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| 6. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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- Flannick, Jason, et al.
(författare)
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Data Descriptor : Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to ~82 K Europeans via the exome chip, and similar to ~90% of low-frequency non-coding variants in similar to ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
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- Thomas, HS, et al.
(författare)
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- 2019
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swepub:Mat__t
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- Kilpelainen, TO, et al.
(författare)
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Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity
- 2019
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Ingår i: Nature communications. - London : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 376-
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Tidskriftsartikel (refereegranskat)abstract
- Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels.
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- Pan, YX, et al.
(författare)
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The apolipoprotein B and apolipoprotein A-I Ratio serves as a strong prognostic factor for the overall survival of patients with colorectal cancer
- 2023
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Ingår i: Frontiers in oncology. - : Frontiers Media SA. - 2234-943X. ; 12, s. 1089688-
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Tidskriftsartikel (refereegranskat)abstract
- The lipid metabolism status of patients with colorectal cancer (CRC) has not been understood comprehensively. The present study investigated the characteristics of lipid metabolism parameters in CRC patients with or without metastases and identified the independent prognostic factors of long-term prognosis.MethodsThe clinicopathological data of 231 CRC patients along with 259 formalin-fixed paraffin-embedded samples with or without liver or lung metastasis were retrieved and stained for apolipoprotein B (apoB) via immunohistochemistry (IHC) in our center. The correlation and multivariable analysis between blood circulating apolipoprotein A-I (apoA1), apoB and overall survival (OS) were analyzed.ResultsIn the multivariable analysis, apoA1, apoB and apolipoprotein B and apolipoprotein A-I (apoB/A) ratio, were identified as independent prognostic factors for OS. Moreover, the apoB/A ratio showed a significantly negative association with OS time (R=-0.187, P=0.004). CRC patients with low apoB/A ratio had better 1-, 3- and 5-year OS rates than those who had high apoB/A ratio (87.1%, 54.3%, and 37.1% vs. 92.5%, 72.0%, and 59.5%, respectively, P=0.001). On histological level, similar expression intensity of apoB between primary CRC and liver metastases indicated better prognostic outcomes than those with different expression levels (100%, 83.3%, and 77.8% vs. 100%, 66.7%, and 33.3%, respectively; P=0.033). Higher level of apoB in the primary CRC interprets into increased incidence of liver metastases. However, the apoB expression levels in the CRC tumor were not parallel to the circulating lipid metabolism parameters.ConclusionsThe apoB/A ratio was a reliable independent prognostic factor for predicting the long-term OS of CRC patients. Moreover, the IHC of the primary CRC and metastatic lesions verified the metastatic potential of apoB through a different aspect. Lipid metabolism status for cancer progression reported in the present study possessed potentially prognostic value, but bench-scale studies are needed for their future clinical applications.
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| 27. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 28. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 29. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 30. |
- Alcorn, J, et al.
(författare)
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Basic instrumentation for Hall A at Jefferson Lab
- 2004
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 522:3, s. 294-346
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Tidskriftsartikel (refereegranskat)abstract
- The instrumentation in Hall A at the Thomas Jefferson National Accelerator Facility was designed to study electro-and photo-induced reactions at very high luminosity and good momentum and angular resolution for at least one of the reaction products. The central components of Hall A are two identical high resolution spectrometers, which allow the vertical drift chambers in the focal plane to provide a momentum resolution of better than 2 x 10(-4). A variety of Cherenkov counters, scintillators and lead-glass calorimeters provide excellent particle identification. The facility has been operated successfully at a luminosity well in excess of 10(38) CM-2 s(-1). The research program is aimed at a variety of subjects, including nucleon structure functions, nucleon form factors and properties of the nuclear medium. (C) 2003 Elsevier B.V. All rights reserved.
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| 31. |
- Buyanova, Irina A, et al.
(författare)
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Unusual effects of hydrogen on electronic and lattice properties of GaNP alloys
- 2006
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Ingår i: Physica. B, Condensed matter. - : Elsevier BV. - 0921-4526 .- 1873-2135. ; 376, s. 568-570
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen incorporation is shown to cause passivation of various N-related localized states and partial neutralization of N-induced changes in the electronic structure of the GaNxP1-x alloys with x < 0.008. According to the performed X-ray diffraction measurements, the hydrogenation is also found to cause strong expansion of the GaNP lattice which even changes from a tensile strain in the as-grown GaNP epilayers to a compressive strain in the post-hydrogenated structures with the highest H concentration. By comparing results obtained using two types of hydrogen treatments, i.e. by implantation from a Kaufman source and by using a remote dc H plasma, the observed changes are shown to be inherent to H due to its efficient complexing with N atoms, whereas possible effects of implantation damage are only marginal. (c) 2005 Elsevier B.V. All rights reserved.
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| 32. |
- Chen, Weimin, et al.
(författare)
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Point defects in dilute nitride III-N-As and III-N-P
- 2006
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Konferensbidrag (refereegranskat)abstract
- We provide a brief review of our recent results from optically detected magnetic resonance studies of grown-in non-radiative defects in two most important dilute nitride system s-Ga(In)NAs grown on GaAs substrates and Ga(Al,In)NP grown on Si and GaP substrates. These results have led to the identification of defect complexes in the alloys, involving intrinsic defects such as As-Ga, antisites and Ga-i self-interstitials. They have also shed light on formation mechanisms of the defects and on their role in non-radiative carrier recombination that is harmful to the performance of potential optoelectronic and photonic devices based on these dilute nitrides. (c) 2005 Elsevier B.V. All rights reserved.
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| 33. |
- Chen, Y, et al.
(författare)
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The role of mitogen-activated protein kinase activation in determining cellular outcomes in polyamine analogue-treated human melanoma cells
- 2003
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Ingår i: Cancer Research. - 1538-7445. ; 63:13, s. 3619-3625
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Tidskriftsartikel (refereegranskat)abstract
- The clinically relevant polyamine analogue N-1,N-11-diethylnorspermine (DENSPM) inhibits cell growth by down-regulating polyamine biosynthesis, up-regulating polyamine catabolism at the level of spermidine/spermine N-1-acetyltransferase (SSAT), and depleting intracellular polyamine pools. Among human melanoma cell lines, the analogue causes rapid apoptosis in SK-MEL-28 cells and a sharp G(1) arrest in MALME-3M cells. This study reveals that DENSPM potently activates the mitogen-activated protein kinase (MAPK) pathways in melanoma cells and investigates the role of this response in determining cellular outcomes. Onset of apoptosis was preceded by an intense phosphorylation of the MAPKs, including extracellular signal-regulated kinase 1/2, c-jun NH2-terminal kinase, and p38 in both SK-MEL-28 and MALME-3M cells. A panel of DENSPM analogues differing only in their ability to induce SSAT was used to show that MAPK activation was causally linked to induction of SSAT. activity and related oxidative events. The latter was confirmed with the polyamine oxidase inhibitor MDL-75275 and the antioxidant N-acetyl-L-cysteine, which when used in combination with DENSPM, decreased MAPK activation and as previously shown, reduced apoptosis. The MAP/extracellular signal-regulated kinase-1 inhibitor PD 98059 reduced activation of all three kinases but failed to alter apoptosis in DENSPM-treated SK-MEL-28 cells. By contrast, the inhibitor prevented p21(waf1/cip1) induction and enhanced apoptosis in MALME-3M cells as indicated by accelerated caspase-3 activation and positive annexin V staining. The generality of this effect was demonstrated in DENSPM-treated A375 and LOX human melanoma cells. Taken together, the importance of the MAPK pathways in determining the biological response to DENSPM treatment is dependent on the genetic environment of the cell.
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| 35. |
- Du, CW, et al.
(författare)
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Arsenic trioxide reduces the invasive and metastatic properties of nasopharyngeal carcinoma cells in vitro
- 2006
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Ingår i: Brazilian journal of medical and biological research. - 0100-879X .- 1414-431X. ; 39:5, s. 677-685
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Tidskriftsartikel (refereegranskat)abstract
- Nasopharyngeal carcinoma (NPC) is notorious for the metastases, which are in close association with Epstein-Barr virus-encoded latent membrane protein 1 (LMP1). Arsenic trioxide (As2O3) has been shown to induce apoptosis and differentiation in NPC xenografts. Then, can it repress the cancer cells' metastasis potential? To elucidate this issue, the present study was performed. LMP1-negative cell line HNE1 and LMP1-positive cell line HNE1-LMP1 were used as in vitro model. Cells (1 × 105/mL) were cultured with or without 3 μM As2O3 for 48 h. Then the survival cells were collected to investigate their potential of colony formation, attachment, invasion, and migration. Both confocal immunofluorescence staining and Western blot were used to detect the changes of LMP1 expression. The changes of MMP-9 were examined by RT-PCR assay and Western blot. The results were as follow: i) the colony formation inhibition rate (75.41 ± 3.9% in HNE1-LMP1 cells vs 37.89 ± 4.9% in HNE1 cells), the rate of attachment (HNE1-LMP1 vs HNE1: 56.40 ± 3.5 vs 65.87 ± 5.9%), the invasion inhibitory rate (HNE1-LMP1 vs HNE1: 56.50 ± 3.7 and 27.91 ± 2.1%), and the migration inhibitory rate (HNE1-LMP1 vs HNE1: 48.70 ± 3.9 vs 29.19 ± 6.27%) were all significantly different between the two cell lines (P < 0.01). ii) LMP1 was down-regulated in As2O3-treated HNE1-LMP1 cells. iii) The reduction of MMP-9 was found in As2O3-treated groups, more evident in HNE1-LMP1 cells. Thus, we conclude that As2O3 can reduce metastasis potential of NPC cells, involving inhibition of MMP-9 expression. LMP1 were also reduced in this process and seemed to enhance anti-metastasis activity of As2O3. © 2006 Brazilian Journal of Medical and Biological Research.
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| 37. |
- Dutta, D, et al.
(författare)
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Nuclear transparency with the gamma n ->pi(-)p process in He-4
- 2003
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 68:2: 021001
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Tidskriftsartikel (refereegranskat)abstract
- We have measured the nuclear transparency of the fundamental process gamman-->pi(-)p in He-4. These measurements were performed at Jefferson Lab in the photon energy range of 1.6-4.5 GeV and at theta(cm)(pi)=70degrees and 90degrees. These measurements are the first of their kind in the study of nuclear transparency in photoreactions. They also provide a benchmark test of Glauber calculations based on traditional models of nuclear physics. The transparency results suggest deviations from the traditional nuclear physics picture. The momentum transfer dependence of the measured nuclear transparency is consistent with Glauber calculations that include the quantum chromodynamics phenomenon of color transparency.
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| 38. |
- Gayou, O, et al.
(författare)
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Measurement of G(Ep)/G(Mp) in (e)over-right-arrowp -> e(p)over-right-arrow to Q(2)=5.6 GeV2
- 2002
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Ingår i: Physical Review Letters. - 1079-7114. ; 88:9
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Tidskriftsartikel (refereegranskat)abstract
- The ratio of the electric and magnetic form factors of the proton G(Ep)/G(Mp), which is an image of its charge and magnetization distributions, was measured at the Thomas Jefferson National Accelerator Facility (JLab) using the recoil polarization technique. The ratio of the form factors is directly proportional to the ratio of the transverse to longitudinal components of the polarization of the recoil proton in the elastic (e) over right arrowp --> e (p) over right arrow reaction. The new data presented span the range 3.5 < Q(2) < 5.6 GeV2 and are well described by a linear Q(2) fit. Also, the ratio rootQ(2) F-2p/F-1p reaches a constant value above Q(2) = 2 GeV2.
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| 43. |
- Gorenek, B, et al.
(författare)
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Device-detected subclinical atrial tachyarrhythmias: definition, implications and management-an European Heart Rhythm Association (EHRA) consensus document, endorsed by Heart Rhythm Society (HRS), Asia Pacific Heart Rhythm Society (APHRS) and Sociedad Latinoamericana de Estimulación Cardíaca y Electrofisiología (SOLEACE)
- 2017
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Ingår i: Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology. - : Oxford University Press (OUP). - 1532-2092 .- 1099-5129. ; 19:9, s. 1556-1578
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Tidskriftsartikel (refereegranskat)
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