| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Gao, Yang, et al.
(författare)
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The Influence of Increased CO2 Concentrations on AMOC Interdecadal Variability Under the LGM Background
- 2024
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Ingår i: JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. - 2169-897X .- 2169-8996. ; 129:3
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Tidskriftsartikel (refereegranskat)abstract
- This study explores the impact of rising CO2 levels on the Atlantic meridional overturning circulation's (AMOC) interdecadal variability within the context of the Last Glacial Maximum (LGM) background climate. Under heightened CO2 concentrations, the AMOC interdecadal variability intensifies dramatically, which is very different from the future warming case that shows a weakening of AMOC interdecadal variability in response to increased CO2 concentration. This unexpected phenomenon primarily results from the extensive retreat of sea ice, which exposes a larger portion of the ocean surface to efficiently feel the heat flux fluctuations from atmospheric processes. These findings underscore the significance of background climate conditions in shaping AMOC responses to increased CO2 and emphasize the necessity of considering these nuances to develop a more accurate understanding of AMOC dynamics in an evolving climate. Plain Language Summary The Atlantic meridional overturning circulation (AMOC) is an important component of the Earth system, and its interdecadal variability is predicted to be significantly weakened under future warming scenarios. In this paper, we analyze the response of AMOC interdecadal variability to rising CO2 levels under the background of the Last Glacial Maximum (LGM) and find that the AMOC interdecadal variability is intensified under increased CO2 , which is totally different from its response at the background of modern climate. Analyses suggest that this unexpected result is mainly caused by dramatic sea ice retreat, which exposes much seawater to efficiently receive large fluctuations of heat flux from atmospheric forcing. The findings reveal that the response of AMOC to increased CO2 and relevant dominant mechanism differs significantly under different climate conditions.
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| 3. |
- Han, Zixuan, et al.
(författare)
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Evaluating the large-scale hydrological cycle response within the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) ensemble
- 2021
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 17:6, s. 2537-2558
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Tidskriftsartikel (refereegranskat)abstract
- The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.
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| 4. |
- Lu, Shen-ning, et al.
(författare)
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Application of an innovative grid-based surveillance strategy to ensure elimination and prevent reintroduction of malaria in high-risk border communities in China
- 2022
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Ingår i: BMC Public Health. - : Springer Nature. - 1471-2458. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- Grid management is a grassroots governance strategy widely implemented in China since 2004 to improve the government's efficiency to actively find and solve problems among populated regions. A grid-based strategy surveillancing high-risk groups, including mobile and migrant populations (MMPs), in the China-Myanmar border region has played an indispensable role in promoting and consolidating the malaria elimination efforts by tracking and timely identification of potential importation or re-establishment of malaria among MMPs. A sequential mixed methods was implementated to explore the operational mechanism and best practices of the grid-based strategy including through the focus group discussions (FGDs), comparison of before and after the implementation of a grid-based strategy in the field sites, and data collection from the local health system.This paper distills the implementation mechanism and highlights the role of the grid-based strategy in the elimination and prevention of re-establishment of malaria transmission.
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| 5. |
- Ma, Wenjing, et al.
(författare)
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Rational construction of perylenequinone annulated porphyrins via cycloaddition reactions
- 2024
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Ingår i: Dyes and pigments. - : ELSEVIER SCI LTD. - 0143-7208 .- 1873-3743. ; 227
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Tidskriftsartikel (refereegranskat)abstract
- Acenequinone-fused porphyrins show remarkable long wavelength absorption, low-lying LUMO orbital and uniform pi,pi-stacking, enabling the potential applications as opto-electronic materials and catalysts. At present, the synthesis of large quinone fused porphyrins remains challenging. To address this, the cycloaddition reactions of naphthoquinone-fused porphyrin (Ni4NQ), followed by oxidative aromatization, have been employed. Through Diels-Alder reaction with perylenes in the presence of chloranil, a series of perylenequinone-fused porphyrins (1Ni-4Ni) have been synthesized with an overall yield above 70 %. Later, the tri-adduct 3Ni underwent 1,3-dipolar cycloaddition with nitrile oxide and the following DDQ oxidation to outcome the unsymmetrical tetra-adduct 5Ni. Although the peripheral perylenequinones fusion in 1Ni-4Ni has limited impact on the absorption with respect to the naphthoquinone-fused counterpart Ni4NQ, introduction of an isoxazole via 1,3-cycloaddition (5Ni) leads to a bathochromic Q band. This result has been rationalized by theoretical calculations. Additionally, the incorporation of perylenequinone units gives rise to intense intermolecular pi,pi-stacking and CH-pi interactions within the crystal packing. The self-assembly behavior using a good/bad solvent strategy are structural dependence. The tri-perylenequinone-fused porphyrins 3Ni formed spherical architecture, while tetraperylenequinone-fused porphyrin 4Ni afforded cubic or petal-type assemblies.
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| 6. |
- Qin, Ning, 1990, et al.
(författare)
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Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast
- 2023
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 186:4, s. 748-763.e15
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Tidskriftsartikel (refereegranskat)abstract
- Although many prokaryotes have glycolysis alternatives, it's considered as the only energy-generating glucose catabolic pathway in eukaryotes. Here, we managed to create a hybrid-glycolysis yeast. Subsequently, we identified an inositol pyrophosphatase encoded by OCA5 that could regulate glycolysis and respiration by adjusting 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP7) levels. 5-InsP7 levels could regulate the expression of genes involved in glycolysis and respiration, representing a global mechanism that could sense ATP levels and regulate central carbon metabolism. The hybrid-glycolysis yeast did not produce ethanol during growth under excess glucose and could produce 2.68 g/L free fatty acids, which is the highest reported production in shake flask of Saccharomyces cerevisiae. This study demonstrated the significance of hybrid-glycolysis yeast and determined Oca5 as an inositol pyrophosphatase controlling the balance between glycolysis and respiration, which may shed light on the role of inositol pyrophosphates in regulating eukaryotic metabolism.
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| 7. |
- Qin, Ning, et al.
(författare)
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Increased CO 2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast
- 2024
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Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- CO2 fixation plays a key role to make biobased production cost competitive. Here, we use 3-hydroxypropionic acid (3-HP) to showcase how CO2 fixation enables approaching theoretical-yield production. Using genome-scale metabolic models to calculate the production envelope, we demonstrate that the provision of bicarbonate, formed from CO2, restricts previous attempts for high yield production of 3-HP. We thus develop multiple strategies for bicarbonate uptake, including the identification of Sul1 as a potential bicarbonate transporter, domain swapping of malonyl-CoA reductase, identification of Esbp6 as a potential 3-HP exporter, and deletion of Uga1 to prevent 3-HP degradation. The combined rational engineering increases 3-HP production from 0.14 g/L to 11.25 g/L in shake flask using 20 g/L glucose, approaching the maximum theoretical yield with concurrent biomass formation. The engineered yeast forms the basis for commercialization of bio-acrylic acid, while our CO2 fixation strategies pave the way for CO2 being used as the sole carbon source.
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| 8. |
- Qin, Ning, et al.
(författare)
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Rewiring Central Carbon Metabolism Ensures Increased Provision of Acetyl-CoA and NADPH Required for 3-OH-Propionic Acid Production
- 2020
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Ingår i: ACS Synthetic Biology. - : American Chemical Society (ACS). - 2161-5063. ; 9:12, s. 3236-3244
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Tidskriftsartikel (refereegranskat)abstract
- The central carbon metabolite acetyl-CoA and the cofactor NADPH are important for the synthesis of a wide array of biobased products. Here, we constructed a platform yeast strain for improved provision of acetyl-CoA and NADPH, and used the production of 3-hydroxypropionic acid (3-HP) as a case study. We first demonstrated that the integration of phosphoketolase and phosphotransacetylase improved 3-HP production by 41.9% and decreased glycerol production by 48.1% compared with that of the control strain. Then, to direct more carbon flux toward the pentose phosphate pathway, we reduced the expression of phosphoglucose isomerase by replacing its native promoter with a weaker promoter, and increased the expression of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase by replacing their native promoters with stronger promoters. This further improved 3-HP production by 26.4%. Furthermore, to increase the NADPH supply we overexpressed cytosolic aldehyde dehydrogenase, and improved 3-HP production by another 10.5%. Together with optimizing enzyme expression of acetyl-CoA carboxylase and malonyl-CoA reductase, the final strain is able to produce 3-HP with a final titer of 864.5 mg/L, which is a more than 24-fold improvement compared with that of the starting strain. Our strategy combines the PK pathway with the oxidative pentose phosphate pathway for the efficient provision of acetyl-CoA and NADPH, which provides both a higher theoretical yield and overall yield than the reported yeast-based 3-HP production strategies via the malonyl-CoA reductase-dependent pathway and sheds light on the construction of efficient platform cell factories for other products.
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| 9. |
- Tian, Songsong, et al.
(författare)
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Continuous transfer of neural network representational similarity for incremental learning
- 2023
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Ingår i: Neurocomputing. - Amsterdam : Elsevier. - 0925-2312 .- 1872-8286. ; 545
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Tidskriftsartikel (refereegranskat)abstract
- The incremental learning paradigm in machine learning has consistently been a focus of academic research. It is similar to the way in which biological systems learn, and reduces energy consumption by avoiding excessive retraining. Existing studies utilize the powerful feature extraction capabilities of pre-trained models to address incremental learning, but there remains a problem of insufficient utilization of neural network feature knowledge. To address this issue, this paper proposes a novel method called Pre-trained Model Knowledge Distillation (PMKD) which combines knowledge distillation of neural network representations and replay. This paper designs a loss function based on centered kernel alignment to transfer neural network representations knowledge from the pre-trained model to the incremental model layer-by-layer. Additionally, the use of memory buffer for Dark Experience Replay helps the model retain past knowledge better. Experiments show that PMKD achieved superior performance on various datasets and different buffer sizes. Compared to other methods, our class incremental learning accuracy reached the best performance. The open-source code is published athttps://github.com/TianSongS/PMKD-IL. © 2023 The Author(s)
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| 10. |
- Wen, Qin, et al.
(författare)
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Separating Direct Heat Flux Forcing and Freshwater Feedback on AMOC Change Under Global Warming
- 2023
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Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 50:22
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Tidskriftsartikel (refereegranskat)abstract
- The Atlantic meridional overturning circulation (AMOC) is predicted to weaken under global warming. Whether it is caused by heat flux or freshwater flux is under debate. Here we separate these two processes in changing the AMOC under global warming. The simulated AMOC is weakened during the first 600years and then gradually recovered to its initial state, with heat flux and freshwater feedback dominating at different timescales. Global warming immediately puts freshwater into the Southern Ocean, which triggers the initial AMOC weakening via altering surface temperature. Concurrently, the extensive heat into the ocean surface increases the temperature over the subpolar North Atlantic, reducing the deep convection and thus the AMOC in the subsequent 50–150years. Meanwhile, the Arctic sea ice melt leads to the AMOC shutdown. Subsequently, the salinity accumulation in the subtropical North Atlantic propagating northward to restart the North Atlantic deep convection is responsible for the AMOC recovery.
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| 11. |
- Xie, Xu-Qin, et al.
(författare)
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miR-124 Intensified Oxaliplatin-Based Chemotherapy by Targeting CAPN2 in Colorectal Cancer
- 2020
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Ingår i: MOLECULAR THERAPY-ONCOLYTICS. - : CELL PRESS. - 2372-7705. ; 17, s. 320-331
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Tidskriftsartikel (refereegranskat)abstract
- Our previous study demonstrated that miR-124 was downregulated in colorectal cancer (CRC) compared with normal mucosa, and the downregulated expression of miR-124 was an independent prognostic factor in CRC patients. However, the function of miR-124 in CRC patients treated with chemotherapy is currently unclear. The aim of this study was to determine the miR-124 expression and its regulative role in oxaliplatin (L-OHP)-based chemotherapy of CRC patients. We observed that low miR-124 expression was correlated with worse overall survival (OS) in the 220 patients who received postoperative chemotherapy of 5-fluorouracil [5-FU] +leucovorin+L-OHP (FOLFOX) or capecitabine+L-OHP (XELOX). miR-124 overexpression promoted L-OHP-induced, but not 5-FU-induced, cytotoxicity and apoptosis in HT29 and SW480 cells. CAPN2 was a direct target of miR124, and its protein expression was reduced by forced expression of miR-124. miR-124 inhibited tumorigenesis and promoted OS of mice bearing xenograft tumors, especially upon L-OHP treatment. miR-124 also promoted L-OHP-induced apoptosis and restrained CAPN2 protein expression in xenograft tumors. Our results suggest that miR-124 could be considered as both a predictor of L-OHP-based chemotherapy for personalized treatment and a therapeutic target for CRC.
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| 12. |
- Yang, Bao, et al.
(författare)
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Long-term decrease in Asian monsoon rainfall and abrupt climate change events over the past 6,700 years
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - Washington : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:30
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Tidskriftsartikel (refereegranskat)abstract
- Asian summer monsoon (ASM) variability and its long-term ecological and societal impacts extending back to Neolithic times are poorly understood due to a lack of high-resolution climate proxy data. Here, we present a precisely dated and well-calibrated treering stable isotope chronology from the Tibetan Plateau with 1- to 5-y resolution that reflects high- to low-frequency ASM variability from 4680 BCE to 2011 CE. Superimposed on a persistent drying trend since the mid-Holocene, a rapid decrease in moisture availability between similar to 2000 and similar to 1500 BCE caused a dry hydroclimatic regime from similar to 1675 to similar to 1185 BCE, with mean precipitation estimated at 42 +/- 4% and 5 +/- 2% lower than during themid-Holocene and the instrumental period, respectively. This second-millennium-BCE megadrought marks the mid-to late Holocene transition, during which regional forests declined and enhanced aeolian activity affected northern Chinese ecosystems. We argue that this abrupt aridification starting similar to 2000 BCE contributed to the shift of Neolithic cultures in northern China and likely triggered human migration and societal transformation.
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| 13. |
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| 14. |
- Zhang, Yiming, 1986, et al.
(författare)
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Expressing a cytosolic pyruvate dehydrogenase complex to increase free fatty acid production in Saccharomyces cerevisiae
- 2020
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Saccharomyces cerevisiae is being exploited as a cell factory to produce fatty acids and their derivatives as biofuels. Previous studies found that both precursor supply and fatty acid metabolism deregulation are essential for enhanced fatty acid synthesis. A bacterial pyruvate dehydrogenase (PDH) complex expressed in the yeast cytosol was reported to enable production of cytosolic acetyl-CoA with lower energy cost and no toxic intermediate. Results: Overexpression of the PDH complex significantly increased cell growth, ethanol consumption and reduced glycerol accumulation. Furthermore, to optimize the redox imbalance in production of fatty acids from glucose, two endogenous NAD+-dependent glycerol-3-phosphate dehydrogenases were deleted, and a heterologous NADP+-dependent glyceraldehyde-3-phosphate dehydrogenase was introduced. The best fatty acid producing strain PDH7 with engineering of precursor and co-factor metabolism could produce 840.5 mg/L free fatty acids (FFAs) in shake flask, which was 83.2% higher than the control strain YJZ08. Profile analysis of free fatty acid suggested the cytosolic PDH complex mainly resulted in the increases of unsaturated fatty acids (C16:1 and C18:1). Conclusions: We demonstrated that cytosolic PDH pathway enabled more efficient acetyl-CoA provision with the lower ATP cost, and improved FFA production. Together with engineering of the redox factor rebalance, the cytosolic PDH pathway could achieve high level of FFA production at similar levels of other best acetyl-CoA producing pathways.
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| 15. |
- Zhang, Yazhou, et al.
(författare)
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Heterogeneous Hydrogenation with Hydrogen Spillover Enabled by Nitrogen Vacancies on Boron Nitride-Supported Pd Nanoparticles
- 2023
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Ingår i: Angewandte Chemie International Edition. - : Wiley-VCH Verlagsgesellschaft. - 1433-7851 .- 1521-3773. ; 62:9
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Tidskriftsartikel (refereegranskat)abstract
- Heterogeneous hydrogenation with hydrogen spillover has been demonstrated as an effective route to achieve high selectivity towards target products. More effort should be paid to understand the complicated correlation between the nature of supports and hydrogenation involving hydrogen spillover. Herein, we report the development of the hydrogenation system of hexagonal boron nitride (h-BN)-supported Pd nanoparticles for the hydrogenation of aldehydes/ketones to alcohols with hydrogen spillover. Nitrogen vacancies in h-BN determine the feasibility of hydrogen spillover from Pd to h-BN. The hydrogenation of aldehydes/ketones with hydrogen spillover from Pd proceeds on nitrogen vacancies on h-BN. The weak adsorption of alcohols to h-BN inhibits the deep hydrogenation of aldehydes/ketones, thus leading to high catalytic selectivity to alcohols. Moreover, the hydrogen spillover-based hydrogenation mechanism makes the catalyst system exhibit a high tolerance to CO poisoning.
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| 16. |
- Zheng, Nianye, et al.
(författare)
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Magnesium facilitates the healing of atypical femoral fractures : A single-cell transcriptomic study
- 2022
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Ingår i: Materials Today. - : Elsevier. - 1369-7021 .- 1873-4103. ; 52, s. 43-62
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Tidskriftsartikel (refereegranskat)abstract
- Bisphosphonates (BPs)-associated atypical femoral fractures (AFFs) present with impaired fracture healing, yet the underlying mechanism is unclear, which prevents the development of effective therapy. Peripheral sensory nerve has been shown to regulate fracture healing via releasing neuropeptides. Here we show that long-term BPs pre-treatment leads to fracture non-union in rats, characterized by reduced expression of calcitonin gene-related peptide (CGRP, a predominant type of neuropeptides) and abundant fibrous tissues in the non-bridged fracture gap, mimicking clinical AFFs. By using single-cell RNA-sequencing, long-term BPs treatment was identified to promote transition of progenitor cells into a specific cluster of fibroblasts that actively deposit dense extracellular matrix (ECM) to prevent fracture callus bridging. Administration of exogenous CGRP at early stages of fracture repair, in contrast, eliminates the ECM-secreting fibroblast cluster, attenuates fibrogenesis, and facilitates callus bridging, suggesting CGRP is a promising agent to facilitate AFF healing. Accordingly, we have developed an innovative magnesium (Mg) containing hybrid intramedullary nail fixation system (Mg-IMN) to effectively rescue BPs-impaired fracture healing via elevating CGRP synthesis and release. Such device optimizes the fracture healing in BPs-pretreated rats, comparable to direct administration of CGRP. These findings address the indispensable role of CGRP in advancing the healing of AFFs and develop translational strategies to accelerate AFF healing by taking advantage of the CGRP-stimulating effect of Mg-based biodegradable orthopedic implant. The study also indicates fibrosis could be targeted by augmenting CGRP expression to accelerate fracture healing even under challenging scenarios where fibroblasts are aberrantly activated.
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