| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Nie, Wei, et al.
(författare)
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NO at low concentration can enhance the formation of highly oxygenated biogenic molecules in the atmosphere
- 2023
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Ingår i: Nature Communications. - Malmö : IVL Svenska Miljöinstitutet AB. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between nitrogen monoxide (NO) and organic peroxy radicals (RO2) greatly impacts the formation of highly oxygenated organic molecules (HOM), the key precursors of secondary organic aerosols. It has been thought that HOM production can be significantly suppressed by NO even at low concentrations. Here, we perform dedicated experiments focusing on HOM formation from monoterpenes at low NO concentrations (0 – 82 pptv). We demonstrate that such low NO can enhance HOM production by modulating the RO2 loss and favoring the formation of alkoxy radicals that can continue to autoxidize through isomerization.These insights suggest that HOM yields from typical boreal forest emissions can vary between 2.5%-6.5%, and HOM formation will not be completely inhibited even at high NO concentrations. Our findings challenge the notion that NO monotonically reduces HOM yields by extending the knowledge of RO2-NO interactions to the low-NO regime. This represents a major advance towards an accurate assessment of HOM budgets, especially in low-NO environments, which prevails in the preindustrial atmosphere, pristine areas, and the upper boundary layer.
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| 4. |
- Zhang, Yanan, et al.
(författare)
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Identifying discriminative features for diagnosis of Kashin-Beck disease among adolescents
- 2021
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Ingår i: BMC Musculoskeletal Disorders. - : BioMed Central. - 1471-2474. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Diagnosing Kashin-Beck disease (KBD) involves damages to multiple joints and carries variable clinical symptoms, posing great challenge to the diagnosis of KBD for clinical practitioners. However, it is still unclear which clinical features of KBD are more informative for the diagnosis of Kashin-Beck disease among adolescent.METHODS: We first manually extracted 26 possible features including clinical manifestations, and pathological changes of X-ray images from 400 KBD and 400 non-KBD adolescents. With such features, we performed four classification methods, i.e., random forest algorithms (RFA), artificial neural networks (ANNs), support vector machines (SVMs) and linear regression (LR) with four feature selection methods, i.e., RFA, minimum redundancy maximum relevance (mRMR), support vector machine recursive feature elimination (SVM-RFE) and Relief. The performance of diagnosis of KBD with respect to different classification models were evaluated by sensitivity, specificity, accuracy, and the area under the receiver operating characteristic (ROC) curve (AUC).RESULTS: Our results demonstrated that the 10 out of 26 discriminative features were displayed more powerful performance, regardless of the chosen of classification models and feature selection methods. These ten discriminative features were distal end of phalanges alterations, metaphysis alterations and carpals alterations and clinical manifestations of ankle joint movement limitation, enlarged finger joints, flexion of the distal part of fingers, elbow joint movement limitation, squatting limitation, deformed finger joints, wrist joint movement limitation.CONCLUSIONS: The selected ten discriminative features could provide a fast, effective diagnostic standard for KBD adolescents.
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| 5. |
- Bao, Haiyan, et al.
(författare)
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Condition of setting surge tanks in hydropower plants - A review
- 2018
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Ingår i: Renewable & sustainable energy reviews. - : Elsevier BV. - 1364-0321 .- 1879-0690. ; 81, s. 2059-2070
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Forskningsöversikt (refereegranskat)abstract
- Hydropower plays an important role in the safe, stable and efficient operation of power systems, especially with current trends toward renewable energy systems. The total global potential of gross, technical, economic, and exploitable hydropower are still enormous in the future, and the developments of new hydropower stations (HPSs) are of great importance. For constructions of new HPSs, the condition of setting surge tanks (CSST) is crucial for various perspectives, e.g. safety, stability and economy of HPSs. In this review, the CSST are summarized and analyzed from the three aspects: regulation assurance, operation stability, and the regulation quality, with an aim of providing a reference and guidance for research and engineering applications regarding surge tanks. Upstream and downstream surge tanks in conventional HPSs and pumped storage power stations are all included. Moreover, a comprehensive comparison of CSST under different conditions is conducted. One of the main focuses of this review is on Chinese studies, for introducing many meaningful results written in Chinese to more readers all over the world.
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| 6. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 7. |
- Guo, Peng, et al.
(författare)
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Ab initio structure determination of interlayer expanded zeolites by single crystal rotation electron diffraction
- 2014
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 43:27, s. 10593-10601
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Tidskriftsartikel (refereegranskat)abstract
- Layered solids often form thin plate-like crystals that are too small to be studied by single-crystal X-ray diffraction. Although powder X-ray diffraction (PXRD) is the conventional method for studying such solids, it has limitations because of peak broadening and peak overlapping. We have recently developed a software-based rotation electron diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Here we demonstrate the ab initio structure determination of two interlayer expanded zeolites, the microporous silicates COE-3 and COE-4 (COE-n stands for International Network of Centers of Excellence-n), from submicron-sized crystals by the RED method. COE-3 and COE-4 are built of ferrierite-type layers pillared by (-O-Si(CH3)(2)-O-) and (-O-Si(OH)(2)-O-) linker groups, respectively. The structures contain 2D intersecting 10-ring channels running parallel to the ferrierite layers. Because both COE-3 and COE-4 are electron-beam sensitive, a combination of RED datasets from 2 to 3 different crystals was needed for the structure solution and subsequent structure refinement. The structures were further refined by Rietveld refinement against the PXRD data. The structure models obtained from RED and PXRD were compared.
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| 8. |
- Li, Constance H., et al.
(författare)
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Sex differences in oncogenic mutational processes
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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| 9. |
- Li, Haiyan, et al.
(författare)
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Fragmentation inside proton-transfer-reaction-based mass spectrometers limits the detection of ROOR and ROOH peroxides
- 2022
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 15:6, s. 1811-1827
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Tidskriftsartikel (refereegranskat)abstract
- Proton transfer reaction (PTR) is a commonly applied ionization technique for mass spectrometers, in which hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later-generation PTR instruments have been designed for better throughput of less volatile species, allowing detection of more functionalized molecules as well. For example, the recently developed Vocus PTR time-of-flight mass spectrometer (PTR-TOF) has been shown to agree well with an iodide-adduct-based chemical ionization mass spectrometer (CIMS) for products with 3-5 O atoms from oxidation of monoterpenes (C10H16). However, while several different types of CIMS instruments (including those using iodide) detect abundant signals also at dimeric species, believed to be primarily ROOR peroxides, no such signals have been observed in the Vocus PTR even though these compounds fulfil the condition of having higher proton affinity than water. More traditional PTR instruments have been limited to volatile molecules as the inlets have not been designed for transmission of easily condensable species. Some newer instruments, like the Vocus PTR, have overcome this limitation but are still not able to detect the full range of functionalized products, suggesting that other limitations need to be considered. One such limitation, well-documented in PTR literature, is the tendency of protonation to lead to fragmentation of some analytes. In this work, we evaluate the potential for PTR to detect dimers and the most oxygenated compounds as these have been shown to be crucial for forming atmospheric aerosol particles. We studied the detection of dimers using a Vocus PTR-TOF in laboratory experiments, as well as through quantum chemical calculations. Only noisy signals of potential dimers were observed during experiments on the ozonolysis of the monoterpene alpha-pinene, while a few small signals of dimeric compounds were detected during the ozonolysis of cyclohexene. During the latter experiments, we also tested varying the pressures and electric fields in the ionization region of the Vocus PTR-TOF, finding that only small improvements were possible in the relative dimer contributions. Calculations for model ROOR and ROOH systems showed that most of these peroxides should fragment partially following protonation. With the inclusion of additional energy from the ion-molecule collisions driven by the electric fields in the ionization source, computational results suggest substantial or nearly complete fragmentation of dimers. Our study thus suggests that while the improved versions of PTR-based mass spectrometers are very powerful tools for measuring hydrocarbons and their moderately oxidized products, other types of CIMS are likely more suitable for the detection of ROOR and ROOH species.
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| 10. |
- Lu, Wei Fang, et al.
(författare)
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Photoluminescence enhancement in nano-textured fluorescent SiC passivated by atomic layer deposited Al2O3 films
- 2016
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Ingår i: Silicon Carbide and Related Materials 2015. ; , s. 493-496
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Konferensbidrag (refereegranskat)abstract
- The influence of thickness of atomic layer deposited Al2O3 films on nanotextured fluorescent 6H-SiC passivation is investigated. The passivation effect on the light emission has been characterized by photoluminescence and time-resolved photoluminescence at room temperature. The results show that 20nm thickness of Al2O3 layer is favorable to observe a large photoluminescence enhancement (25.9%) and long carrier lifetime (0.86ms). This is a strong indication for an interface hydrogenation that takes place during post-thermal annealing. These result show that an Al2O3 layer could serve as passivation in fluorescent SiC based white LEDs applications.
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