| 1. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 4. |
- Ge, Xiaodong, et al.
(författare)
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Amelioration of type 2 diabetes by the novel 6, 8-guanidyl luteolin quinone-chromium coordination via biochemical mechanisms and gut microbiota interaction
- 2023
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Ingår i: JOURNAL OF ADVANCED RESEARCH. - : Elsevier. - 2090-1232 .- 2090-1224. ; 46, s. 173-188
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Luteolin is a plant-derived flavonoid that exhibits a broad range of pharmacological activ-ities. Studies on luteolin have mainly focused on its use for hyperlipidaemia prevention, whereas the capacity of the flavonoid to hinder hyperglycaemia development remains underexplored.Objectives: To probe the anti-hyperglycemic mechanism of 6,8-guanidyl luteolin quinone-chromium coordination (GLQ.Cr), and to assess its regulatory effect on intestinal microbiota in type 2 diabetes mel-litus (T2DM) mice.Methods: High-sucrose/high-fat diet-induced and intraperitoneal injection of streptozotocin was used to develop a T2DM model. Glycometabolism related indicators, histopathology, and gut microbiota compo-sition in caecum samples were evaluated, and RNA sequencing (RNA-seq) of liver samples was con-ducted. Faecal microbiota transplantation (FMT) was further used to verify the anti-hyperglycemic activity of intestinal microbiota.Results: The administration of GLQ.Cr alleviated hyperglycaemia symptoms by improving liver and pan-creatic functions and modulating gut microbe communities (Lactobacillus, Alistipes, Parabacteroides, Lachnoclostridium, and Desulfovibrio). RNA-seq analysis showed that GLQ.Cr mainly affected the peroxi-some proliferative activated receptor (PPAR) signalling pathway in order to regulate abnormal glucose metabolism. FMT significantly modulated the abundance of Lactobacillus, Alloprevotella, Alistipes, Bacteroides, Ruminiclostridium, Brevundimonas and Pseudomonas in the caecum to balance blood glucose levels and counteract T2DM mice inflammation.Conclusion: GLQ.Cr improved the abnormal glucose metabolism in T2DM mice by regulating the PPAR signalling pathway and modulating intestinal microbial composition. FMT can improve the intestinal microecology of the recipient and in turn ameliorate the symptoms of T2DM-induced hyperglycaemia.
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| 5. |
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| 6. |
- Hao, Qian, et al.
(författare)
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Organic blue carbon sequestration in vegetated coastal wetlands: Processes and influencing factors
- 2024
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Ingår i: Earth-Science Reviews. - 0012-8252 .- 1872-6828. ; 255, s. 104853-104853
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Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands play a vital role in carbon (C) sequestration, named ‘blue carbon’. The review aims to disentangle the processes and influencing factors, including elevated atmospheric CO2, global climate warming, sea level rise and anthropogenic activities. Firstly, we provided an overview of C processes, including input, output, and deposition, in coastal wetlands. We then summarized the impacts of different factors on C processes by modifying soil physicochemical properties, plant growth, vegetation type, and microbial community composition. Vegetation composition was a major contributor to C inputs, and C outputs was mainly controlled by microbial decomposition. Increased atmospheric CO2 concentration and associated climate warming often enhanced vegetation growth, while climate warming also promoted soil C decomposition. As a result, C storage could increase under mild warming conditions in the short-term, but decrease in the long-term as the severity of warming intensifies. Elevated salinity, caused by sea level rise, can be harmful to plant growth and inhibit organic C decomposition because of the reduced biomass and the weakened metabolic capacity of microorganisms. Most of human activities, such as reclamation, can lead to less C input and more C output, resulting in decreased C storage in coastal wetlands. Additionally, we also illustrate various coastal wetland restoration methods aimed at enhancing C sequestration, including legal frameworks, scientific theories, vegetation management, hydrological restoration, and other relevant constructions. Vegetation management could benefit plant growth and enhance C input effectively, and hydrological restoration can maintain the harmonious development of coastal wetland ecosystems. Other constructions, including breakwater, spillway, and dredged material, could protect coastal wetlands, especially facing sea level rise. This review offers valuable theoretical support and scientific references for the sustainable development and management of coastal wetlands in a changing climate.
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| 7. |
- He, Guojing, et al.
(författare)
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Shear Behavior Study on Timber-Concrete Composite Structures with Bolts
- 2016
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Ingår i: BioResources. - : BioResources. - 1930-2126. ; 11:4, s. 9205-9218
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Tidskriftsartikel (refereegranskat)abstract
- The key point of design for timber-concrete composite structure is to ensure the reliability of shear connectors. This study examined the mechanical properties of bolt-type connectors in timber-concrete composite structures theoretically and experimentally. The theoretical study was based on the Johansen yield theory (European Yield Model). Push-out specimens with different bolt dimensions were tested to determine the shear capacity and slip modulus. According to the experimental results, bolts yielded without timber or concrete cracks when the stiffness of bolts was not very great. The shear capacity and slip modulus of the bolt connectors were directly proportional to the diameter of the bolt. The strength of concrete was found to significantly affect the shear capacity of bolt connectors. Comparison between the theoretical and the experimental shear strength results showed reasonable agreement.
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| 8. |
- He, Shijun, et al.
(författare)
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GLP-1 Receptor Activation Abrogates β-Cell Dysfunction by PKA Cα-Mediated Degradation of Thioredoxin Interacting Protein
- 2019
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Ingår i: Frontiers in Pharmacology. - : Frontiers Media SA. - 1663-9812. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Glucagon-like peptide 1 receptor (GLP-1R) agonist (Exendin-4) is a well-known agent used to improve β-cell dysfunctions via protein kinase A (PKA), but the detailed downstream molecular mechanisms are still elusive. We have now found that PKA Cα mediated- TXNIP phosphorylation and degradation played a vital role in the β-cell protective role of exendin-4. After PKA activator (Exendin-4 or FSK) treatment, PKA Cα could directly interact with TXNIP by bimolecular fluorescence complementation and Co-IP assays in INS-1 cells. And PKA Cα overexpression decreased TXNIP level, whereas TXNIP level was largely increased in PKA Cα-KO β-cells by CRISPR-Cas9. Interestingly, TXNIP overexpression or PKA Cα-KO has impaired β-cell functions, including loss of insulin secretion and activation of inflammation. PKA Cα directly phosphorylated TXNIP at Ser307 and Ser308 positions, leading to its degradation via activation of cellular proteasome pathway. Consistent with this observation, TXNIP (S307/308A) mutant resisted the degradation effects of PKA Cα. However, exendin-4 neither affected TXNIP level in TXNIP (S307/308A) mutant overexpressed β-cells nor in PKA Cα-KO β-cells. Moreover, exendin-4 treatment reduced the inflammation gene expression in TXNIP overexpressed β-cells, but exendin-4 treatment has no effect on the inflammation gene expression in TXNIP (S307/308A) overexpressed β-cells. In conclusion, our study reveals the integral role of PKA Cα/TXNIP signaling in pancreatic β-cells and suggests that PKA Cα-mediated TXNIP degradation is vital in β-cell protective effects of exendin-4.
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| 9. |
- He, Tao, et al.
(författare)
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Kinetically Controlled Reticular Assembly of a Chemically Stable Mesoporous Ni(II)-Pyrazolate Metal-Organic Framework
- 2020
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:31, s. 13491-13499
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Tidskriftsartikel (refereegranskat)abstract
- The application scope of metal-organic frameworks (MOFs) is severely restricted by their weak chemical stability and limited pore size. A robust MOF with large mesopores is highly desired, yet poses a great synthetic challenge. Herein, two chemically stable Ni(II)-pyrazolate MOFs, BUT-32 and -33, were constructed from a conformation-matched elongated pyrazolate ligand through the isoreticular expansion. The two MOFs share the same sodalite-type net, but have different pore sizes due to the network interpenetration in BUT-32. Controlled syntheses of the two MOFs have been achieved through precisely tuning reaction conditions, where the microporous BUT-32 was demonstrated to be a thermodynamically stable product while the mesoporous BUT-33 is kinetically favored. To date, BUT-32 represents the first example of Ni-4-pyrazolate MOF whose structure was unambiguously determined by single-crystal X-ray diffraction. Interestingly, the kinetic product BUT-33 integrates 2.6 nm large mesopores with accessible Ni(II) active sites and remarkable chemical stability even in 4 M NaOH aqueous solution and 1 M Grignard reagent. This MOF thus demonstrated an excellent catalytic performance in carbon-carbon coupling reactions, superior to other Ni(II)-MOFs including BUT-32. These findings highlight the importance of kinetic control in the reticular synthesis of mesoporous MOFs, as well as their superiority in heterogeneous catalysis.
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| 10. |
- He, Xiaodong, et al.
(författare)
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Exponential Set-Point Stabilization of Underactuated Vehicles Moving in Three-Dimensional Space
- 2022
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Ingår i: IEEE/CAA Journal of Automatica Sinica. - 2329-9266. ; 9:2, s. 270-282
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Tidskriftsartikel (refereegranskat)abstract
- This paper investigates the stabilization of underactuated vehicles moving in a three-dimensional vector space. The vehicle's model is established on the matrix Lie group SE(3), which describes the configuration of rigid bodies globally and uniquely. We focus on the kinematic model of the underactuated vehicle, which features an underactuation form that has no sway and heave velocity. To compensate for the lack of these two velocities, we construct additional rotation matrices to generate a motion of rotation coupled with translation. Then, the state feedback is designed with the help of the logarithmic map, and we prove that the proposed control law can exponentially stabilize the underactuated vehicle to the identity group element with an almost global domain of attraction. Later, the presented control strategy is extended to set-point stabilization in the sense that the underactuated vehicle can be stabilized to an arbitrary desired configuration specified in advance. Finally, simulation examples are provided to verify the effectiveness of the stabilization controller.
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