| 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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