| 1. |
- 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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| 2. |
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| 3. |
- Wessel, Jennifer, et al.
(författare)
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Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
- 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
- Fasting glucose and insulin are intermediate traits for type 2 diabetes. Here we explore the role of coding variation on these traits by analysis of variants on the HumanExome BeadChip in 60,564 non-diabetic individuals and in 16,491 T2D cases and 81,877 controls. We identify a novel association of a low-frequency nonsynonymous SNV in GLP1R (A316T; rs10305492; MAF = 1.4%) with lower FG (beta = -0.09 +/- 0.01 mmol l(-1), P = 3.4 x 10(-12)), T2D risk (OR[95% CI] = 0.86[0.76-0.96], P = 0.010), early insulin secretion (beta = -0.07 +/- 0.035 pmol(insulin) mmol(glucose)(-1), P = 0.048), but higher 2-h glucose (beta = 0.16 +/- 0.05 mmol l(-1), P = 4.3 x 10(-4)). We identify a gene-based association with FG at G6PC2 (p(SKAT) = 6.8 x 10(-6)) driven by four rare protein-coding SNVs (H177Y, Y207S, R283X and S324P). We identify rs651007 (MAF = 20%) in the first intron of ABO at the putative promoter of an antisense lncRNA, associating with higher FG (beta = 0.02 +/- 0.004 mmol l(-1), P = 1.3 x 10(-8)). Our approach identifies novel coding variant associations and extends the allelic spectrum of variation underlying diabetes-related quantitative traits and T2D susceptibility.
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| 4. |
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| 5. |
- Wang, J., et al.
(författare)
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Final report of the CCQM-K145 : Toxic and essential elements in bovine liver
- 2020
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Ingår i: Metrologia. - : IOP Publishing Ltd. - 0026-1394 .- 1681-7575. ; 57:1 A
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Tidskriftsartikel (refereegranskat)abstract
- Liver plays a major role in metabolism and acts as a source of energy for the body by storing glycogen. With the growing interest and investigation in the biological effects in recent years, it is important and necessary to develop accurate and comparable analytical methods for elements in bio-samples. It has, however, been 10 years since the tissue sample (bovine liver) of CCQM-K49 key comparison. The purpose of CCQM-K145 is to ensure the comparable and traceable measurement results for essential and toxic elements such as P, S, Zn, Mn, Ni, Mo, Sr, Cr, Co, Pb, As and Hg in bovine liver among NMIs and other designated measurement bodies worldwide. The comparison was agreed by IAWG as 6th IAWG Benchmarking Exercise with Zn and Ni as exemplary elements at the meeting in Korea in the early October 2016. The results of CCQM-K145 are expected to cover the measurement capability and support CMCs claiming for inorganic elements in the similar biological tissue materials and food samples. 30 NMIs and DIs registered in CCQM-K145. With respect to the methodology, a variety of techniques such as IDMS, ICP-OES, ICP-MS(non-ID), AAS and NAA were adopted by the participants. For Zn, Ni, Sr, Pb and Hg measurements, most participants chose ID-ICP-MS method, which showed the better performance in terms of consistency and reliability of the measurement results. In aspect of the traceability for the measurement results in CCQM-K145, most participants used their own (in house) CRMs or other NMI's CRMs to guarantee trace to SI unit. Most participants used similar matrix CRMs for quality control or method validation. Base on different statistic way to calculate the reference mass fraction values and associated uncertainties for each measurand, removal of the suspected extreme values, and discussion at the IAWG meetings, the median values are proposed as the KCRV for Zn, Ni, Mn, Mo, Cr, Pb and Hg; the arithmetic mean values are proposed as the KCRV for P, S, Sr, Co and As. In general, the performances of the majority of CCQM-K145 participants are very good, illustrating their measurement capabilities for Zn, Ni, P, S, Mn, Mo, Sr, Cr, As, Co, Pb and Hg in a complex biological tissue matrix. Bovine liver contains many kinds of nutrients and microelements, it can be regarded as a typical representative material of biological tissue and food. In CCQM-K145, the analytes involved alkali metals and transition elements, metalloids/semi-metals and non metals with a range of mass fraction from mg/g to μg/kg. CCQM-K145 also tested the ability of NMIs/DIs to determine elements that were easy to be lost and polluted, and interfered significantly. The chemical pretreatment methods of samples used in the comparison is suitable for general food and biological matrix samples. A variety of measurement methods used in the comparison represent the main instrumental technology for elemental analysis. Therefore, for supporting CMC claim, CCQM-K145 is readily applicable to measurement of more elements in a wide range of biological materials (including liquids and solids) and meat products. Main text To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
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| 6. |
- Kang, JS, et al.
(författare)
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Risk prediction for malignant intraductal papillary mucinous neoplasm of the pancreas: logistic regression versus machine learning
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1, s. 20140-
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Tidskriftsartikel (refereegranskat)abstract
- Most models for predicting malignant pancreatic intraductal papillary mucinous neoplasms were developed based on logistic regression (LR) analysis. Our study aimed to develop risk prediction models using machine learning (ML) and LR techniques and compare their performances. This was a multinational, multi-institutional, retrospective study. Clinical variables including age, sex, main duct diameter, cyst size, mural nodule, and tumour location were factors considered for model development (MD). After the division into a MD set and a test set (2:1), the best ML and LR models were developed by training with the MD set using a tenfold cross validation. The test area under the receiver operating curves (AUCs) of the two models were calculated using an independent test set. A total of 3,708 patients were included. The stacked ensemble algorithm in the ML model and variable combinations containing all variables in the LR model were the most chosen during 200 repetitions. After 200 repetitions, the mean AUCs of the ML and LR models were comparable (0.725 vs. 0.725). The performances of the ML and LR models were comparable. The LR model was more practical than ML counterpart, because of its convenience in clinical use and simple interpretability.
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| 7. |
- Haridas, Anupriya K., et al.
(författare)
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A flexible and free-standing FeS/sulfurized polyacrylonitrile hybrid anode material for high-rate sodium-ion storage
- 2020
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Ingår i: Chemical Engineering Journal. - : Elsevier BV. - 1385-8947. ; 385:1 April
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Tidskriftsartikel (refereegranskat)abstract
- Sodium-ion based energy storage systems have attracted extensive attention due to the similarities in the mechanism of operation with lithium-ion batteries along with the additional benefit of low cost and high abundance of sodium resources. Iron sulfide-based electrodes that operate via conversion mechanism have shown ample potential for high energy sodium-ion storage. However, the problems related with tremendous volume changes and the dissolution of sodium polysulfides in the electrolyte deteriorate the cycle life and limit their application in sodium-ion batteries (SIBs). Herein, a hybrid anode material, FeS/SPAN-HNF, with iron sulfide (FeS) nanoparticles decorated in a sulfurized polyacrylonitrile (SPAN) fiber matrix is demonstrated as flexible and free-standing anode material for high-rate SIBs. Unlike previous strategies in which FeS is encapsulated in an electrochemically inactive carbon matrix, this study utilizes SPAN, an electrochemically active material, as a dual functional matrix that can efficiently buffer volume expansion and sulfur dissolution of FeS nanoparticles as well as provide significant capacity improvement. The as-designed electrode is self-standing and flexible, without current collectors, binders or additional conductive agents, thus rendering enhanced practical capacity and energy density. This electrode showed a high reversible capacity of 782.8 mAh g−1 at 200 mA g−1 with excellent high rate capability, maintaining 327.5 mAh g−1 after 500 cycles at 5 A g−1, emphasizing promising prospects for the development of flexible and high energy density SIBs.
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| 8. |
- Haridas, Anupriya K., et al.
(författare)
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Boosting High Energy Density Lithium-Ion Storage via the Rational Design of an FeS-Incorporated Sulfurized Polyacrylonitrile Fiber Hybrid Cathode
- 2019
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Ingår i: ACS Applied Materials & Interfaces. - : American Chemical Society (ACS). - 1944-8252 .- 1944-8244. ; 11:33, s. 29924-29933
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Tidskriftsartikel (refereegranskat)abstract
- In order to satisfy the escalating energy demands, it is inevitable to improve the energy density of current Li-ion batteries. As the development of high-capacity cathode materials is of paramount significance compared to anode materials, here we have designed for the first time a unique synergistic hybrid cathode material with enhanced specific capacity, incorporating cost-effective iron sulfide (FeS) nanoparticles in a sulfurized polyacrylonitrile (SPAN) nanofiber matrix through a rational in situ synthesis strategy. Previous reports on FeS cathodes are scarce and consist of an amorphous carbon matrix to accommodate the volume changes encountered during the cycling process. However, this inactive buffering matrix eventually increases the weight of the cell, reducing the overall energy density. By the rational design of this hybrid composite cathode, we ensure that the presence of covalently bonded sulfur in SPAN guarantees high sulfur utilization, while effectively buffering the volume changes in FeS. Meanwhile, FeS can compensate for the conductivity issues in the SPAN, thereby realizing a synergistically driven dual-active cathode material improving the overall energy density of the composite. Simultaneous in situ generation of FeS nanoparticles within the SPAN fiber matrix was carried out via electrospinning followed by a one-step heating procedure. The developed hybrid cathode material displays enhanced lithium-ion storage, retaining 688.6 mA h g(FeS@SPAN composite)-1 at the end of 500 cycles at 1 A g-1 even within a narrow voltage range of 1-3.0 V. A high discharge energy density > 900 W h kg(FeS@SPAN composite)-1, much higher than the theoretical energy density of the commercial LiCoO2 cathode, was also achieved, revealing the promising prospects of this hybrid cathode material for high energy density applications.
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| 9. |
- Agostini, Marco, 1987, et al.
(författare)
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Rational Design of Low Cost and High Energy Lithium Batteries through Tailored Fluorine-free Electrolyte and Nanostructured S/C Composite
- 2018
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Ingår i: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 11:17, s. 2981-2986
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Tidskriftsartikel (refereegranskat)abstract
- We report a new Li–S cell concept based on an optimized F-free catholyte solution and a high loading nanostructured C/S composite cathode. The Li2S8present in the electrolyte ensures both buffering against active material dissolution and Li+conduction. The high S loading is obtained by confining elemental S (≈80 %) in the pores of a highly ordered mesopores carbon (CMK3). With this concept we demonstrate stabilization of a high energy density and excellent cycling performance over 500 cycles. This Li–S cell has a specific capacity that reaches over 1000 mA h g−1, with an overall S loading of 3.6 mg cm−2and low electrolyte volume (i.e., 10 μL cm−2), resulting in a practical energy density of 365 Wh kg−1. The Li–S system proposed thus meets the requirements for large scale energy storage systems and is expected to be environmentally friendly and have lower cost compared with the commercial Li-ion battery thanks to the removal of both Co and F from the overall formulation.
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