| 1. |
- Chen, Chao, et al.
(författare)
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Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients
- 2020
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Ingår i: Aging. - : Impact Journals, LLC. - 1945-4589. ; 12:11, s. 10642-10662
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Tidskriftsartikel (refereegranskat)abstract
- DNA methylation changes during aging, but it remains unclear whether the effect of DNA methylation on lung cancer survival varies with age. Such an effect could decrease prediction accuracy and treatment efficacy. We performed a methylation-age interaction analysis using 1,230 early-stage lung adenocarcinoma patients from five cohorts. A Cox proportional hazards model was used to investigate lung adenocarcinoma and squamous cell carcinoma patients for methylation-age interactions, which were further confirmed in a validation phase. We identified one adenocarcinoma-specific CpG probe, cg14326354PRODH, with effects significantly modified by age (HRinteraction = 0.989; 95% CI: 0.986-0.994; P = 9.18×10-7). The effect of low methylation was reversed for young and elderly patients categorized by the boundary of 95% CI standard (HRyoung = 2.44; 95% CI: 1.26-4.72; P = 8.34×10-3; HRelderly = 0.58; 95% CI: 0.42-0.82; P = 1.67×10-3). Moreover, there was an antagonistic interaction between low cg14326354PRODH methylation and elderly age (HRinteraction = 0.21; 95% CI: 0.11-0.40; P = 2.20×10-6). In summary, low methylation of cg14326354PRODH might benefit survival of elderly lung adenocarcinoma patients, providing new insight to age-specific prediction and potential drug targeting.
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| 2. |
- Chen, Kai, et al.
(författare)
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Room-temperature multiferroic properties in NiBi2O4
- 2010
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Ingår i: Europhysics letters. - : European Physical Society. - 0295-5075 .- 1286-4854. ; 89:2
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Tidskriftsartikel (refereegranskat)abstract
- Magnetism and ferroelectricity at room temperature are observed in the NiBi2O4 ceramics. Both the time reversal and the inversion symmetry of the structure (space group F-43m) are broken. The saturation magnetization is 0.028 emu/g and the saturation polarization 2P(s) similar to 4.0 mu C/cm(2). NiBi2O4 also shows other room-temperature multiferroic properties, e. g. the piezoelectric coefficient (d(33)), the polarized dielectric character, the magneto-dielectric response and the magnetoelectric effect. Copyright (C) EPLA, 2010
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| 3. |
- Dong, Weiwei, et al.
(författare)
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Fe0.79Si0.07B0.14 metallic glass gaskets for high-pressure research beyond 1 Mbar
- 2022
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Ingår i: Journal of Synchrotron Radiation. - : Wiley-Blackwell Publishing Ltd. - 0909-0495 .- 1600-5775. ; 29, s. 1167-1179
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Tidskriftsartikel (refereegranskat)abstract
- A gasket is an important constituent of a diamond anvil cell (DAC) assembly, responsible for the sample chamber stability at extreme conditions for X-ray diffraction studies. In this work, we studied the performance of gaskets made of metallic glass Fe0.79Si0.07B0.14 in a number of high-pressure X-ray diffraction (XRD) experiments in DACs equipped with conventional and toroidal-shape diamond anvils. The experiments were conducted in either axial or radial geometry with X-ray beams of micrometre to sub-micrometre size. We report that Fe0.79Si0.07B0.14 metallic glass gaskets offer a stable sample environment under compression exceeding 1 Mbar in all XRD experiments described here, even in those involving small-molecule gases (e.g. Ne, H-2) used as pressure-transmitting media or in those with laser heating in a DAC. Our results emphasize the materials importance for a great number of delicate experiments conducted under extreme conditions. They indicate that the application of Fe0.79Si0.07B0.14 metallic glass gaskets in XRD experiments for both axial and radial geometries substantially improves various aspects of megabar experiments and, in particular, the signal-to-noise ratio in comparison to that with conventional gaskets made of Re, W, steel or other crystalline metals.
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| 4. |
- Dong, Xuesi, et al.
(författare)
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Trans-omics biomarker model improves prognostic prediction accuracy for early-stage lung adenocarcinoma
- 2019
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Ingår i: Aging. - : Impact Journals, LLC. - 1945-4589. ; 11:16, s. 6312-6335
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Tidskriftsartikel (refereegranskat)abstract
- Limited studies have focused on developing prognostic models with trans-omics biomarkers for early-stage lung adenocarcinoma (LUAD). We performed integrative analysis of clinical information, DNA methylation, and gene expression data using 825 early-stage LUAD patients from 5 cohorts. Ranger algorithm was used to screen prognosis-associated biomarkers, which were confirmed with a validation phase. Clinical and biomarker information was fused using an iCluster plus algorithm, which significantly distinguished patients into high- and low-mortality risk groups (Pdiscovery = 0.01 and Pvalidation = 2.71×10-3). Further, potential functional DNA methylation-gene expression-overall survival pathways were evaluated by causal mediation analysis. The effect of DNA methylation level on LUAD survival was significantly mediated through gene expression level. By adding DNA methylation and gene expression biomarkers to a model of only clinical data, the AUCs of the trans-omics model improved by 18.3% (to 87.2%) and 16.4% (to 85.3%) in discovery and validation phases, respectively. Further, concordance index of the nomogram was 0.81 and 0.77 in discovery and validation phases, respectively. Based on systematic review of published literatures, our model was superior to all existing models for early-stage LUAD. In summary, our trans-omics model may help physicians accurately identify patients with high mortality risk.
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| 5. |
- Ji, Xinyu, et al.
(författare)
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Epigenetic–smoking interaction reveals histologically heterogeneous effects of TRIM27 DNA methylation on overall survival among early-stage NSCLC patients
- 2020
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Ingår i: Molecular Oncology. - : Wiley. - 1574-7891 .- 1878-0261. ; 14:11, s. 2759-2774
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Tidskriftsartikel (refereegranskat)abstract
- Tripartite motif containing 27 (TRIM27) is highly expressed in lung cancer, including non-small-cell lung cancer (NSCLC). Here, we profiled DNA methylation of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tumours from 613 early-stage NSCLC patients and evaluated associations between CpG methylation of TRIM27 and overall survival. Significant CpG probes were confirmed in 617 samples from The Cancer Genome Atlas. The methylation of the CpG probe cg05293407TRIM27 was significantly associated with overall survival in patients with LUSC (HR = 1.65, 95% CI: 1.30–2.09, P = 4.52 × 10−5), but not in patients with LUAD (HR = 1.08, 95% CI: 0.87–1.33, P = 0.493). As incidence of LUSC is associated with higher smoking intensity compared to LUAD, we investigated whether smoking intensity impacted on the prognostic effect of cg05293407TRIM27 methylation in NSCLC. LUSC patients had a higher average pack-year of smoking (37.49LUAD vs 54.79LUSC, P = 1.03 × 10−19) and included a higher proportion of current smokers than LUAD patients (28.24%LUAD vs 34.09%LUSC, P = 0.037). cg05293407TRIM27 was significantly associated with overall survival only in NSCLC patients with medium–high pack-year of smoking (HR = 1.58, 95% CI: 1.26–1.96, P = 5.25 × 10−5). We conclude that cg05293407TRIM27 methylation is a potential predictor of LUSC prognosis, and smoking intensity may impact on its prognostic value across the various types of NSCLC.
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| 6. |
- Khandarkhaeva, Saiana, et al.
(författare)
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Testing the performance of secondary anvils shaped with focused ion beam from the single-crystal diamond for use in double-stage diamond anvil cells
- 2022
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 93:3
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Tidskriftsartikel (refereegranskat)abstract
- The success of high-pressure research relies on the inventive design of pressure-generating instruments and materials used for their construction. In this study, the anvils of conical frustum or disk shapes with flat or modified culet profiles (toroidal or beveled) were prepared by milling an Ia-type diamond plate made of a (100)-oriented single crystal using the focused ion beam. Raman spectroscopy and synchrotron x-ray diffraction were applied to evaluate the efficiency of the anvils for pressure multiplication in different modes of operation: as single indenters forced against the primary anvil in diamond anvil cells (DACs) or as pairs of anvils forced together in double-stage DACs (dsDACs). All types of secondary anvils performed well up to about 250 GPa. The pressure multiplication factor of single indenters appeared to be insignificantly dependent on the shape of the anvils and their culets profiles. The enhanced pressure multiplication factor found for pairs of toroidally shaped secondary anvils makes this design very promising for ultrahigh-pressure experiments in dsDACs.
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| 7. |
- Wang, Guo-Dong, et al.
(författare)
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Out of southern East Asia : the natural history of domestic dogs across the world
- 2016
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Ingår i: Cell Research. - : Nature Publishing Group. - 1001-0602 .- 1748-7838. ; 26:1, s. 21-33
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Tidskriftsartikel (refereegranskat)abstract
- The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.
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| 8. |
- Wang, Guo-dong, et al.
(författare)
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The genomics of selection in dogs and the parallel evolution between dogs and humans
- 2013
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 4, s. 1860-
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Tidskriftsartikel (refereegranskat)abstract
- The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.
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| 9. |
- Yang, Fengmei, et al.
(författare)
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Li2FePO4F and its metal-doping for Li-ion batteries : an ab initio study
- 2014
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Ingår i: RSC Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 4:91, s. 50195-50201
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Tidskriftsartikel (refereegranskat)abstract
- The electrochemical properties of three isotopic Li2FePO4F compounds, as cathode materials under different space groups Pbcn, P (1) over bar and Pnma were investigated using first principle calculations. Their structures and average open circuit voltages for step delithiation reactions were explored, and the results are in good agreement with the reported experimental data. We estimate the substitution effect of Fe by Co in Pnma-Li2FePO4F. The substitution of Fe by Co in Li2Fe1-xCoxPO4F may enhance the discharge potential of the materials, and the rate of its volume change during the redox process is between 0.6% and 2.1%. Furthermore, from the projected density of states for Li2Fe0.5Co0.5PO4F, we found strong hybridization for Fe-3d and Co-3d bands near the Fermi level, which implies that the Co-doped Li2Fe1-xCoxPO4F may possess better electronic conductivity than the pure phase.
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| 10. |
- Zhang, Ruyang, et al.
(författare)
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EGLN2 DNA methylation and expression interact with HIF1A to affect survival of early-stage NSCLC
- 2019
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Ingår i: Epigenetics. - : Informa UK Limited. - 1559-2294 .- 1559-2308. ; 14:2, s. 118-129
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Tidskriftsartikel (refereegranskat)abstract
- Hypoxia occurs frequently in human cancers and promotes stabilization and activation of hypoxia inducible factor (HIF). HIF-1α is specific for the hypoxia response, and its degradation mediated by three enzymes EGLN1, EGLN2 and EGLN3. Although EGLNs expression has been found to be related to prognosis of many cancers, few studies examined DNA methylation in EGLNs and its relationship to prognosis of early-stage non-small cell lung cancer (NSCLC). We analyzed EGLNs DNA methylation data from tumor tissue samples of 1,230 early-stage NSCLC patients, as well as gene expression data from The Cancer Genome Atlas. The sliding windows sequential forward feature selection method and weighted random forest were used to screen out the candidate CpG probes in lung adenocarcinomas (LUAD) and lung squamous cell carcinomas patients, respectively, in both discovery and validation phases. Then Cox regression was performed to evaluate the association between DNA methylation and overall survival. Among the 34 CpG probes in EGLNs, DNA methylation at cg25923056EGLN2 was identified to be significantly associated with LUAD survival (HR = 1.02, 95% CI: 1.01–1.03, P = 9.90 × 10–5), and correlated with EGLN2 expression (r =–0.36, P = 1.52 × 10–11). Meanwhile, EGLN2 expression was negatively correlated with HIF1A expression in tumor tissues (r =–0.30, P = 4.78 × 10–8) and significantly (P = 0.037) interacted with HIF1A expression on overall survival. Therefore, DNA methylation of EGLN2- HIF1A is a potential marker for LUAD prognosis and these genes are potential treatment targets for further development of HIF-1α inhibitors in lung cancer therapy.
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