240 results on '"Li, Songyuan"'
Search Results
202. SimLuator: A multi-core CPU simulator with dynamic language Lua.
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Ye, John, Li, Songyuan, Chen, Tianzhou, Wu, Minghui, and Liu, Li
- Published
- 2014
203. Adsorption and sensing performances of Rh-embedded PtSe2 monolayer upon CO and HCHO in dry-type reactors: A first-principles study.
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Zhao, Qi, Li, Songyuan, Man, Yuyan, Li, Suya, Li, Lin, Li, Nan, and Ning, Qi
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FIELD-effect transistors , *GAS detectors , *ADSORPTION (Chemistry) , *MONOMOLECULAR films , *POISONS , *CHEMISORPTION - Abstract
• Rh-embedding behaviors on a pristine PtSe 2 monolayer are studied. • The sensing mechanisms of Rh-PtSe 2 monolayer upon CO and HCHO are expounded. • The sensing potential of Rh-PtSe 2 monolayer in dry-type reactors is explored. Based on the first-principles method, we theoretically analyze the Rh-embedded PtSe 2 (Rh-PtSe 2) monolayer as a potential gas sensor in this paper, for detection of CO and HCHO in the dry-type reactor to evaluate its operation status. The Rh-embedding behavior is performed by substituting a Se atom at the topmost Se layer of the pristine PtSe 2 monolayer, and we find that the Rh atom can be stably and energy-favorably embedded in the PtSe 2 monolayer with the formation energy (E form) of −0.53 eV. Chemisorption is identified for the CO and HCHO system, with the adsorption energy (E ad) as −1.89 and −1.05 eV, respectively. The electronic property analysis reveals that the Rh-PtSe 2 monolayer can be a promising resistance-type sensor or a field-effect transistor sensor for detection of two gas species, with good sensing response or selectivity. This theoretical work can pave the way to further investigate the sensing application of Rh-PtSe 2 monolayer upon toxic gases in the dry-type reactors, and related experimental research can verify our findings and to confirm that Rh-PtSe 2 monolayer is a promising sensing candidate to evaluate the operation status of the dry-type reactors in the power system. [ABSTRACT FROM AUTHOR]
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- 2022
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204. Ni-Doped Janus HfSSe monolayer as a promising HCHO and C2H3Cl sensors in Dry-Type Reactor: A First-Principles theory.
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Zhao, Qi, Man, Yuyan, Li, Suya, Li, Songyuan, Li, Lin, Li, Nan, and Ning, Qi
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GAS absorption & adsorption ,GAS detectors ,HAZARDOUS substances ,DENSITY of states ,DETECTORS ,MONOMOLECULAR films - Abstract
[Display omitted] • Ni-embedding behaviors on pristine HfSSe monolayer is studied. • Expound the sensing mechanism of Ni-HfSSe monolayer upon HCHO and C 2 H 3 Cl. • Explore the sensing potential of Ni-HfSSe monolayer in dry-type reactors. This work using the first-principles theory studies the Ni-doping behavior on the pristine HfSSe monolayer and the potential of Ni-doped HfSSe (Ni-HfSSe) monolayer for HCHO and C 2 H 3 Cl detection in the dry-type reactors. Results indicates that the Ni dopant is more likely to be doped on the Se-surface, and the formation energy (E f) is 0.99 eV. The most stable configurations for gas adsorption and Hirshfeld analysis reveal the better adsorption behavior in the HCHO system with the adsorption energy (E ad) of −0.976 eV, slightly larger than that in the C 2 H 3 Cl system with E ad of −0.973 eV. The charge density difference (CDD) and atomic density of state (DOS) support the strong binding force of the new-formed bonds. The band structure (BS) and work function (WF) analysis reveal the potential of Ni-HfSSe monolayer to detect two gases as a resistance type gas sensor or the Kelvin Probe system. This paper proposes a novel sensing material for detection of toxic gases and is meaningful for possible application in the power system to evaluate the operation status of the electrical devices. [ABSTRACT FROM AUTHOR]
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- 2022
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205. Effect of Laser-Textured Cu Foil with Deep Ablation on Si Anode Performance in Li-Ion Batteries.
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Wang, Jingbo, Cao, Li, Li, Songyuan, Xu, Jiejie, Xiao, Rongshi, and Huang, Ting
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LITHIUM-ion batteries , *COPPER , *ANODES , *INTERFACIAL resistance , *FEMTOSECOND lasers , *SILICON nanowires , *CHARGE exchange - Abstract
Si is a highly promising anode material due to its superior theoretical capacity of up to 3579 mAh/g. However, it is worth noting that Si anodes experience significant volume expansion (>300%) during charging and discharging. Due to the weak adhesion between the anode coating and the smooth Cu foil current collector, the volume-expanded Si anode easily peels off, thus damaging anode cycling performance. In the present study, a femtosecond laser with a wavelength of 515 nm is used to texture Cu foils with a hierarchical microstructure and nanostructure. The peeling and cracking phenomenon in the Si anode are successfully reduced, demonstrating that volume expansion is effectively mitigated, which is attributed to the high specific surface area of the nanostructure and the protection of the deep-ablated microgrooves. Moreover, the hierarchical structure reduces interfacial resistance to promote electron transfer. The Si anode achieves improved cycling stability and rate capability, and the influence of structural features on the aforementioned performance is studied. The Si anode on the 20 μm-thick Cu current collector with a groove density of 75% and a depth of 15 μm exhibits a capacity of 1182 mAh/g after 300 cycles at 1 C and shows a high-rate capacity of 684 mAh/g at 3 C. [ABSTRACT FROM AUTHOR]
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- 2023
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206. Photo-inactive ZIF-8 is applied to significantly enhance the photocatalytic water reduction by forming a built-in electric field with g-C3N4 and the mechanism analysis.
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Chen, Pinghua, Li, Songyuan, Tang, Xiaoqiu, Zheng, Huitao, Shi, Jinwen, Wen, Linyuan, Xu, Yong, Fominski, Vyacheslav, and Jiang, Hualin
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ELECTRIC fields ,PHOTOREDUCTION ,CHARGE exchange ,CHARGE transfer ,PHOTOCATALYSTS - Abstract
It has been found in this study that the combination of ZIF-8 and g-C 3 N 4 turns the photo-inactive ZIF-8 into "active" and significantly enhances the photocatalytic performance for H 2 production. The experimental results such as contact potential difference (CPD) and photodeposition analysis suggest that a built-in electric field exists at the interface of g-C 3 N 4 and ZIF-8, and the direction is from ZIF-8 to g-C 3 N 4. Furthermore, the theoretical calculation of charge density difference and work functions uncover the potential forming mechanism of the built-in electric field. The mechanism analysis exhibits that the built-in electric field is conducive to promote the directional transfer of photo-induced electrons from g-C 3 N 4 to ZIF-8, which significantly boosts the catalytic ability. Hence, the construction of a built-in electric field is considered to be an effective strategy to synthesize robust photocatalysts, and the strategy can be extended to prepare a range of advanced catalysts needing directional charge transfer. [Display omitted] • Photo-inactive ZIF-8 is turned into "active" by built-in electric field. • Photo-inactive ZIF-8 become "active" and acts as the photo-reduction site. • The incorporation of ZIF-8 and g-C 3 N 4 improve the photocatalytic ability for 10 times. • The mechanism was detailly uncovered by the consistent experiments and calculations. [ABSTRACT FROM AUTHOR]
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- 2022
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207. CNTs with nano-confined TiO2 and surface loading Co3O4: The analysis of its performance and mechanism of PMS activation for ECs degradation under visible light.
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Fan, Dongdong, Hu, Meihua, Li, Songyuan, Chen, Pinghua, Jiang, Hualin, Tu, Xinman, Li, Xibao, and Luo, Xubiao
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EMERGING contaminants , *TITANIUM dioxide , *ELECTRON pairs , *CHARGE exchange , *CARBON nanotubes - Abstract
[Display omitted] • Rational design of nanoparticles distributed inside and outside the CNTs. • Nanoconfined TiO 2 generate radical species. • Surface loading Co 3 O 4 generate non-radical species-1O 2. • TiO 2 -in-CNT/Co 3 O 4 system has excellent anti-interference and stability. • TiO 2 -in-CNT/Co 3 O 4 can degrade ECs in broad-spectrum. The efficient activation of peroxymonosulfate for degrading emerging contaminants has become a focal point in recent decades, emphasizing the development of novel materials and efficient strategies for high-performance degradation. This study explores a spatial confinement strategy, where TiO 2 is confined inside carbon nanotubes with Co 3 O 4 loading outside, is performed to prepare the nano-confined composite TiO 2 -in-CNT/Co 3 O 4. Norfloxacin is chosen as the primary target pollutant, revealing a degradation rate exceeding 97 % within 30 min. The non-radical 1O 2 species were confirmed to be generated in nano-confined catalyst, but not observed in the control non-confined catalyst. Additionally, the quantity of original radical active species significantly increases in nano-confined catalyst compared to non-confined catalyst. TiO 2 -in-CNT/Co 3 O 4 has excellent reusability and application universality. Wonderful stability is observed in real water and anti-ion interference experiments, highlighting its robust stability. Experimental and DFT calculation results also demonstrate that the spatial confinement strategy prevents nanoparticle aggregation, accelerates electron transfer efficiency, and promotes the cycling of Co2+/Co3+ electron pairs. This work provides insights into the regulation of confined effects in activating PMS and offers a feasible strategy for the synergistic activation of PMS for water environment remediation through a radical and non-radical mixed mechanism. [ABSTRACT FROM AUTHOR]
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- 2025
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208. Key errors analysis and simulation of a 3-PUU parallel CMM
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Ye, Shenghua, Fei, Yetai, Li, Shuaipeng, Li, Songyuan, Zhao, Peng, and Hu, Penghao
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- 2013
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209. Photo-inactive ZIF-8 is applied to significantly enhance the photocatalytic water reduction by forming a built-in electric field with g-C3N4and the mechanism analysis
- Author
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Chen, Pinghua, Li, Songyuan, Tang, Xiaoqiu, Zheng, Huitao, Shi, Jinwen, Wen, Linyuan, Xu, Yong, Fominski, Vyacheslav, and Jiang, Hualin
- Abstract
It has been found in this study that the combination of ZIF-8 and g-C3N4turns the photo-inactive ZIF-8 into “active” and significantly enhances the photocatalytic performance for H2production. The experimental results such as contact potential difference (CPD) and photodeposition analysis suggest that a built-in electric field exists at the interface of g-C3N4and ZIF-8, and the direction is from ZIF-8 to g-C3N4. Furthermore, the theoretical calculation of charge density difference and work functions uncover the potential forming mechanism of the built-in electric field. The mechanism analysis exhibits that the built-in electric field is conducive to promote the directional transfer of photo-induced electrons from g-C3N4to ZIF-8, which significantly boosts the catalytic ability. Hence, the construction of a built-in electric field is considered to be an effective strategy to synthesize robust photocatalysts, and the strategy can be extended to prepare a range of advanced catalysts needing directional charge transfer.
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- 2022
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210. Author Correction: Universal toxin-based selection for precise genome engineering in human cells.
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Li, Songyuan, Akrap, Nina, Cerboni, Silvia, Porritt, Michelle J., Wimberger, Sandra, Lundin, Anders, Möller, Carl, Firth, Mike, Gordon, Euan, Lazovic, Bojana, Sieńska, Aleksandra, Pane, Luna Simona, Coelho, Matthew A., Ciotta, Giovanni, Pellegrini, Giovanni, Sini, Marcella, Xu, Xiufeng, Mitra, Suman, Bohlooly-Y, Mohammad, and Taylor, Benjamin J. M.
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ERGONOMICS ,HUMAN genome ,AUTHORS - Abstract
These authors contributed equally: Nina Akrap, Silvia Cerboni. In the original version of this Article the Acknowledgements failed to state support from the European Union's Horizon 2020 research and innovation program by grant number 814316. [Extracted from the article]
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- 2021
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211. Learnable Depth-Sensitive Attention for Deep RGB-D Saliency Detection with Multi-modal Fusion Architecture Search.
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Sun, Peng, Zhang, Wenhu, Li, Songyuan, Guo, Yilin, Song, Congli, and Li, Xi
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ATTENTION , *FEATURE extraction , *DISTRACTION - Abstract
RGB-D salient object detection (SOD) is usually formulated as a problem of classification or regression over two modalities, i.e. , RGB and depth. Hence, effective RGB-D feature modeling and multi-modal feature fusion both play a vital role in RGB-D SOD. In this paper, we propose a depth-sensitive RGB feature modeling scheme using the depth-wise geometric prior of salient objects. In principle, the feature modeling scheme is carried out in a Depth-Sensitive Attention Module (DSAM), which leads to the RGB feature enhancement as well as the background distraction reduction by capturing the depth geometry prior. Furthermore, we extend and enhance the original DSAM to DSAMv2 by proposing a novel Depth Attention Generation Module (DAGM) to generate learnable depth attention maps for more robust depth-sensitive RGB feature extraction. Moreover, to perform effective multi-modal feature fusion, we further present an automatic neural architecture search approach for RGB-D SOD, which does well in finding out a feasible architecture from our specially designed multi-modal multi-scale search space. Extensive experiments on nine standard benchmarks have demonstrated the effectiveness of the proposed approach against the state-of-the-art. We name the enhanced learnable Depth-Sensitive Attention and Automatic multi-modal Fusion framework DSA 2 Fv2. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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212. An optimized genome-wide, virus-free CRISPR screen for mammalian cells
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Xiong, Kai, Karottki, Karen Julie la Cour, Hefzi, Hooman, Li, Songyuan, Grav, Lise Marie, Li, Shangzhong, Spahn, Philipp, Lee, Jae Seong, Ventina, Ildze, Lee, Gyun Min, Lewis, Nathan E., Kildegaard, Helene Faustrup, and Pedersen, Lasse Ebdrup
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- 2021
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213. Structure-conditioned adversarial learning for unsupervised domain adaptation.
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Wang, Hui, Tian, Jian, Li, Songyuan, Zhao, Hanbin, Wu, Fei, and Li, Xi
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KNOWLEDGE transfer - Abstract
Unsupervised domain adaptation (UDA) typically carries out knowledge transfer from a label-rich source domain to an unlabeled target domain by adversarial learning. In principle, existing UDA approaches mainly focus on the global distribution alignment between domains while ignoring the intrinsic local distribution properties. Motivated by this observation, we propose an end-to-end structure-conditioned adversarial learning scheme (SCAL) that is able to preserve the intra-class compactness during domain distribution alignment. By using local structures as structure-aware conditions, the proposed scheme is implemented in a structure-conditioned adversarial learning pipeline. The above learning procedure is iteratively performed by alternating between local structures establishment and structure-conditioned adversarial learning. Experimental results demonstrate the effectiveness of the proposed scheme in UDA scenarios. [ABSTRACT FROM AUTHOR]
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- 2022
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214. Conceptual Examination of Pt Atom-Adorned WTe 2 for Improved Adsorption and Identification of CO and C 2 H 4 in Dissolved Gas Analysis.
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Zhao, Qi, Li, Suya, He, Jin, Man, Yuyan, and Li, Songyuan
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INSULATING oils , *DENSITY functional theory , *ADSORPTION (Chemistry) , *GAS detectors , *TRANSFORMER insulation , *MONOMOLECULAR films - Abstract
The online monitoring of transformer insulation is crucial for ensuring power system stability and safety. Dissolved gas analysis (DGA), employing highly sensitive gas sensors to detect dissolved gas in transformer oil, offers a promising means to assess equipment insulation performance. Based on density functional theory (DFT), platinum modification of a WTe2 monolayer was studied and the adsorption behavior of CO and C2H4 on the Pt-WTe2 monolayer was simulated. The results showed that the Pt atom could be firmly anchored to the W atoms in the WTe2 monolayer, with a binding energy of −3.12 eV. The Pt-WTe2 monolayer showed a trend toward chemical adsorption to CO and C2H4 with adsorption energies of −2.46 and −1.88 eV, respectively, highlighting a stronger ability of Pt-WTe2 to adsorb CO compared with C2H4. Analyses of the band structure (BS) and density of states (DOS) revealed altered electronic properties in the Pt-WTe2 monolayer after gas adsorption. The bandgap decreased to 1.082 eV in the CO system and 1.084 eV in the C2H4 system, indicating a stronger interaction of Pt-WTe2 with CO, corroborated by the analysis of DOS. Moreover, the observed change in work function (WF) was more significant in CO systems, suggesting the potential of Pt-WTe2 as a WF-based gas sensor for CO detection. This study unveils the gas-sensing potential of the Pt-WTe2 monolayer for transformer status evaluation, paving the way for the development of gas sensor preparation for DGA. [ABSTRACT FROM AUTHOR]
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- 2024
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215. An optimized filter design approach for enhancing imaging quality in industrial linear accelerator.
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Chen, Gang, Zhang, Zehuan, Xu, Shuo, Jiang, Shibo, Liu, Ximing, Tang, Peng, Li, Songyuan, and Xiang, Xincheng
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COMPUTED tomography , *PHOTON counting , *RADIATION sources , *SYSTEMS design , *LINEAR accelerators , *GRAPHITE - Abstract
BACKGROUND: The polychromatic X-rays generated by a linear accelerator (Linac) often result in noticeable hardening artifacts in images, posing a significant challenge to accurate defect identification. To address this issue, a simple yet effective approach is to introduce filters at the radiation source outlet. However, current methods are often empirical, lacking scientifically sound metrics. OBJECTIVE: This study introduces an innovative filter design method that optimizes filter performance by balancing the impact of ray intensity and energy on image quality. MATERIALS AND METHODS: Firstly, different spectra under various materials and thicknesses of filters were obtained using GEometry ANd Tracking (Geant4) simulation. Subsequently, these spectra and their corresponding incident photon counts were used as input sources to generate different reconstructed images. By comprehensively comparing the intensity differences and noise in images of defective and non-defective regions, along with considering hardening indicators, the optimal filter was determined. RESULTS: The optimized filter was applied to a Linac-based X-ray computed tomography (CT) detection system designed for identifying defects in graphite materials within high-temperature gas-cooled reactor (HTR), with defect dimensions of 2 mm. After adding the filter, the hardening effect reduced by 22%, and the Defect Contrast Index (DCI) reached 3.226. CONCLUSION: The filter designed based on the parameters of Average Difference (AD) and Defect Contrast Index (DCI) can effectively improve the quality of defect images. [ABSTRACT FROM AUTHOR]
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- 2024
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216. Research on the combined prediction model of milling sound pressure level based on force-thermal-vibration multi-feature fusion.
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Hu, Yuting, Li, Shuncai, Li, Songyuan, and Popov, Eugene
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SOUND pressure , *PREDICTION models , *LEAST squares , *ROOT-mean-squares , *DATA fusion (Statistics) , *DISCRETIZATION methods - Abstract
In order to establish the combined prediction model of milling noise based on force-thermal-vibration multi-feature fusion, a simultaneous milling noise-vibration-thermal-force test system was established. Based on the gray correlation theory and test data, the relationship between milling sound pressure and milling parameters, milling vibration, milling force, and milling thermal was analyzed. Based on the least square method, three single prediction models of milling sound pressure level for three-directional vibration, milling thermal, and three-directional milling force were established. Then, the weight coefficients of the combined model are determined by the standard errors of the three single models, and the linear combination model of the mean square root of milling sound pressure level expressed by the three single prediction models and the corresponding weight coefficients was established. The correlation coefficient of the combined prediction model of sound pressure is 0.95, which is larger than the correlation coefficient of three single prediction models. It shows that the combined prediction model of sound pressure level with multiple features can better predict milling noise and provide theoretical guidance for milling tool condition monitoring. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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217. Real-Time Semantic Segmentation via Auto Depth, Downsampling Joint Decision and Feature Aggregation.
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Sun, Peng, Wu, Jiaxiang, Li, Songyuan, Lin, Peiwen, Huang, Junzhou, and Li, Xi
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CELL aggregation , *COMPUTER vision , *DEEP learning - Abstract
To satisfy the stringent requirements for computational resources in the field of real-time semantic segmentation, most approaches focus on the hand-crafted design of light-weight segmentation networks. To enjoy the ability of model auto-design, Neural Architecture Search (NAS) has been introduced to search for the optimal building blocks of networks automatically. However, the network depth, downsampling strategy, and feature aggregation method are still set in advance and nonadjustable during searching. Moreover, these key properties are highly correlated and essential for a remarkable real-time segmentation model. In this paper, we propose a joint search framework, called AutoRTNet, to automate all the aforementioned key properties in semantic segmentation. Specifically, we propose hyper-cells to jointly decide the network depth and the downsampling strategy via a novel cell-level pruning process. Furthermore, we propose an aggregation cell to achieve automatic multi-scale feature aggregation. Extensive experimental results on Cityscapes and CamVid datasets demonstrate that the proposed AutoRTNet achieves the new state-of-the-art trade-off between accuracy and speed. Notably, our AutoRTNet achieves 73.9% mIoU on Cityscapes and 110.0 FPS on an NVIDIA TitanXP GPU card with input images at a resolution of 768 × 1536 . [ABSTRACT FROM AUTHOR]
- Published
- 2021
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218. CO and HCHO Sensing by Single Au Atom-Decorated WS 2 Monolayer for Diagnosis of Thermal Aging Faults in the Dry-Type Reactor: A First-Principles Study.
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Zhao, Qi, Man, Yuyan, He, Jin, Li, Songyuan, and Li, Lin
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CARBON monoxide detectors , *GAS detectors , *GAS absorption & adsorption , *THERMAL insulation , *DENSITY of states , *MONOMOLECULAR films , *RECOVERY rooms - Abstract
CO and HCHO are the main pyrolysis gases in long-term running dry-type reactors, and thus the diagnosis of thermal insulation faults inside such devices can be realized by sensing these gases. In this paper, a single Au atom-decorated WS2 (Au-WS2) monolayer is proposed as an original sensing material for CO or HCHO detection to evaluate the operation status of dry-type reactors. It was found that the Au atom prefers to be adsorbed at the top of the S atom of the pristine WS2 monolayer, wherein the binding force is calculated as −3.12 eV. The Au-WS2 monolayer behaves by chemisorption upon the introduction of CO and HCHO molecules, with the adsorption energies of −0.82 and −1.01 eV, respectively. The charge density difference was used to analyze the charge-transfer and bonding behaviors in the gas adsorptions, and the analysis of density of state as well as band structure indicate gas-sensing mechanisms. As calculated, the sensing responses of the Au-WS2 monolayer upon CO and HCHO molecule introduction were 58.7% and −74.4%, with recovery times of 0.01 s and 11.86 s, respectively. These findings reveal the favorable potential of the Au-WS2 monolayer to be a reusable and room-temperature sensing candidate for CO and HCHO detections. Moreover, the work function of the Au-WS2 monolayer was decreased by 13.0% after the adsorption of CO molecules, while it increased by 1.2% after the adsorption of HCHO molecules, which implies its possibility to be a work-function-based gas sensor for CO detection. This theoretical report paves the way for further investigations into WS2-based gas sensors in some other fields, and it is our hope that our findings can stimulate more reports on novel gas-sensing materials for application in evaluating the operation conditions of dry-type reactors. [ABSTRACT FROM AUTHOR]
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- 2024
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219. Effects of order and disorder on the defect evolution of NiFe binary alloys from atomistic simulations.
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Ge, Guojia, Chen, Feida, Tang, Xiaobin, Li, Changyuan, Gao, Jing, Li, Songyuan, and Geng, Zhenlong
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BINARY metallic systems , *THERMAL conductivity , *MOLECULAR dynamics , *TETRAHEDRA - Abstract
The effects of the ordered and disordered arrangements of elements on radiation-induced defects production and evolution in NiFe alloys were investigated through atomistic simulations. Results present a sluggish evolution of the overall microstructure in ordered L1 0 NiFe. Although the disordered phase has fewer Frankel pair accumulation in cascade simulation attributed to the low thermal conductivity reduced by the intrinsic chemical disorder, the difference is negligible when PKA energy increases because of the direct formation of clusters. Interstitial diffusion is restricted in the ordered phase, where Ni and Fe layers are alternately arranged. This condition delays interstitials accumulation and leads to the formation of more Shockley partial loops rather than Frank loops which favor in the disordered phase. The higher stacking fault energy in the ordered phase renders it difficult to form stacking fault tetrahedra [ABSTRACT FROM AUTHOR]
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- 2021
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220. One stone three birds: Simultaneous detection, adsorption and photocatalysis, the novel coordinated treating strategy towards complicated pollution system and the mechanism analysis.
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Jiang, Hualin, Fan, Dongdong, Qiu, Xianhua, Li, Songyuan, Tu, Xinman, Ye, Long, Zhang, Weiwei, Xie, Yang, Chen, Pinghua, and Luo, Xubiao
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PHOTOCATALYSIS , *TITANIUM dioxide , *SEWAGE , *DENSITY functional theory , *ADSORPTION (Chemistry) , *POLLUTION , *BIRD conservation - Abstract
[Display omitted] • Cd2+ can be fast qualitatively/quantitatively detect and adsorbed to be removed. • Tetracycline can be effectively degraded to be removed by visible light irradiation. • The above two performances can be simultaneously achieved by using TiO 2 /DAT. • TiO 2 /DAT is highly potential to treat complex pollution thanks to its trifunction. Waste water is difficult to treat, mainly because of the co-existence of organic and inorganic contaminants, attracting much attention. Herein, a novel nanohybrid of TiO 2 /dicarboxylate 1,5-diphenyl-3-thiocarbazone(III) (denoted as TiO 2 /DAT) was facilely synthesized. TiO 2 /DAT was used to treat the waste water with the co-existence of tetracycline (TC) and Cd2+. The results indicated that TiO 2 /DAT can qualitatively/quantitatively detect Cd2+ via colorimetry, and the Cd2+ adsorption can boost the TC degradation by TiO 2 /DAT. It was found that the co-existence of TC does not affect the detection and adsorption of Cd2+. Furthermore, whether Cd2+ being adsorbed in advance or co-existent with TC, the TC degradation manners over TiO 2 /DAT were similar. A reasonable deduction for these phenomena is that Cd2+ was adsorbed by TiO 2 /DAT before TC, which was confirmed by density functional theory (DFT) calculations. So TC and Cd2+ will not compete the surface active sites of TiO 2 /DAT when treated simultaneously by TiO 2 /DAT, and that is why TiO 2 /DAT can effectively treat TC and Cd2+ co-existent waste water. Upon TiO 2 /DAT, the treating strategies of detection, adsorption and degradation are combined into one functional material. This one stone three birds strategy can simplify the treating process of complex pollution systems, exhibiting highly promising in practical applications. [ABSTRACT FROM AUTHOR]
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- 2024
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221. Universal toxin-based selection for precise genome engineering in human cells
- Author
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Mohammad Bohlooly-Y, Nina Akrap, Benjamin J. M. Taylor, Euan Gordon, Grzegorz Sienski, Mike Firth, Giovanni Ciotta, Anders Lundin, Matthew A. Coelho, Silvia Cerboni, Aleksandra Sieńska, Marcella Sini, Marcello Maresca, Luna Simona Pane, Giovanni Pellegrini, Xiufeng Xu, Songyuan Li, Suman Mitra, Bojana Lazovic, Sandra Wimberger, Carl Möller, Michelle J. Porritt, University of Zurich, Li, Songyuan, Sienski, Grzegorz, and Maresca, Marcello
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0301 basic medicine ,Science ,Population ,10184 Institute of Veterinary Pathology ,General Physics and Astronomy ,1600 General Chemistry ,Genetics and Molecular Biology ,Computational biology ,Gene delivery ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Genome engineering ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Genome editing ,1300 General Biochemistry, Genetics and Molecular Biology ,Recombinase ,education ,Gene ,education.field_of_study ,Multidisciplinary ,Biological techniques ,General Chemistry ,3100 General Physics and Astronomy ,030104 developmental biology ,chemistry ,General Biochemistry ,Genetic engineering ,570 Life sciences ,biology ,Stem cell ,Genetic techniques ,030217 neurology & neurosurgery ,DNA ,Biotechnology - Abstract
Prokaryotic restriction enzymes, recombinases and Cas proteins are powerful DNA engineering and genome editing tools. However, in many primary cell types, the efficiency of genome editing remains low, impeding the development of gene- and cell-based therapeutic applications. A safe strategy for robust and efficient enrichment of precisely genetically engineered cells is urgently required. Here, we screen for mutations in the receptor for Diphtheria Toxin (DT) which protect human cells from DT. Selection for cells with an edited DT receptor variant enriches for simultaneously introduced, precisely targeted gene modifications at a second independent locus, such as nucleotide substitutions and DNA insertions. Our method enables the rapid generation of a homogenous cell population with bi-allelic integration of a DNA cassette at the selection locus, without clonal isolation. Toxin-based selection works in both cancer-transformed and non-transformed cells, including human induced pluripotent stem cells and human primary T-lymphocytes, as well as it is applicable also in vivo, in mice with humanized liver. This work represents a flexible, precise, and efficient selection strategy to engineer cells using CRISPR-Cas and base editing systems., Genome engineering in cell lines or human stem cells often has poor efficiency, limiting the development of research and therapeutic applications. Here, the authors use a toxin-based selection system for precise bi-allelic engineering in cells and in vivo.
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- 2021
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222. Community structure and diversity of myxobacteria in soils from Inner Mongolia, China.
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Wu Z, Li S, Wang X, and Liu H
- Abstract
Myxobacteria are a special kind of Gram-negative bacteria that can slide and produce a variety of bioactive substances against bacteria, fungi, and viruses. It has great development and research value in medicine and agriculture. Although myxobacteria have become a research hotspot at home and abroad, there are few systematic studies on the relationship between its diversity, geographical location, and environment factors. In order to solve these problems, 133 soil samples were collected from the east to the west of Inner Mongolia Autonomous Region and divided into five groups. The water content, pH, organic matter, available phosphorus, hydrolytic nitrogen, and available potassium content of soil samples were determined by national standards and other methods. The quantitative assessment of the abundance of myxobacteria in the soil sample was performed by quantitative real-time PCR. The composition of myxobacteria in the soil was determined by 16S rRNA high-throughput sequencing technology to analyze the differences in the community structure of myxobacteria among different groups, explore the relationship between the diversity of myxobacteria resources and the distribution and physical and chemical properties of the soil, and predict and analyze its community function. The results showed that there were abundant myxobacteria resources in the soils of Inner Mongolia, and the average relative abundance of myxobacteria in the soil samples from the central part of Inner Mongolia was higher than that in the eastern and western parts, but the richness and diversity of samples from the central to eastern regions were significantly higher than those from the western regions. The myxobacteria resources in the whole region included 10 families and 22 genera, among which the dominant genera were Labilitrix , Sandaracinus , Archangium , and Haliangium . The analysis of the species composition of myxobacteria among different groups found that the distribution of soil and soil type had an impact on the species composition of the samples. The species with significant differences in relative abundance among the five groups of samples were Labilitrix , Archangium , Sandaracinus , Minicystis , Polyangium , and Myxococcus . In addition, the latitude and longitude of the sampling point and the soil pH, water content, available phosphorus content and organic matter content had a greater impact on the myxobacteria community structure of samples, while the altitude of the soil sample and the contents of available potassium and alkaline nitrogen had a relatively small impact. Our data suggest that the distribution, type and nutrient composition of soil samples have an impact on the relative abundance and species composition of myxobacteria community. The completion of this work can provide basic data for the in-depth study of myxobacteria in the soil., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2025 Wu, Li, Wang and Liu.)
- Published
- 2025
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223. Optimized prime editing of the Alzheimer's disease-associated APOE4 mutation.
- Author
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Rottner AK, Lundin A, Li S, Firth M, Maresca M, and Sienski G
- Subjects
- Humans, RNA, Guide, CRISPR-Cas Systems genetics, HEK293 Cells, Alzheimer Disease genetics, Gene Editing methods, Apolipoprotein E4 genetics, Induced Pluripotent Stem Cells metabolism, Mutation, CRISPR-Cas Systems
- Abstract
Gene editing strategies to safely and robustly modify the Alzheimer's disease-associated APOE4 isoform are still lacking. Prime editing (PE) enables the precise introduction of genetic variants with minimal unintended editing and without donor templates. However, it requires optimization for each target site and has not yet been applied to APOE4 gene editing. Here, we screened PE guide RNA (pegRNA) parameters and PE systems for introducing the APOE4 variant and applied the optimized PE strategy to generate disease-relevant human induced pluripotent stem cell models. We show that introducing a single-nucleotide difference required for APOE4 correction inhibits PE activity. To advance efficient and robust genome engineering of precise genetic variants, we further present a reliable PE enrichment strategy based on diphtheria toxin co-selection. Our work provides an optimized and reproducible genome engineering pipeline to generate APOE4 disease models and outlines novel strategies to accelerate genome editing in cellular disease model generation., Competing Interests: Declaration of interests A.K.R., A.L., S.L., M.F., M.M., and G.S. are employees and shareholders of AstraZeneca. M.M. and S.L. are listed as co-inventors in an AstraZeneca patent application (application number: WO2019099943A1, WO2020208185A1, and WO2021204877A2) related to this work. S.L. is now an employee of AccurEdit Therapeutics., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2025
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224. CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium.
- Author
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Rong Y, Frey A, Özdemir E, Sainz de la Maza Larrea A, Li S, Nielsen AT, and Jensen SI
- Subjects
- Anaerobiosis, Aerobiosis, Acetates metabolism, Glucose metabolism, Xylitol metabolism, CRISPR-Cas Systems, Fermentation, Escherichia coli metabolism, Escherichia coli genetics, Metabolic Engineering methods, Bioreactors microbiology
- Abstract
Replacing petrochemicals with compounds from bio-based manufacturing processes remains an important part of the global effort to move towards a sustainable future. However, achieving economic viability requires both optimized cell factories and innovative processes. Here, we address this challenge by developing a fermentation platform, which enables two concurrent fermentations in one bioreactor. We first construct a xylitol producing Escherichia coli strain in which CRISPRi-mediated gene silencing is used to switch the metabolism from aerobic to anaerobic, even when the bacteria are under oxic conditions. The switch also decouples growth from production, which further increases the yield. The strain produces acetate as a byproduct, which is subsequently metabolized under oxic conditions by a secondary E. coli strain. Through constraint-based metabolic modelling this strain is designed to co-valorize glucose and the excreted acetate to a secondary product. This unique syntrophic consortium concept facilitates the implementation of "two fermentations in one go", where the concurrent fermentation displays similar titers and productivities as compared to two separate single strain fermentations., (© 2024. The Author(s).)
- Published
- 2024
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225. High photoluminescence quantum yield and stability achieved by encapsulating MAPbBr 3 QDs in UIO-66 and their application in LEDs.
- Author
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Liu J, Li S, Han J, and Huang M
- Abstract
Lead halide perovskite quantum dots (QDs) have been extensively studied due to their excellent photoelectric performance. However, the stability of MAPbBr
3 QDs is affected by inevitable factors such as light, heat, and moisture, which limits their practical applications. In this work, stable metal-organic framework UIO-66 was synthesized via a solvothermal method, and the composite MAPbBr3 @UIO-66 was prepared through an in-situ growth method. Owing to the wide bandgap, small pore size, and regular geometric structure, UIO-66 can confine the size and uniformity of the perovskite QDs encapsulated within the framework, maximally preserving the luminescent properties of the perovskite QDs. Furthermore, UIO-66 isolates the perovskite QDs from contact with polar water molecules in the air, significantly enhancing the stability of the perovskite QDs. The synthesized composite material exhibits high stability and excellent optical performance, with a photoluminescence quantum yield (PLQY) of up to 78.9% in an air environment. After being stored under natural conditions for 35 days, it still retains 65% of its high luminescence intensity and fluorescence quantum efficiency. When packaged into green and white LEDs, the LEDs demonstrate high brightness and good monochromaticity, maintaining stable brightness even after 2.5 hours of continuous operation. These superior characteristics indicate that the composite material MAPbBr3 @UIO-66 has great potential for application in LED technology.- Published
- 2024
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226. Correction: Human iPSC and CRISPR targeted gene knock-in strategy for studying the somatic TIE2L914F mutation in endothelial cells.
- Author
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Lazovic B, Nguyen HT, Ansarizadeh M, Wigge L, Kohl F, Li S, Carracedo M, Kettunen J, Krimpenfort L, Elgendy R, Richter K, De Silva L, Bilican B, Singh P, Saxena P, Jakobsson L, Hong X, Eklund L, and Hicks R
- Published
- 2024
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- View/download PDF
227. Human iPSC and CRISPR targeted gene knock-in strategy for studying the somatic TIE2 L914F mutation in endothelial cells.
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Lazovic B, Nguyen HT, Ansarizadeh M, Wigge L, Kohl F, Li S, Carracedo M, Kettunen J, Krimpenfort L, Elgendy R, Richter K, De Silva L, Bilican B, Singh P, Saxena P, Jakobsson L, Hong X, Eklund L, and Hicks R
- Subjects
- Humans, Mutation genetics, CRISPR-Cas Systems genetics, Vascular Malformations genetics, Vascular Malformations pathology, Vascular Malformations metabolism, Induced Pluripotent Stem Cells metabolism, Receptor, TIE-2 genetics, Receptor, TIE-2 metabolism, Endothelial Cells metabolism, Gene Knock-In Techniques
- Abstract
Induced pluripotent stem cell (iPSC) derived endothelial cells (iECs) have emerged as a promising tool for studying vascular biology and providing a platform for modelling various vascular diseases, including those with genetic origins. Currently, primary ECs are the main source for disease modelling in this field. However, they are difficult to edit and have a limited lifespan. To study the effects of targeted mutations on an endogenous level, we generated and characterized an iPSC derived model for venous malformations (VMs). CRISPR-Cas9 technology was used to generate a novel human iPSC line with an amino acid substitution L914F in the TIE2 receptor, known to cause VMs. This enabled us to study the differential effects of VM causative mutations in iECs in multiple in vitro models and assess their ability to form vessels in vivo. The analysis of TIE2 expression levels in TIE2
L914F iECs showed a significantly lower expression of TIE2 on mRNA and protein level, which has not been observed before due to a lack of models with endogenous edited TIE2L914F and sparse patient data. Interestingly, the TIE2 pathway was still significantly upregulated and TIE2 showed high levels of phosphorylation. TIE2L914F iECs exhibited dysregulated angiogenesis markers and upregulated migration capability, while proliferation was not affected. Under shear stress TIE2L914F iECs showed reduced alignment in the flow direction and a larger cell area than TIE2WT iECs. In summary, we developed a novel TIE2L914F iPSC-derived iEC model and characterized it in multiple in vitro models. The model can be used in future work for drug screening for novel treatments for VMs., (© 2024. The Author(s).)- Published
- 2024
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228. Conformal Graphs as Twisted Partition Functions.
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Karydas M, Li S, Petkou AC, and Vilatte M
- Abstract
We show that a class of L-loop conformal ladder graphs are intimately related to twisted partition functions of free massive complex scalars in d=2L+1 dimensions. The graphs arise as four-point functions in certain two- and four-dimensional conformal fishnet models. The twisted thermal two-point function of the scalars becomes a generator of conformal ladder graphs for all loops. We argue that this correspondence is seeded by a system of two decoupled harmonic oscillators twisted by an imaginary chemical potential. We find a number of algebraic and differential relations among the conformal graphs that mirror the underlying free dynamics.
- Published
- 2024
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229. Highly sensitive and selective fluorescent "turn-on" sensor for Ag+ detection using MAPbBr3@PCN-221(Fe): An efficient Ag+-bridged energy transfer from perovskite to MOF.
- Author
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Li S, Zhao G, Sun X, Zheng J, Liu J, and Huang M
- Abstract
Metal ion-induced water pollution is attracting increasing public attention. Perovskite quantum dots and metal-organic frameworks (MOFs), owing to their outstanding properties, hold promise as ideal probes for detecting metal ions. In this study, a composite material, MAPbBr3@PCN-221(Fe), was prepared by encapsulating MAPbBr3 quantum dots with PCN-221(Fe), demonstrating high chemical stability and good reusability. The composite material shows a sensitive fluorescence turn-on signal in the presence of silver ions. The fluorescence intensity of the composite material exhibits a linear relationship with the concentration of Ag+ in the solution, with a low detection limit of 8.68 µM. Moreover, the fluorescence signal exhibits a strong selectivity for Ag+, enabling the detection of Ag+ concentration. This fluorescence turn-on signal originates from the Ag+-bridged energy transfer from the conductive band of MAPbBr3 to the excited state of the MOF, which is directly proportional to the concentration of silver ions. Simultaneously, this finding may open up a new possibility in artificial controlled energy transfer from perovskite to MOF for future development., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)
- Published
- 2024
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230. Corrigendum: Active substances of myxobacteria against plant diseases and their action mechanisms.
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Zhang L, Bao L, Li S, Liu Y, and Liu H
- Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1294854.]., (Copyright © 2024 Zhang, Bao, Li, Liu and Liu.)
- Published
- 2024
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231. Water-stable perovskite CsPb 2 Br 5 /CdSe quantum dot-based photoelectrochemical sensors for the sensitive determination of dopamine.
- Author
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Zhao G, Sun X, Li S, Zheng J, Liu J, and Huang M
- Abstract
A heterojunction of CdSe quantum dots in situ grown on the perovskite CsPb
2 Br5 (CsPb2 Br5 /CdSe) for water-stable photoelectrochemical (PEC) sensing was simply synthesized using the hot-injection method. Due to the inherent built-in electric field and the matching band structure between CsPb2 Br5 and CdSe, the CsPb2 Br5 /CdSe p-n heterojunction demonstrates enhanced photoelectrochemical properties. Accelerated interfacial charge transfer and increased electron-hole pair separation enable hydrolysis-resistant CsPb2 Br5 /CdSe sensors to exhibit heightened sensitivity with an ultra-low detection limit (0.0124 μM) and a wide linear range (0.4-303.9 μM) in subsequent dopamine detection. Moreover, the CsPb2 Br5 /CdSe sensors show excellent anti-interference ability, as well as remarkable stability and reproducibility in water solvent. It is noteworthy that this work is conducted in an aqueous environment, which provides an inspiring and convenient way for photoelectric and photoelectrocatalysis applications based on water-resistant perovskites.- Published
- 2024
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232. Active substances of myxobacteria against plant diseases and their action mechanisms.
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Zhang L, Bao L, Li S, Liu Y, and Liu H
- Abstract
Myxobacteria have a complex life cycle and unique social behavior, and obtain nutrients by preying on bacteria and fungi in soil. Chitinase, β-1,3 glucanase and β-1,6 glucanase produced by myxobacteria can degrade the glycosidic bond of cell wall of some plant pathogenic fungi, resulting in a perforated structure in the cell wall. In addition, isooctanol produced by myxobacteria can lead to the accumulation of intracellular reactive oxygen species in some pathogenic fungi and induce cell apoptosis. Myxobacteria can also perforate the cell wall of some plant pathogenic oomycetes by β-1,3 glucanase, reduce the content of intracellular soluble protein and protective enzyme activity, affect the permeability of oomycete cell membrane, and aggravate the oxidative damage of pathogen cells. Small molecule compounds such as diisobutyl phthalate and myxovirescin produced by myxobacteria can inhibit the formation of biofilm and lipoprotein of bacteria, and cystobactamids can inhibit the activity of DNA gyrase, thus changing the permeability of bacterial cell membrane. Myxobacteria, as a new natural compound resource bank, can control plant pathogenic fungi, oomycetes and bacteria by producing carbohydrate active enzymes and small molecular compounds, so it has great potential in plant disease control., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lele, Liangliang, Songyuan, Yang and Huirong.)
- Published
- 2024
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233. MLMG-SGG: Multilabel Scene Graph Generation With Multigrained Features.
- Author
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Li X, Miao P, Li S, and Li X
- Abstract
As an important and challenging problem in computer vision, scene graph generation (SGG) aims to find out the underlying semantic relationships among objects from a given image for scene understanding. Usually, prevalent SGG approaches adopt a learning pipeline with the assumption that there exists only a single relationship for a particular object pair. Considering the common phenomenon that a pair of objects can be attached by multiple relationships, we propose a multi-label scene graph generation pipeline with multi-grained features (MLMG-SGG), which formulates the relationship detection as a multi-label classification problem during training while generating multigraphs at inference time. In order to better model the fine-grained relationships, the proposed pipeline encodes the feature representation of SGG on different spatial scales by a specially designed Multi-Grained Module (MGM), resulting in the multi-grained (i.e., object-level and region-level) features of objects. Experimental results over the benchmark dataset demonstrate the significant performance gain of the proposed pipeline used as a plug-in for the state-of-the-art methods.
- Published
- 2024
- Full Text
- View/download PDF
234. IDNet: Information Decomposition Network for Fast Panoptic Segmentation.
- Author
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Lin G, Li S, Chen Y, and Li X
- Abstract
Traditional CNN-based pipelines for panoptic segmentation decompose the task into two subtasks, i.e., instance segmentation and semantic segmentation. In this way, they extract information with multiple branches, perform two subtasks separately and finally fuse the results. However, excessive feature extraction and complicated processes make them time-consuming. We propose IDNet to decompose panoptic segmentation at information level. IDNet only extracts two kinds of information and directly completes panoptic segmentation task, saving the efforts to extract extra information and to fuse subtasks. By decomposing panoptic segmentation into category information and location information and recomposing them with a serial pipeline, the process for panoptic segmentation is simplified greatly and unified with regard to stuff and things. We also adopt two correction losses specially designed for our serial pipeline, guaranteeing the overall predicting performance. As a result, IDNet strikes a better balance between effectiveness and efficiency, achieving the fastest inference speed of 24.2 FPS at a resolution of 800×1333 on a Tesla V100 GPU and a PQ of 43.8, which is comparable in one-stage CNN-based methods. The code will be released at https://github.com/AronLin/IDNet.
- Published
- 2024
- Full Text
- View/download PDF
235. A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo.
- Author
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Bestas B, Wimberger S, Degtev D, Madsen A, Rottner AK, Karlsson F, Naumenko S, Callahan M, Touza JL, Francescatto M, Möller CI, Badertscher L, Li S, Cerboni S, Selfjord N, Ericson E, Gordon E, Firth M, Chylinski K, Taheri-Ghahfarokhi A, Bohlooly-Y M, Snowden M, Pangalos M, Nuttall B, Akcakaya P, Sienski G, and Maresca M
- Subjects
- Animals, Mice, CRISPR-Cas Systems genetics, Mutation, Endonucleases genetics, Streptococcus pyogenes genetics, Translocation, Genetic, Proprotein Convertase 9 genetics
- Abstract
Streptococcus pyogenes Cas9 (SpCas9) and derived enzymes are widely used as genome editors, but their promiscuous nuclease activity often induces undesired mutations and chromosomal rearrangements. Several strategies for mapping off-target effects have emerged, but they suffer from limited sensitivity. To increase the detection sensitivity, we develop an off-target assessment workflow that uses Duplex Sequencing. The strategy increases sensitivity by one order of magnitude, identifying previously unknown SpCas9's off-target mutations in the humanized PCSK9 mouse model. To reduce off-target risks, we perform a bioinformatic search and identify a high-fidelity Cas9 variant of the II-B subfamily from Parasutterella secunda (PsCas9). PsCas9 shows improved specificity as compared to SpCas9 across multiple tested sites, both in vitro and in vivo, including the PCSK9 site. In the future, while PsCas9 will offer an alternative to SpCas9 for research and clinical use, the Duplex Sequencing workflow will enable a more sensitive assessment of Cas9 editing outcomes., (© 2023. Springer Nature Limited.)
- Published
- 2023
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- View/download PDF
236. Simultaneous inhibition of DNA-PK and Polϴ improves integration efficiency and precision of genome editing.
- Author
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Wimberger S, Akrap N, Firth M, Brengdahl J, Engberg S, Schwinn MK, Slater MR, Lundin A, Hsieh PP, Li S, Cerboni S, Sumner J, Bestas B, Schiffthaler B, Magnusson B, Di Castro S, Iyer P, Bohlooly-Y M, Machleidt T, Rees S, Engkvist O, Norris T, Cadogan EB, Forment JV, Šviković S, Akcakaya P, Taheri-Ghahfarokhi A, and Maresca M
- Subjects
- Protein Kinases genetics, DNA Repair genetics, DNA genetics, Gene Editing, CRISPR-Cas Systems genetics
- Abstract
Genome editing, specifically CRISPR/Cas9 technology, has revolutionized biomedical research and offers potential cures for genetic diseases. Despite rapid progress, low efficiency of targeted DNA integration and generation of unintended mutations represent major limitations for genome editing applications caused by the interplay with DNA double-strand break repair pathways. To address this, we conduct a large-scale compound library screen to identify targets for enhancing targeted genome insertions. Our study reveals DNA-dependent protein kinase (DNA-PK) as the most effective target to improve CRISPR/Cas9-mediated insertions, confirming previous findings. We extensively characterize AZD7648, a selective DNA-PK inhibitor, and find it to significantly enhance precise gene editing. We further improve integration efficiency and precision by inhibiting DNA polymerase theta (Polϴ). The combined treatment, named 2iHDR, boosts templated insertions to 80% efficiency with minimal unintended insertions and deletions. Notably, 2iHDR also reduces off-target effects of Cas9, greatly enhancing the fidelity and performance of CRISPR/Cas9 gene editing., (© 2023. Springer Nature Limited.)
- Published
- 2023
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- View/download PDF
237. Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing.
- Author
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Peterka M, Akrap N, Li S, Wimberger S, Hsieh PP, Degtev D, Bestas B, Barr J, van de Plassche S, Mendoza-Garcia P, Šviković S, Sienski G, Firth M, and Maresca M
- Subjects
- Animals, CRISPR-Cas Systems, DNA Repair, Endonucleases metabolism, Gene Editing, Mammals genetics, DNA Breaks, Double-Stranded, DNA End-Joining Repair
- Abstract
Prime editing recently emerged as a next-generation approach for precise genome editing. Here we exploit DNA double-strand break (DSB) repair to develop two strategies that install precise genomic insertions using an SpCas9 nuclease-based prime editor (PEn). We first demonstrate that PEn coupled to a regular prime editing guide RNA (pegRNA) efficiently promotes short genomic insertions through a homology-dependent DSB repair mechanism. While PEn editing leads to increased levels of by-products, it can rescue pegRNAs that perform poorly with a nickase-based prime editor. We also present a small molecule approach that yields increased product purity of PEn editing. Next, we develop a homology-independent PEn editing strategy, which installs genomic insertions at DSBs through the non-homologous end joining pathway (NHEJ). Lastly, we show that PEn-mediated insertions at DSBs prevent Cas9-induced large chromosomal deletions and provide evidence that continuous Cas9-mediated cutting is one of the mechanisms by which Cas9-induced large deletions arise. Altogether, this work expands the current prime editing toolbox by leveraging distinct DNA repair mechanisms including NHEJ, which represents the primary pathway of DSB repair in mammalian cells., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
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238. Erratum: An optimized genome-wide, virus-free CRISPR screen for mammalian cells.
- Author
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Xiong K, Karottki KJC, Hefzi H, Li S, Grav LM, Li S, Spahn P, Lee JS, Ventina I, Lee GM, Lewis NE, Kildegaard HF, and Pedersen LE
- Abstract
[This corrects the article DOI: 10.1016/j.crmeth.2021.100062.]., (© 2021 The Authors.)
- Published
- 2021
- Full Text
- View/download PDF
239. The Correlative Factors and Probable Mechanism of Epidural Fluid Collection After Cranioplasty.
- Author
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Zhang S, Li S, Wei L, Chen H, Wang S, and Wang W
- Subjects
- Dura Mater surgery, Humans, Retrospective Studies, Ventriculoperitoneal Shunt adverse effects, Epidural Space diagnostic imaging, Postoperative Complications, Skull surgery
- Abstract
Objective: Epidural fluid collection (EFC) is one of the postoperative complications of cranioplasty and is easily ignored. Not only the predictive factors of EFC formation are unknown, the pathologic mechanisms are also unknown. We determined to analyze the predictive factors and the mechanism of EFC formation., Methods: A total of 340 patients underwent cranioplasty were retrospectively analyzed in this study. A series of factors were compared in the EFC and none-EFC groups and farther compared in the progress epidural fluid collection (PEFC) and none-PEFC subgroups to determine the predictive factors. The t test, χ test, and logistic regression analysis were used in statistical analysis., Results: The rate of EFC formation was 34.41%, and the size of skull defect, preoperative volume of collapse, intraoperative dura suspending, a pre- or intraoperative ventriculoperitoneal shunt (V-P shunt), and an postoperative air bubble in epidural space were predictive factors for EFC formation. Furthermore, the incidence of PEFC was 10.29%, the size of skull defects and intraoperative dura suspending were predictive factors for PEFC formation. The protein ratio and lactate dehydrogenase (LDH) ratio of effusion to serum were >0.5 and 0.6, respectively. There was no adverse prognosis., Conclusions: Although EFC can be treated with conservative therapy, we need to emphasize EFC incidence and development. As neurosurgeons, it is necessary to analyze the preoperative predictive factors of EFC, pay attention to the intraoperative details such as dura suspending to prevent PEFC formation, and the early intervention should be performed in the postoperative.
- Published
- 2020
- Full Text
- View/download PDF
240. Awakening dormant glycosyltransferases in CHO cells with CRISPRa.
- Author
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Karottki KJC, Hefzi H, Xiong K, Shamie I, Hansen AH, Li S, Pedersen LE, Li S, Lee JS, Lee GM, Kildegaard HF, and Lewis NE
- Subjects
- Animals, CHO Cells, Cricetinae, Cricetulus, Glycosylation, Phenotype, Polysaccharides analysis, Polysaccharides chemistry, CRISPR-Cas Systems genetics, Gene Editing methods, Glycosyltransferases genetics
- Abstract
Chinese hamster ovary (CHO) cells are the preferred workhorse for the biopharmaceutical industry, and CRISPR/Cas9 has proven powerful for generating targeted gene perturbations in CHO cells. Here, we expand the CRISPR engineering toolbox with CRISPR activation (CRISPRa) to increase transcription of endogenous genes. We successfully increased transcription of Mgat3 and St6gal1, and verified their activity on a functional level by subsequently detecting that the appropriate glycan structures were produced. This study demonstrates that CRISPRa can make targeted alterations of CHO cells for desired phenotypes., (© 2019 Wiley Periodicals, Inc.)
- Published
- 2020
- Full Text
- View/download PDF
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