| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Berger, Ashton C, et al.
(författare)
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A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.
- 2018
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Ingår i: Cancer Cell. - : Elsevier BV. - 1535-6108 .- 1878-3686. ; 33:4, s. 690-705.e9
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Tidskriftsartikel (refereegranskat)abstract
- We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.
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| 3. |
- Feng, Tao, et al.
(författare)
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Adaptive finite element methods for parameter estimation problems in linear elasticity
- 2009
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Ingår i: International Journal of Numerical Analysis & Modeling. - 1705-5105. ; 6:1, s. 17-32
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, the Lame coefficients in the linear elasticity problem are estimated by using the measurements of displacement. Some a posteriori error estimators for the approximation error of the parameters are derived, and then adaptive finite element schemes are developed for the discretization of the parameter estimation problem, based on the error estimators. The Gauss-Newton method is employed to solve the discretized nonlinear least-squares problem. Some numerical results are presented.
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| 4. |
- Feng, Tao, et al.
(författare)
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Adaptive finite element methods for the identification of distributed parameters in elliptic equation
- 2008
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Ingår i: Advances in Computational Mathematics. - : Springer Science and Business Media LLC. - 1019-7168 .- 1572-9044. ; 29:1, s. 27-53
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, adaptive finite element method is developed for the estimation of distributed parameter in elliptic equation. Both upper and lower error bound are derived and used to improve the accuracy by appropriate mesh refinement. An efficient preconditioned project gradient algorithm is employed to solve the nonlinear least-squares problem arising in the context of parameter identification problem. The efficiency of our error estimators is demonstrated by some numerical experiments
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| 5. |
- Guo, Feilong, et al.
(författare)
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How Early-Life Gut Microbiota Alteration Sets Trajectories for Health and Inflammatory Bowel Disease?
- 2021
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Ingår i: Frontiers in Nutrition. - : Frontiers Media S.A.. - 2296-861X. ; 8
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Forskningsöversikt (refereegranskat)abstract
- Inflammatory bowel disease (IBD) is a recurrent chronic inflammatory condition of the intestine without any efficient therapeutic regimens. Gut microbiota, which plays an instrumental role in the development and maturation of the immune system, has been implicated in the pathogenesis of IBD. Emerging evidence has established that early-life events particularly maternal influences and antibiotic treatment are strongly correlated with the health or susceptibility to disease of an individual in later life. Thus, it is proposed that there is a critical period in infancy, during which the environmental exposures bestow a long-term pathophysiological imprint. This notion sheds new light on the development of novel approaches for the treatment, i.e., early interventions, more precisely, the prevention of many uncurable chronic inflammatory diseases like IBD. In this review, we have integrated current evidence to describe the feasibility of the "able-to-be-regulated microbiota," summarized the underlying mechanisms of the "microbiota-driven immune system education," explored the optimal intervention time window, and discussed the potential of designing early-probiotic treatment as a new prevention strategy for IBD.
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| 6. |
- He, Huihui, et al.
(författare)
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Sex-related differences in the hypertriglyceridemic-waist phenotype in association with hyperuricemia : a longitudinal cohort study
- 2023
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Ingår i: Lipids in Health and Disease. - : Springer Nature. - 1476-511X. ; 22
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is limited longitudinal evidence supporting the association between the hypertriglyceridemic-waist (HTGW) phenotype and hyperuricemia. This study aimed to examine the longitudinal relationship between hyperuricemia and the HTGW phenotype among males and females.Methods: A total of 5562 hyperuricemia-free participants aged 45 or over from the China Health and Retirement Longitudinal Study (mean age: 59.0) were followed for 4 years. The HTGW phenotype was defined as having elevated triglyceride levels and enlarged waist circumference (cutoffs for males: 2.0 mmol/L and 90 cm; females: 1.5 mmol/L and 85 cm). Hyperuricemia was determined by uric acid cutoffs (males: 7 mg/dl; females: 6 mg/dl. Multivariate logistic regression models were used to assess the association between the HTGW phenotype and hyperuricemia. The joint effect of the HTGW phenotype and sex on hyperuricemia was quantified, and the multiplicative interaction was assessed.Results: During the four-year follow-up, 549 (9.9%) incident hyperuricemia cases were ascertained. Compared with those with normal levels of triglycerides and waist circumference, participants with the HTGW phenotype had the highest risk of hyperuricemia (OR: 2.67; 95% CI: 1.95 to 3.66), followed by an OR of 1.96 (95% CI: 1.40 to 2.74) for only higher triglyceride levels and 1.39 (95% CI: 1.03 to 1.86) for only greater waist circumference. The association between HTGW and hyperuricemia was more prominent among females (OR = 2.36; 95% CI: 1.77 to 3.15) than males (OR = 1.29; 95% CI: 0.82 to 2.04), with evidence of a multiplicative interaction (P = 0.006).Conclusions: Middle-aged and older females with the HTGW phenotype may at the highest risk of hyperuricemia. Future hyperuricemia prevention interventions should be primarily targeted for females with the HTGW phenotype.
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| 7. |
- He, Jia, et al.
(författare)
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A population-based survey of the epidemiology of symptom-defined gastroesophageal reflux disease : the Systematic Investigation of Gastrointestinal Diseases in China
- 2010
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Ingår i: BMC Gastroenterology. - 1471-230X. ; 10, s. 94-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The epidemiology of gastroesophageal reflux disease (GERD) has yet to be investigated using the symptomatic threshold criteria recommended by the Montreal Definition. This study aimed to determine the prevalence of symptom-defined GERD across five regions of China, and to investigate variables associated with GERD. Methods: A representative sample of 18 000 adults (aged 18-80 years) were selected equally from rural and urban areas in each region (n = 1800). According to the Montreal Definition, GERD is present when mild symptoms of heartburn and/ or regurgitation occur on >= 2 days a week, or moderate-to-severe symptoms of heartburn and/or regurgitation occur on >= 1 day a week. Results: In total, 16 091 participants completed the survey (response rate: 89.4%) and 16 078 responses were suitable for analysis. Applying the Montreal criteria, the prevalence of symptom-defined GERD was 3.1% and varied significantly (p < 0.001) among the five regions (from 1.7% in Guangzhou to 5.1% in Wuhan) and between rural and urban populations (3.8% vs 2.4%). Factors significantly associated with GERD included living in a rural area and a family history of gastrointestinal diseases. Conclusions: This population-based survey found that the prevalence of symptom-defined GERD in China was 3.1%, which is lower than that found in Western countries.
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| 8. |
- Lamichhaney, Sangeet, 1984-, et al.
(författare)
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Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
- 2016
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 48:1, s. 84-88
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Tidskriftsartikel (refereegranskat)abstract
- The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females1,2,3,4. This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles5,6. Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.
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| 9. |
- Li, Zhiqi, et al.
(författare)
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Efficient perovskite solar cells enabled by ion-modulated grain boundary passivation with a fill factor exceeding 84%
- 2019
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Ingår i: Journal of Materials Chemistry A. - : ROYAL SOC CHEMISTRY. - 2050-7488 .- 2050-7496. ; 7:39, s. 22359-22365
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Tidskriftsartikel (refereegranskat)abstract
- Alkali metal cation modulation toward high-electronic-quality perovskite films requires strict control over trap densities in the devices. By introducing tailor-made potassium cation (K+)-functionalized carbon nanodots (CNDs@K) into the perovskite precursor solution, we succeeded in defect passivation and crystallization control of the perovskite film. X-ray diffraction indicated that the binding effect of carbon dots confined the K+ ions in the grain boundary and prevented excessive cations from occupying interstitial sites, thereby reducing the microstrain of the polycrystalline film. Consequently, the synergistic effect of the tailored crystal size and suppressed grain boundary defects could reduce the charge trap density, facilitate charge generation, and lengthen the carrier lifetime, leading to a boosted efficiency of 21.01% with a high fill factor of 84%. This performance is among the best reported for carbon dot-doped PSCs.
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| 10. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 11. |
- Liu, Mengling, et al.
(författare)
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Estimation and selection of complex covariate effects in pooled nested case-control studies with heterogeneity
- 2013
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Ingår i: Biostatistics. - : Oxford University Press. - 1465-4644 .- 1468-4357. ; 14:4, s. 682-694
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge in cancer epidemiologic studies, especially those of rare cancers, is observing enough cases. To address this, researchers often join forces by bringing multiple studies together to achieve large sample sizes, allowing for increased power in hypothesis testing, and improved efficiency in effect estimation. Combining studies, however, renders the analysis difficult owing to the presence of heterogeneity in the pooled data. In this article, motivated by a collaborative nested case-control (NCC) study of ovarian cancer in three cohorts from United States, Sweden, and Italy, we investigate the use of penalty regularized partial likelihood estimation in the context of pooled NCC studies to achieve two goals. First, we propose an adaptive group lasso (gLASSO) penalized approach to simultaneously identify important variables and estimate their effects. Second, we propose a composite agLASSO penalized approach to identify variables with heterogeneous effects. Both methods are readily implemented with the group coordinate gradient decent algorithm and shown to enjoy the oracle property. We conduct simulation studies to evaluate the performance of our proposed approaches in finite samples under various heterogeneity settings, and apply them to the pooled ovarian cancer study.
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| 12. |
- Martínez Barrio, Álvaro, et al.
(författare)
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
- 2016
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Ingår i: eLIFE. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.
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| 13. |
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| 14. |
- Nie, Junsheng, et al.
(författare)
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Loess Plateau storage of Northeastern Tibetan Plateau-derived Yellow River sediment
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Marine accumulations of terrigenous sediment are widely assumed to accurately record climatic- and tectonic-controlled mountain denudation and play an important role in understanding late Cenozoic mountain uplift and global cooling. Underpinning this is the assumption that the majority of sediment eroded from hinterland orogenic belts is transported to and ultimately stored in marine basins with little lag between erosion and deposition. Here we use a detailed and multi-technique sedimentary provenance dataset from the Yellow River to show that substantial amounts of sediment eroded from Northeast Tibet and carried by the river/'s upper reach are stored in the Chinese Loess Plateau and the western Mu Us desert. This finding revises our understanding of the origin of the Chinese Loess Plateau and provides a potential solution for mismatches between late Cenozoic terrestrial sedimentation and marine geochemistry records, as well as between global CO2 and erosion records.
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| 15. |
- Nie, Junsheng, et al.
(författare)
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Provenance of the upper Miocene–Pliocene Red Clay deposits of the Chinese loess plateau
- 2014
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Ingår i: Earth and Planetary Science Letters. - : Elsevier BV. - 0012-821X .- 1385-013X. ; 407, s. 35-47
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Tidskriftsartikel (refereegranskat)abstract
- A clear understanding of the provenance of late Cenozoic Chinese loess and the underlying Red Clay deposits will shed light on the history and mechanisms of Asian aridification. Although much progress has been made in understanding the source of Quaternary loess on the Chinese Loess Plateau (CLP), the provenance of the underlying upper Miocene-Pliocene Red Clay sequence is largely unknown. Here we present the first provenance history of the Red Clay sequence based on zircon U-Pb ages from the central CLP. Visual and statistical analyses of the U-Pb age populations and comparison with results from potential source regions reveals that (I) the lowermost Red Clay of the late Miocene (depositional age of similar to 8 Ma) is likely sourced from the nearby Liupan Mountains and the Qaidam Basin; (2) the middle Red Clay (5.5-4 Ma) of the early-mid Pliocene is sourced mainly from the Taklamakan desert, transported via lower-level westerly winds; (3) the upper Red Clay of the late Pliocene (similar to 3 Ma) is sourced from mixed areas, although western source materials from middle-northern Tibetan plateau (including Qaidam Desert sediments and materials eroded from the Qilian Mountains) sediments appear to dominate; and (4) the Quaternary loess is also sourced from mixed source regions, albeit with dominant northern CLP proximal desert sediments transported via winter monsoon winds, which in turn may be transported from mountain source regions of the northeastern Tibet and Gobi Altai via major river systems. This long term shift in sources suggests a progressive eastward aridification during the Pliocene in Asia with the specific timing of provenance shifts synchronous with large-scale climatic transitions and Tibetan uplift, demonstrating that Asian desertification is controlled by both factors.
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| 16. |
- Shang, Shulian, et al.
(författare)
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Partially linear single index Cox regression model in nested case-control studies
- 2013
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Ingår i: Computational Statistics & Data Analysis. - : Elsevier BV. - 0167-9473 .- 1872-7352. ; 67, s. 199-212
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Tidskriftsartikel (refereegranskat)abstract
- The nested case-control (NCC) design is widely used in epidemiologic studies as a cost-effective subcohort sampling method to study the association between a disease and its potential risk factors. NCC data are commonly analyzed using Thomas' partial likelihood approach under the Cox proportional hazards model assumption. However, the linear modeling form in the Cox model may be insufficient for practical applications, especially when there are a large number of risk factors under investigation. In this paper, we consider a partially linear single index proportional hazards model, which includes a linear component for covariates of interest to yield easily interpretable results and a nonparametric single index component to adjust for multiple confounders effectively. We propose to approximate the nonparametric single index function by polynomial splines and estimate the parameters of interest using an iterative algorithm based on the partial likelihood. Asymptotic properties of the resulting estimators are established. The proposed methods are evaluated using simulations and applied to an NCC study of ovarian cancer.
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| 17. |
- Shi, Tian-Le, et al.
(författare)
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Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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| 18. |
- Sun, Yuanyuan, et al.
(författare)
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Types of Water Rights Systems in China: A Zoning Scheme Applied
- 2023
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Ingår i: Sustainability. - 2071-1050. ; 15:23
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Tidskriftsartikel (refereegranskat)abstract
- This article analyzes the appropriate types of water rights systems for different regions with varying water resource conditions in China. The most appropriate water rights systems for various zones were determined by comparing the value of influencing factors with corresponding thresholds in China’s second-class zones of water resources. It is shown that a riparian rights system under water withdrawals permission could be adopted in most regions of southern China. For most northern Chinese regions, the quantity proportional water rights systems should be adopted and further improved. In contrast to the implementation of a single quantity proportional water rights system, this paper innovatively proposes a zoning scheme for China’s water rights system. The appropriate type of water rights system can be identified according to the region’s specific water resource conditions. It can provide a scientific reference for the reform of water rights systems in China and other countries or regions.
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| 19. |
- Xu, Chao-Qun, et al.
(författare)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 20. |
- Zhang, Lei, et al.
(författare)
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A window–space-directed assembly strategy for the construction of supertetrahedron-based zeolitic mesoporous metal–organic frameworks with ultramicroporous apertures for selective gas adsorption
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 12:16, s. 5767-5773
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Tidskriftsartikel (refereegranskat)abstract
- Despite their scarcity due to synthetic challenges, supertetrahedron-based metal–organic frameworks (MOFs) possess intriguing architectures, diverse functionalities, and superb properties that make them in‑demand materials. Employing a new window–space-directed assembly strategy, a family of mesoporous zeolitic MOFs have been constructed herein from corner-shared supertetrahedra based on homometallic or heterometallic trimers [M3(OH/O)(COO)6] (M3 = Co3, Ni3 or Co2Ti). These MOFs consisted of close-packed truncated octahedral cages possessing a sodalite topology and large β-cavity mesoporous cages (~22 Å diameter) connected by ultramicroporous apertures (~5.6 Å diameter). Notably, the supertetrahedron-based sodalite topology MOF composed with the Co2Ti trimer exhibited high thermal and chemical stability as well as the ability to efficiently separate acetylene (C2H2) from carbon dioxide (CO2).
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