| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 4. |
- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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| 5. |
- Bo, Li, et al.
(författare)
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Deformation behavior of disclosed sandstone fractures subjects to normal stresses
- 2021
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Ingår i: Robotics and Biomimetics. - : SCIENCE PRESS. - 1000-7598 .- 2197-3768. ; 42:7, s. 1850-1860
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Tidskriftsartikel (refereegranskat)abstract
- Subject to geological processes, natural rock fractures can be dislocated to some extent, and the normal deformation behavior of such dislocated fractures has not been quantitatively estimated, and the applicability of classic deformation models has not been verified against experiments and numerical simulations. The deformation and failure behavior of dislocated sandstone fractures were studied via compression tests and elastic-plastic contact simulations. The obtained stress-displacement curves were fitted by a hyperbolic model, an exponential model and a logarithmic model, respectively and the coefficients involved in these models were estimated. The results show that the experimentally and numerically obtained stress-displacement curves agree well with each other, and the surface damage areas are also consistent, which verified the reliability of the elastic-plastic contact model. The hyperbolic and logarithmic models do not fit the curves well under relatively low stress levels, while the exponential model well accommodates the simulation results in the whole loading process by introducing a coefficient n. The maximum closure V-max. is positively correlated with the maximum local aperture, the initial normal stiffness K-ni is positively correlated with the elastic modulus and negatively correlated with the fracture roughness and dislocating ratio, and n is positively correlated with the fracture roughness and dislocating ratio. A model was established to predict the three coefficients, and the prediction values agree well with the experimental results.
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| 6. |
- Li, Yang, 1984, et al.
(författare)
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Electrochemical Model-Based Fast Charging: Physical Constraint-Triggered PI Control
- 2021
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Ingår i: IEEE Transactions on Energy Conversion. - 1558-0059 .- 0885-8969. ; 36:4, s. 3208-3220
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Tidskriftsartikel (refereegranskat)abstract
- This paper proposes a new fast charging strategy for lithium-ion (Li-ion) batteries. The approach relies on an experimentally validated high-fidelity model describing battery electrochemical and thermal dynamics that determine the fast charging capability. Such a high-dimensional nonlinear dynamic model can be intractable to compute in real-time if it is fused with the extended Kalman filter or the unscented Kalman filter that is commonly used in the community of battery management. To significantly save computational efforts and achieve rapid convergence, the ensemble transform Kalman filter (ETKF) is selected and tailored to estimate the nonuniform Li-ion battery states. Then, a health- and safety-aware charging protocol is proposed based on successively applied proportional-integral (PI) control actions. The controller regulates charging rates using online battery state information and the imposed constraints, in which each PI control action automatically comes into play when its corresponding constraint is triggered. The proposed physical constraint-triggered PI charging control strategy with the ETKF is evaluated and compared with several prevalent alternatives. It shows that the derived controller can achieve close to the optimal solution in terms of charging time and trajectory, as determined by a nonlinear model predictive controller, but at a drastically reduced computational cost.
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| 7. |
- Wang, Zhihang, 1989, et al.
(författare)
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Chip-scale solar thermal electrical power generation
- 2022
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Ingår i: Cell Reports Physical Science. - : Elsevier BV. - 2666-3864. ; 3:3
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Tidskriftsartikel (refereegranskat)abstract
- There is an urgent need for alternative compact technologies that can derive and store energy from the sun, especially the large amount of solar heat that is not effectively used for power generation. Here, we report a combination of solution- and neat-film-based molecular solar thermal (MOST) systems, where solar energy can be stored as chemical energy and released as heat, with microfabricated thermoelectric generators to produce electricity when solar radiation is not available. The photophysical properties of two MOST couples are characterized both in liquid with a catalytical cycling setup and in a phase-interconvertible neat film. Their suitable photophysical properties let us combine them individually with a microelectromechanical ultrathin thermoelectric chip to use the stored solar energy for electrical power generation. The generator can produce, as a proof of concept, a power output of up to 0.1 nW (power output per unit volume up to 1.3 W m−3). Our results demonstrate that such a molecular thermal power generation system has a high potential to store and transfer solar power into electricity and is thus potentially independent of geographical restrictions.
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| 8. |
- Yang, Zhi Peng, et al.
(författare)
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Deterministic one-way logic gates on a cloud quantum computer
- 2022
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Ingår i: Physical Review A. - 2469-9934 .- 2469-9926. ; 105:4
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Tidskriftsartikel (refereegranskat)abstract
- One-way quantum computing is a promising candidate for fault-tolerant quantum computing. Here, we propose protocols to realize a deterministic one-way controlled-not (cnot) gate and one-way X rotations on current quantum-computing platforms. By applying a delayed-choice scheme, we overcome a limit of most currently available quantum computers, which are unable to implement further operations on measured qubits or operations conditioned on measurement results from other qubits. Moreover, we decrease the error rate of the one-way logic gates, compared to the original protocol using local operations and classical communication. In addition, we apply our deterministic one-way cnot gate in the Deutsch-Jozsa algorithm to show the feasibility of our proposal. We demonstrate all these one-way gates and algorithms by running experiments on the cloud quantum-computing platform IBM Quantum Experience.
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| 9. |
- Zhang, Jinbao, 1987-, et al.
(författare)
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Electrochemically polymerized poly (3, 4-phenylenedioxythiophene) as efficient and transparent counter electrode for dye sensitized solar cells
- 2019
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Ingår i: Electrochimica Acta. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0013-4686 .- 1873-3859. ; 300, s. 482-488
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Tidskriftsartikel (refereegranskat)abstract
- A new conducting polymer poly (3, 4-phenylenedioxythiophene) is synthesized by the electrochemical polymerization technique with different solvents. We find that solvents used in electrochemical polymerization play important roles for the catalytic activity and morphology of the formed conducting polymers. The obtained poly (3, 4-phenylenedioxythiophene) is for the first time employed as counter electrode electrocatalyst in dye sensitized solar cells with cobalt-based electrolytes. We demonstrate that a polymer prepared from a mixed acetonitrile-dichloromethane solvent exhibit higher catalytic activity for redox reactions, as compared to that from a single solvent, dichloromethane. The devices based on this mixed solvent-based polymer from a mixed solvents show a high power conversion efficiency of 5.97%. An additional advantageous feature of the electrochemically polymerized poly (3, 4-phenylenedioxythiophene) for solar cell applications is the high transparency in the visible and nearinfrared region. We also investigate the beneficial effect of the poly (3, 4-phenylenedioxythiophene) layer thickness on device performance, and concluded that the series resistance and charge transfer resistance are greatly influenced by the thickness of polymer, as evidenced by electrochemical impedance spectroscopy measurements. The optimal thickness for poly (3, 4-phenylenedioxythiophene) is about 100 nm. Furthermore, the high catalytic activity and transparency of the new conducting polymer as counter electrode shows great promise for other optoelectronic applications.
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| 10. |
- Araujo, Rafael B., et al.
(författare)
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Assessing Electrochemical Properties of Polypyridine and Polythiophene for Prospective Application in Sustainable Organic Batteries
- 2017
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 19:4, s. 3307-3314
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Tidskriftsartikel (refereegranskat)abstract
- Conducting polymers are being considered promising candidates for sustainable organic batteries mainly due to their fast electron transport properties and high recyclability. In this work, key properties of polythiophene and polypyridine have been assessed through a combined theoretical and experimental study focusing on such applications. A theoretical protocol has been developed to calculate redox potentials in solution within the framework of the density functional theory and using continuous solvation models. Here, the evolution of the electrochemical properties of solvated oligomers as a function of the length of the chain is analyzed and then the polymer properties are estimated via linear regressions using ordinary least square. The predicted values were verified against our electrochemical experiments. This protocol can now be employed to screen a large database of compounds in order to identify organic electrodes with superior properties.
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