| 1. |
- Buus, Richard, et al.
(författare)
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Novel 18-gene signature for predicting relapse in ER-positive, HER2-negative breast cancer
- 2018
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Ingår i: Breast Cancer Research. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Several prognostic signatures for early oestrogen receptor-positive (ER+) breast cancer have been established with a 10-year follow-up. We tested the hypothesis that signatures optimised for 0-5-year and 5-10-year follow-up separately are more prognostic than a single signature optimised for 10 years. Methods: Genes previously identified as prognostic or associated with endocrine resistance were tested in publicly available microarray data set using Cox regression of 747 ER+/HER2- samples from post-menopausal patients treated with 5 years of endocrine therapy. RNA expression of the selected genes was assayed in primary ER+/HER2- tumours from 948 post-menopausal patients treated with 5 years of anastrozole or tamoxifen in the TransATAC cohort. Prognostic signatures for 0-10, 0-5 and 5-10 years were derived using a penalised Cox regression (elastic net). Signature comparison was performed with likelihood ratio statistics. Validation was done by a case-control (POLAR) study in 422 samples derived from a cohort of 1449. Results: Ninety-three genes were selected by the modelling of microarray data; 63 of these were significantly prognostic in TransATAC, most similarly across each time period. Contrary to our hypothesis, the derived early and late signatures were not significantly more prognostic than the 18-gene 10-year signature. The 18-gene 10-year signature was internally validated in the TransATAC validation set, showing prognostic information similar to that of Oncotype DX Recurrence Score, PAM50 risk of recurrence score, Breast Cancer Index and IHC4 (score based on four IHC markers), as well as in the external POLAR case-control set. Conclusions: The derived 10-year signature predicts risk of metastasis in patients with ER+/HER2- breast cancer similar to commercial signatures. The hypothesis that early and late prognostic signatures are significantly more informative than a single signature was rejected.
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| 2. |
- Hu, Jiwen, et al.
(författare)
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A new ratiometric fluorescent chemodosimeter based on an ICT modulation for the detection of Hg2
- 2016
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Ingår i: Sensors and actuators. B, Chemical. - : ELSEVIER SCIENCE SA. - 0925-4005 .- 1873-3077. ; 230, s. 639-644
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Tidskriftsartikel (refereegranskat)abstract
- We design and synthesize a new ratiometric fluorescent chemodosimeter (S1) for the selective and sensitive detection of Hg2+. Upon addition of Hg2+, the emission of the S1 exhibits a large bathochromic shift from 393 to 515 nm (up to 122 nm) which is ascribed to an intramolecular charge transfer process in the resultant. The Hg2+-induced dethioacetalization for sensing mechanism has been demonstrated by using high-performance liquid chromatography analysis of the sensing process. The interference experiments further demonstrate that S1 exhibits very high selectivity towards Hg2+ over other coexisting cations/anions. Subsequently, a good linearity of the concentrations of Hg2+ (0-15 mu M) vs the ratiometric signals (I-515/I-393) allows a fluorogenic method for the quantitative detection of Hg2+, with the limitation of detection determined to be 5.22 x 10(-7) M. (C) 2016 Elsevier B.V. All rights reserved.
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| 3. |
- Hu, Zhang-Jun, et al.
(författare)
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A TPA-caged precursor of (imino)coumarin for "turn-on" fluorogenic detection of Cu
- 2016
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Ingår i: Analytica Chimica Acta. - : ELSEVIER SCIENCE BV. - 0003-2670 .- 1873-4324. ; 933, s. 189-195
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Tidskriftsartikel (refereegranskat)abstract
- We strategize to utilize the precursors of (imino) coumarin fluorophores to deliver novel reactive Cu+ probes, where tris[(2-pyridyl)-methyl] amine (TPA) works as a reactive receptor towards Cu+. To verify this strategy, CP1, a representative probe and relevant sensing behaviors towards Cu+ are presented here. CP1 features good solubility and fast response for monitoring labile copper in aqueous solution and live cells. The sensing mechanism of CP1 is determined by HPLC titration and mass spectrometric analysis. The probe CP1 exhibits a 60-fold fluorescence enhancement and a detection limitation of 10.8 nM upon the detection of Cu+. CP1 is further applied for imaging labile copper in live cells. This work provides a starting point for future development of Cu+ probes, based on in situ formation of (imino) coumarin scaffolds, as well as their further investigations of copper signaling and biological events. (C) 2016 Elsevier B.V. All rights reserved.
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| 4. |
- Li, Man, et al.
(författare)
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SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function
- 2017
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Ingår i: Journal of the American Society of Nephrology: JASN. - 1533-3450. ; 28:3, s. 981-994
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3.7×10-7), of which most were common and annotated as nonsynonymous variants. Gene-based analysis identified associations of functional rare variants in three genes with eGFRcrea, including a novel association with the SOS Ras/Rho guanine nucleotide exchange factor 2 gene, SOS2 (P=5.4×10-8 by sequence kernel association test). Experimental follow-up in zebrafish embryos revealed changes in glomerular gene expression and renal tubule morphology in the embryonic kidney of acp1- and sos2-knockdowns. These developmental abnormalities associated with altered blood clearance rate and heightened prevalence of edema. This study expands the number of loci associated with kidney function and identifies novel genes with potential roles in kidney formation.
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| 5. |
- O’Sullivan, John F., et al.
(författare)
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Dimethylguanidino valeric acid is a marker of liver fat and predicts diabetes
- 2017
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Ingår i: Journal of Clinical Investigation. - 0021-9738. ; 127:12, s. 4394-4402
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Tidskriftsartikel (refereegranskat)abstract
- Unbiased, “nontargeted” metabolite profiling techniques hold considerable promise for biomarker and pathway discovery, in spite of the lack of successful applications to human disease. By integrating nontargeted metabolomics, genetics, and detailed human phenotyping, we identified dimethylguanidino valeric acid (DMGV) as an independent biomarker of CT-defined nonalcoholic fatty liver disease (NAFLD) in the offspring cohort of the Framingham Heart Study (FHS) participants. We verified the relationship between DMGV and early hepatic pathology. Specifically, plasma DMGV levels were correlated with biopsy-proven nonalcoholic steatohepatitis (NASH) in a hospital cohort of individuals undergoing gastric bypass surgery, and DMGV levels fell in parallel with improvements in post-procedure cardiometabolic parameters. Further, baseline DMGV levels independently predicted future diabetes up to 12 years before disease onset in 3 distinct human cohorts. Finally, we provide all metabolite peak data consisting of known and unidentified peaks, genetics, and key metabolic parameters as a publicly available resource for investigations in cardiometabolic diseases.
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| 6. |
- Sheng, Rongrong, et al.
(författare)
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Does hot weather affect work-related injury? A case-crossover study in Guangzhou, China
- 2018
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Ingår i: International Journal of Hygiene and Environmental Health. - : Elsevier BV. - 1438-4639. ; 221:3, s. 423-428
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Tidskriftsartikel (refereegranskat)abstract
- Background: Despite increasing concerns about the health effects of climate change, the extent to which workers are affected by hot weather is not well documented. This study aims to investigate the association between high temperatures and work-related injuries using data from a large subtropical city in China. Methods: We used workers’ compensation claims to identify work-related injuries in Guangzhou, China during 2011–2012. To feature the heat effect, the study period was restricted to the warm seasons in Guangzhou (1 May-31 October). We conducted a time-stratified case-crossover study to examine the association between ambient outdoor temperatures, including daily maximum and minimum temperatures, and cases of work-related injury. The relationships were assessed using conditional Poisson regression models. Results: Overall, a total of 5418 workers’ compensation claims were included over the study period. Both maximum and minimum temperatures were significantly associated with work-related injuries, but associations varied by subgroup. One °C increase in maximum temperature was associated with a 1.4% (RR = 1.014, 95%CIs 1.012–1.017) increase in daily injury claims. Significant associations were seen for male and middle-aged workers, workers in small and medium-sized enterprises, and those working in manufacturing sector. And 1 °C increase in minimum temperature was associated with 1.7% (RR = 1.017, 95%CIs 1.012–1.021) increase in daily injury claims. Significant associations were observed for female and middle-aged workers, workers in large-sized enterprises, and those working in transport and construction sectors. Conclusions: We found a higher risk of work-related injuries due to hot weather in Guangzhou, China. This study provides important epidemiological evidence for policy-makers and industry that may assist in the formulation of occupational safety and climate adaptation strategies.
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| 7. |
- Wuttke, Matthias, et al.
(författare)
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A catalog of genetic loci associated with kidney function from analyses of a million individuals
- 2019
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Ingår i: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 51:6, s. 957-972
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Tidskriftsartikel (refereegranskat)abstract
- Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
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| 8. |
- 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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