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  • Davidsson, Marcus, et al. (författare)
  • A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
  • 2016
  • Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
  • Tidskriftsartikel (refereegranskat)abstract
    • Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.
  • Davidsson, Marcus, et al. (författare)
  • A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism
  • 2019
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 1091-6490. ; 116:52, s. 27053-27062
  • Tidskriftsartikel (refereegranskat)abstract
    • Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Most approaches to date depend on random screening, enrichment, and serendipity. The approach explored here, called BRAVE (barcoded rational AAV vector evolution), enables efficient selection of engineered capsid structures on a large scale using only a single screening round in vivo. The approach stands in contrast to previous methods that require multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide, derived from a protein, of known function on the AAV capsid surface, and a unique molecular barcode in the packaged genome. The sequencing of RNA-expressed barcodes from a single-generation in vivo screen allows the mapping of putative binding sequences from hundreds of proteins simultaneously. Using the BRAVE approach and hidden Markov model-based clustering, we present 25 synthetic capsid variants with refined properties, such as retrograde axonal transport in specific subtypes of neurons, as shown for both rodent and human dopaminergic neurons.
  • Davidsson, Marcus, et al. (författare)
  • Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing
  • 2018
  • Ingår i: RNA. - : Cold Spring Harbor Laboratory Press (CSHL). - 1355-8382 .- 1469-9001. ; 24:5, s. 673-687
  • Tidskriftsartikel (refereegranskat)abstract
    • Genome editing has proven to be highly potent in the generation of functional gene knockouts in dividing cells. In the CNS however, efficient technologies to repair sequences are yet to materialize. Reprogramming on the mRNA level is an attractive alternative as it provides means to perform in situ editing of coding sequences without nuclease dependency. Furthermore, de novo sequences can be inserted without the requirement of homologous recombination. Such reprogramming would enable efficient editing in quiescent cells (e.g., neurons) with an attractive safety profile for translational therapies. In this study, we applied a novel molecular-barcoded screening assay to investigate RNA trans-splicing in mammalian neurons. Through three alternative screening systems in cell culture and in vivo, we demonstrate that factors determining trans-splicing are reproducible regardless of the screening system. With this screening, we have located the most permissive trans-splicing sequences targeting an intron in the Synapsin I gene. Using viral vectors, we were able to splice full-length fluorophores into the mRNA while retaining very low off-target expression. Furthermore, this approach also showed evidence of functionality in the mouse striatum. However, in its current form, the trans-splicing events are stochastic and the overall activity lower than would be required for therapies targeting loss-of-function mutations. Nevertheless, the herein described barcode-based screening assay provides a unique possibility to screen and map large libraries in single animals or cell assays with very high precision.
  • Deng, Bin, et al. (författare)
  • Modelling asymmetric deformation along a curved strike-slip basement-fault system
  • 2021
  • Ingår i: International journal of earth sciences. - : SPRINGER. - 1437-3254 .- 1437-3262. ; 110, s. 165-182
  • Tidskriftsartikel (refereegranskat)abstract
    • Large-scale curved strike-slip fault systems along which significant amounts of displacement have taken place are common in nature. Scaled analogue experiments were used in this study to investigate strike-slip deformation in cover units above a curved basement-fault system simulated by a rigid plate with an in-built curvature depicting a half-circular fault. The model results show that en-echelon, right-stepping Riedel shears and low-angle synthetic shears (Y-shears) always form at the beginning of deformation, and grow outwards with splay faults, most of which evolve into thrusts at later stages of deformation. Digital image correlation (DIC) analyses of the surface displacement vectors show that a diffuse zone of deformation progressively changes into en-echelon shears, which gradually develop into throughgoing shear zones with further deformation. The geometries of Riedel shears along two sides of the basement fault (i.e. concave and convex sides) show significant differences in fault shape and intersection angles between the faults and the curved basement fault, indicating an asymmetry in deformation with a much wider deformation zone occurring on the concave side. As a result, en-echelon and/or overlapping flower structures develop along the curved basement strike-slip fault system. In particular, Riedel shears with a upward-convex geometry are localised in both sides of the curved basement fault and a continuous reverse oblique-slip fault forms at the concave side. When compared with the geometry of curved strike-slip faults in nature (e.g. the Daliangshan shear zone in Xichang basin and the Red River shear zone in the Yinggehai basin, China) the model results depict the asymmetric evolution pattern of the faults on either side of curved basement faults.
  • Dong, Xixi, et al. (författare)
  • A quantitative strategy for achieving the high thermal conductivity of die-cast Mg-Al-based alloys
  • 2022
  • Ingår i: Materialia. - : Elsevier. - 2589-1529.
  • Tidskriftsartikel (refereegranskat)abstract
    • A quantitative strategy was reported to design and develop Mg-Al-based alloys to achieve high thermal conductivity, in which the specific RE elements can be introduced to reduce the Al concentration in Mg matrix and to suppress the formation of Mg17Al12 phase through the formation of new intermetallic phases. Based on quantitative calculations, the strategy was demonstrated by a novel die-cast Mg3.2Al4.4La0.4Nd (in wt.%) alloy, which provided the thermal conductivity of 114.3 W/(m∙K) at ambient temperature and 137.5 W/(m∙K) at 300 °C, ∼25% higher than the commercial Mg4Al4RE (AE44) alloy. Meanwhile, the alloy also offered excellent ambient yield strength of 143.2 MPa and elongation of 8.2%, and superior strength and ductility than the AE44 alloy at elevated temperatures.
  • Dong, Xinyang, et al. (författare)
  • Flexible Mixed-Criticality Scheduling with Dynamic Slack Management
  • 2021
  • Ingår i: Journal of Circuits, Systems and Computers. - : WORLD SCIENTIFIC PUBL CO PTE LTD. - 0218-1266. ; 30:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Mixed-criticality (MC) system has attracted a lot of research attention in the past few years for its resource efficiency. Recent work attempted to provide a new MC model, the so-called Flexible Mixed-Criticality (FMC) task model, to relax the pessimistic assumptions in classic MC scheduling. However, in FMC, the behavior of MC tasks is still analyzed in offline stage. The run-time behavior such as dynamic slack has not yet been studied in FMC scheduling framework. In this paper, we present a utilization-based slack scheduling framework for FMC tasks. In particular, we monitor task execution on run time and collect dynamic slacks generated by task early completion. And these slacks can then be used either by high-criticality tasks to reduce mode-switches, or by low-criticality tasks so that less suspensions are triggered with more execution time, and thus quality of service is improved. We evaluate our approach with extensive simulations, and experiment results demonstrate the effectiveness of the proposed approaches.
  • Du, Yijun, et al. (författare)
  • Design of Sharp Roll-Off Band Notch with Fragment-Type Pattern Etched on UWB Antenna
  • 2018
  • Ingår i: IEEE Antennas and Wireless Propagation Letters. - 1536-1225 .- 1548-5757. ; 17:12, s. 2404-2408
  • Tidskriftsartikel (refereegranskat)abstract
    • Fragment-type etch patterns are proposed and designed on ultra-wideband planar antenna to acquire sharp roll-off band notch. Multi-objective evolutionary algorithm is applied to achieve the optimization searching of the best fragment-type etch pattern by setting multiple objectives to acquire the exact notched band and challenge the roll-off criterion (ROC) of band notch. Efficiency of the design can be improved by properly presetting slits on the patch radiator. For demonstration, designs with different slit presetting are implemented and tested. With single slit preset, band notch of ROC=0.72 at the WLAN band ranging from 5.15 GHz to 5.85GHz is acquired. 
  • Du, Yijun, et al. (författare)
  • Design of ultra-wideband antenna with high-selectivity band notches using fragment-type etch pattern
  • 2020
  • Ingår i: Microwave and optical technology letters (Print). - : Wiley. - 0895-2477 .- 1098-2760. ; 62:2, s. 912-918
  • Tidskriftsartikel (refereegranskat)abstract
    • By specifying objective functions defining the two bands to be notched with high roll-off criteria (ROCs), optimization searching for the best fragment-type etch pattern on ultra-wideband (UWB) antenna is implemented by using multi-objective optimization. The optimization with too many objective functions requires special treatment to improve the searching efficiency. In this design, two slits are preset on appropriate positions on different sides of the UWB radiator to constrain the decision space for etch pattern searching and yield two initial notched bands to speed up the optimization. For demonstration, a UWB patch antenna is designed with dual-band notches of ROC = 0.63 at WiMAX band and ROC = 0.65 at WLAN band. Both the simulation and measurement results indicate that there is significant improvement of the selectivity of the dual-band notches.
  • Elsayed, Ahmed H., et al. (författare)
  • Multilayer information spillover networks between oil shocks and banking sectors: Evidence from oil-rich countries
  • 2023
  • Ingår i: International Review of Financial Analysis. - : ELSEVIER SCIENCE INC. - 1057-5219 .- 1873-8079. ; 87
  • Tidskriftsartikel (refereegranskat)abstract
    • There is no doubt that oil price shocks significantly affect oil-producing countries macroeconomic fundamentals and financial stability, mainly in crisis times. The recent oil price shocks, coupled with the COVID-19 pandemic, motivated us to investigate the connectedness and risk transmission among oil shocks and banking sectors in the Gulf Cooperation Council (GCC) economies from June 30, 2006, to September 9, 2021. Thus, we construct multilayer information spillover networks between oil price shocks and GCC banking sectors. The empirical results show that the Bahrain banking sector depicts the highest connectedness and risk transmission with oil price shocks on the extreme risk spillover layer. In addition, Kuwait and the United Arab Emirates are highly connected to oil demand shocks. Furthermore, we find a substantial increase in extreme risk spillover and volatility spillover layers during the COVID-19 period. The results of this paper have some important implica-tions for regional portfolio risk management, alleviating systemic risk, and developing hedging and investment strategies.
  • Faber, Zachary J, et al. (författare)
  • The genomic landscape of core-binding factor acute myeloid leukemias
  • 2016
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
  • Tidskriftsartikel (refereegranskat)abstract
    • Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
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