic photovoltaic (OPV) materials by enhancing the intramolecular push-pull effect is a general and effective method to improve the power conversion efficiencies of OPV cells. However, in terms of the electron acceptors, the most common molecular design strategy of halogenation usually results in down-shifted molecular energy levels, thereby leading to decreased open-circuit voltages in the devices. Herein, we report a chlorinated non-fullerene acceptor, which exhibits an extended optical absorption and meanwhile displays a higher voltage than its fluorinated counterpart in the devices. This unexpected phenomenon can be ascribed to the reduced non-radiative energy loss (0.206 eV). Due to the simultaneously improved short-circuit current density and open-circuit voltage, a high efficiency of 16.5% is achieved. This study demonstrates that finely tuning the OPV materials to reduce the bandgap-voltage offset has great potential for boosting the efficiency.
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| 9. |
- Dong, Jianbo, et al.
(författare)
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Venice: Exploring Server Architectures for Effective Resource Sharing
- 2016
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Ingår i: Proceedings - International Symposium on High-Performance Computer Architecture. - 1530-0897. - 9781467392112 ; 2016-April, s. 507-518
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Konferensbidrag (refereegranskat)abstract
- Consolidated server racks are quickly becoming the backbone of IT infrastructure for science, engineering, and business, alike. These servers are still largely built and organized as when they were distributed, individual entities. Given that many fields increasingly rely on analytics of huge datasets, it makes sense to support flexible resource utilization across servers to improve cost-effectiveness and performance. We introduce Venice, a family of data-center server architectures that builds a strong communication substrate as a first-class resource for server chips. Venice provides a diverse set of resource-joining mechanisms that enables user programs to efficiently leverage non-local resources.To better understand the implications of design decisionsabout system support for resource sharing we have constructed a hardware prototype that allows us to more accurately measure end-to-end performance of at-scale applications and to explore tradeoffs among performance, power, and resource-sharing transparency. We present results from our initial studies analyzing these tradeoffs when sharing memory, accelerators, or NICs. We find that it is particularly important to reduce or hide latency, that data-sharing access patterns should match the features of the communication channels employed, and that inter-channel collaboration can be exploited for better performance.
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