1,191 results on '"Xu Gu"'
Search Results
152. Development and Application of Computational Methods in Biology and Medicine
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Ruo-Xu Gu and Zunnan Huang
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Pharmacology ,Development (topology) ,Management science ,Drug Discovery ,Organic Chemistry ,Computational Biology ,Humans ,Medicine ,Molecular Medicine ,Biochemistry - Published
- 2020
153. Effects of an ionic liquid and processing conditions on the β-polymorph crystal formation in poly(vinylidene fluoride)
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Chaoying Wan, Xu Gu, Ellen L. Heeley, and Tom Pickford
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TP ,Materials science ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Electrospinning ,0104 chemical sciences ,law.invention ,Crystal ,chemistry.chemical_compound ,Crystallinity ,chemistry ,Chemical engineering ,law ,Nanofiber ,Phase (matter) ,Ionic liquid ,QD ,General Materials Science ,Lamellar structure ,Crystallization ,0210 nano-technology - Abstract
The piezoelectric properties of poly(vinylidene fluoride) (PVDF) are determined by the prevalence and orientation of its polar β-crystal phase, which can be tuned by processing conditions, additives, mechanical stretching or post-treatment. Here, the effects of three types of processing conditions on the crystalline structure evolution of PVDF was investigated; electrospinning, solution-casting and melt-compression. An ionic liquid (1-allyl-3-methylimidazolium chloride (AMIM)) used as an additive in aiding the electrospinning process, also affected the crystalline structure of the electrospun PVDF nanofibers. The total crystallinity, crystalline phase content and dielectric properties of the PVDF samples prepared by the different conditions were evaluated. The FTIR and DSC analyses show that the melt-compressed PVDF contains a high proportion of the paraelectric α-phase with a low total crystallinity, whereas the solution-cast PVDF contains a high proportion of polar γ-phase and a higher total crystallinity. In the case of the electrospun PVDF nanofibres, the addition of AMIM improved the morphology, uniformity and promoted the formation of the polar β and γ crystalline phases. X-Ray scattering analysis refined the crystal phase contents derived from FTIR, and also determined the ordered lamellar macromorphology formed by the three processing techniques. Furthermore, AMIM enhanced the a.c. conductivity and relative permittivity of the electrospun PVDF nanofibres by an order of magnitude, showing the effectiveness of using the ionic liquid AMIM, to improve the morphology and properties of electrospun PVDF nanofibers.\ud \ud
- Published
- 2019
154. Effects of seasonal hydrological regulation of cascade dams on the functional diversity of zooplankton: Implications for the management of massive reservoirs and dams
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Jiachen Shen, Ge Qin, Xu Gu, Yan Liu, Shuqing An, Run Liu, Xin Leng, and Yun Wan
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Water Science and Technology - Published
- 2022
155. Visualization of the mechanosensitive ion channel MscS under membrane tension
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Csaba Daday, Boris Martinac, Charles D. Cox, Ruo-Xu Gu, Thomas Walz, Bert L. de Groot, and Yixiao Zhang
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0303 health sciences ,Multidisciplinary ,Mechanosensation ,Chemistry ,Tension (physics) ,Mesenchymal stem cell ,03 medical and health sciences ,0302 clinical medicine ,Membrane ,Mechanosensitive ion channel ,Biophysics ,Mechanosensitive channels ,Mechanotransduction ,Lipid bilayer ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Mechanosensitive channels sense mechanical forces in cell membranes and underlie many biological sensing processes1-3. However, how exactly they sense mechanical force remains under investigation4. The bacterial mechanosensitive channel of small conductance, MscS, is one of the most extensively studied mechanosensitive channels4-8, but how it is regulated by membrane tension remains unclear, even though the structures are known for its open and closed states9-11. Here we used cryo-electron microscopy to determine the structure of MscS in different membrane environments, including one that mimics a membrane under tension. We present the structures of MscS in the subconducting and desensitized states, and demonstrate that the conformation of MscS in a lipid bilayer in the open state is dynamic. Several associated lipids have distinct roles in MscS mechanosensation. Pore lipids are necessary to prevent ion conduction in the closed state. Gatekeeper lipids stabilize the closed conformation and dissociate with membrane tension, allowing the channel to open. Pocket lipids in a solvent-exposed pocket between subunits are pulled out under sustained tension, allowing the channel to transition to the subconducting state and then to the desensitized state. Our results provide a mechanistic underpinning and expand on the 'force-from-lipids' model for MscS mechanosensation4,11.
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- 2021
156. Time-course observation of the reconstruction of stem cell niche in the intact root
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Renyin Wang, Meizhi Xu, Qiaozhi Yu, Shuang Wu, Xu Gu, Yuting Liu, Meina Yang, and Xinxin Bian
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0106 biological sciences ,endocrine system ,Time Factors ,animal structures ,Regular Issue ,Cell division ,Genotype ,Physiology ,Meristem ,Arabidopsis ,Plant Science ,Cell fate determination ,01 natural sciences ,Plant Roots ,03 medical and health sciences ,chemistry.chemical_compound ,Auxin ,Genetics ,Arabidopsis thaliana ,Stem Cell Niche ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,biology ,Arabidopsis Proteins ,Regeneration (biology) ,Genetic Variation ,Cell Differentiation ,biology.organism_classification ,Cell biology ,chemistry ,nervous system ,Stele ,Cytokinin ,sense organs ,Cell Division ,hormones, hormone substitutes, and hormone antagonists ,010606 plant biology & botany - Abstract
The stem cell niche (SCN) is critical in maintaining continuous postembryonic growth of the plant root. During their growth in soil, plant roots are often challenged by various biotic or abiotic stresses, resulting in damage to the SCN. This can be repaired by the reconstruction of a functional SCN. Previous studies examining the SCN’s reconstruction often introduce physical damage including laser ablation or surgical excision. In this study, we performed a time-course observation of the SCN reconstruction in pWOX5:icals3m roots, an inducible system that causes non-invasive SCN differentiation upon induction of estradiol on Arabidopsis (Arabidopsis thaliana) root. We found a stage-dependent reconstruction of SCN in pWOX5:icals3m roots, with division-driven anatomic reorganization in the early stage of the SCN recovery, and cell fate specification of new SCN in later stages. During the recovery of the SCN, the local accumulation of auxin was coincident with the cell division pattern, exhibiting a spatial shift in the root tip. In the early stage, division mostly occurred in the neighboring stele to the SCN position, while division in endodermal layers seemed to contribute more in the later stages, when the SCN was specified. The precise re-positioning of SCN seemed to be determined by mutual antagonism between auxin and cytokinin, a conserved mechanism that also regulates damage-induced root regeneration. Our results thus provide time-course information about the reconstruction of SCN in intact Arabidopsis roots, which highlights the stage-dependent re-patterning in response to differentiated quiescent center.
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- 2021
157. Editorial: Computational Approaches in Drug Discovery and Precision Medicine
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Xiao Jun Yao, Ruo-Xu Gu, and Zunnan Huang
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lcsh:Chemistry ,lcsh:QD1-999 ,Computer science ,Drug discovery ,molecular modeling ,precision medicine ,General Chemistry ,data mining ,Precision medicine ,artificial intelligence ,Data science ,drug discovery - Published
- 2021
158. A Software Suite for Self-Paced Learning.
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Meng Zhang, Zi Xu Gu, Amer, Adan, Sidhu, Gaganpreet, and Srinivasan, Seshasai
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FINITE element method ,PREREQUISITES (Education) ,EDUCATIONAL resources ,MATHEMATICAL physics ,PRIOR learning - Abstract
The faculty of engineering at McMaster University is very diverse with students coming from a variety of socio-economic backgrounds and nationalities. There is an expected level of prerequisite knowledge for courses in the program, especially for subjects in mathematics and physics. Yet, a significant number of students struggle to reach the same level of prior knowledge as their peers due to a lack of educational resources or due to language barriers. Entering lectures without the expected baseline understanding of the concepts increases the risk of cognitive overload because these students exert additional mental effort in retaining the pre-lecture information along with the lecture content. As a solution to this problem, we present a suite of web-based interactive programs that are accessible to the students outside the class. The Software Suite will provide supplementary material to assist with self-paced learning in a 3rd year undergraduate engineering course, i.e., Finite Element Analysis, at McMaster University's W Booth School of Engineering Practice and Technology. It will enable students design and analyze various engineering applications, namely, Spring System, Trusses, Beams, Frames, and Heat Transfer along one or two dimensions. The purpose of the interactive platform with several programs is to actively engage the students with this cognitive tool to cement their understanding of the concepts instead of passively perceiving it as a tutor or repository of information. [ABSTRACT FROM AUTHOR]
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- 2022
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159. The influence of compression on the lattice stability of α-FAPbI3 revealed by numerical simulation.
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Wang, Ryan Taoran, Xu, Alex Fan, Zhang, Weiwei, and Xu, Gu
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COMPUTER simulation ,GIBBS' free energy ,SOLAR cells ,SCIENTIFIC community - Abstract
The ambient stability of α-FAPbI
3 perovskite remains one of the biggest barriers to its commercialization, despite many attempts to enhance its lifetime. Due to the difficulties in experimentally investigating the transition kinetics, numerical simulation was performed. Surprising results were uncovered that the unstable α phase could be maintained in ambient conditions under compression, caused by the reduced Gibbs free energy of this phase. By analysing the transition rate, the detailed kinetic parameters have also been obtained, enabling us to construct a more complete phase map as a function of temperature and stress, offering a possible path towards stable high PCE perovskite solar devices, which opens an unprecedented avenue in perovskite solar cell research, and will hopefully be of intrinsic interest to the broad materials research community as well. [ABSTRACT FROM AUTHOR]- Published
- 2022
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160. Cardiovascular Dysfunction in Offspring of Ovarian-Hyperstimulated Women and Effects of Estradiol and Progesterone: A Retrospective Cohort Study and Proteomics Analysis
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Xu, Gu-Feng, Zhang, Jun-Yu, Pan, Hai-Tao, Tian, Shen, Liu, Miao-E, Yu, Tian-Tian, Li, Jing-Yi, Ying, Wei-Wen, Yao, Wei-Miao, Lin, Xian-Hua, Lv, Yuan, Su, Wen-Wen, Ye, Xiao-Qun, Zhang, Fang-Hong, Pan, Jie-Xue, Liu, Ye, Zhou, Cheng-Liang, Zhang, Dan, Liu, Xin-Mei, Zhu, Yi-Min, Sheng, Jian-Zhong, and Huang, He-Feng
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- 2014
161. Effects of Amomum villosum polysaccharide on physicochemical and in vitro digestibility properties of wheat starch
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KANG Zhimin, GENG Ningning, HE Mengying, XU Guozhen, WANG Zhiwei, and ZHANG Kangyi
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amomum villosum polysaccharide ,wheat starch ,physicochemical properties ,digestion properties ,Food processing and manufacture ,TP368-456 - Abstract
[Objective] This study aimed to explore the mechanism of action between Amomum villosum polysaccharide (AVP) and wheat starch and reveal the dose-effect relationship of AVP on the quality of wheat starch. [Methods] an AVP-wheat starch compound system with different concentrations of AVP was prepared. The effects of different concentrations of AVP on the gelatinization characteristics, rheological properties, thermodynamic properties, crystal structure and digestion characteristics of wheat starch were studied. [Results] The AVP could increase the viscosity and gelatinization temperature of the wheat starch compound system, reduce the leaching of amylose during gelatinization and the damage degree of the crystalline region during wheat starch gelatinization, and delay the gelatinization process. When the concentration of AVP was 1.00%, the disintegration value of the compound system was 299 mPa·s, the retrogradation value was 532 mPa·s, and the gelatinization enthalpy was 666.29 J/g, indicating that the anti-aging effect and the stability were the best. Fourier infrared spectrum analysis showed that there was a hydrogen bond interaction between AVP and wheat, and the bond was the strongest when the mass concentration of AVP was 1.00%. The results of in vitro simulated digestion showed that AVP could inhibit the digestion of wheat starch. [Conclusion] Adding AVP can effectively improve the thermal stability of wheat starch and reduce the digestibility of wheat starch.
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- 2024
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162. Inhibitory effect of aqueous extract of Scrophularia ningpoensis on β-cell pyroptosis in diabetic mice
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Xu Guo, Yanguo Gao, Xiaohan Li, Shiqi Chen, Jun Zhou, Wei Lu, Xiangxiang Fu, Qin Xiang, Yu Zhang, Yonghong Zhang, Qibin Wang, Li Chen, and Tao Zheng
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Scrophularia ningpoensis Hemsl. ,Diabetes ,β-cells ,Pyroptosis ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Scrophularia ningpoensis Hemsl. (SN) is an herbal medicine used as a functional food in China. SN has traditionally been used to treat diabetes mellitus (DM), but its mechanism of action is not well understood. Our previous study indicated that the aqueous extract of SN can reduce hepatic insulin resistance and correct the irregular shape of pancreatic islets in diabetic mice. This study aims to investigate whether the aqueous extract of SN can regulate pyroptosis in pancreatic β-cells and explore its underlying mechanisms. Db/db mice were orally given an aqueous extract of SN for eight weeks. Subsequently, their pancreatic tissues were collected for histopathological analysis and immunoblotting. Rat insulinoma (INS-1) cells were cultured either alone or with the aqueous extract of SN and evaluated for cell viability, pyroptotic body formation, AMP-activated protein kinase (AMPK) activity, the NACHT, LRR, and PYD domain-containing protein 3 (NLRP3) inflammasome and gasdermin D (GSDMD) activation, and reactive oxygen species (ROS) production under high glucose (HG) exposure conditions. The aqueous extract of SN reduced insulitis and pancreatic β-cell death in db/db mice. Increased AMPK phosphorylation and decreased NLRP3 inflammasome and GSDMD activation were observed in pancreatic tissues after administration of the aqueous extract of SN. In vitro, the aqueous extract of SN increased cell viability and AMPK phosphorylation in a concentration-dependent manner. Additionally, the aqueous extract of SN corrected excessive ROS generation, NLRP3 inflammasome and GSDMD activation, and pyroptotic body formation. Inhibition of AMPK negated these beneficial effects of the aqueous extract of SN on INS-1 cells. The study concluded that the aqueous extract of SN alleviates β-cell pyroptosis by inhibiting NLRP3/GSDMD activation in an AMPK-dependent manner.
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- 2024
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163. Peptides derived from growth factors: Exploring their diverse impact from antimicrobial properties to neuroprotection
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Zhang Hai-na, Jiang Jun-jie, and Xu Guang-meng
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Growth factors ,Peptides derived from growth factors ,Immune modulation ,Antimicrobial effects ,Anticancer effects ,Neuroprotective ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Growth factor-derived peptides are bioactive molecules that play a crucial role in various physiological processes within the human body. Over the years, extensive research has revealed their diverse applications, ranging from antimicrobial properties to their potential in neuroprotection and treating various diseases. These peptides exhibit innate immune responses and have been found to possess potent antimicrobial properties against a wide range of pathogens. Growth factor-derived peptides have demonstrated the ability to promote neuronal survival, prevent cell death, and stimulate neural regeneration. As a result, they hold immense promise in the treatment of various neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis, as well as in the management of traumatic brain injuries. Moreover, growth factor-derived peptides have shown potential for supporting tissue repair and wound healing processes. By enhancing cell proliferation and migration, these peptides contribute to the regeneration of damaged tissues and promote a more efficient healing response. The applications of growth factor-derived peptides extend beyond their therapeutic potential in health; they also have a role in various disease conditions. For example, researchers have explored their influence on cancer cells, where some peptides have demonstrated anti-cancer properties, inhibiting tumor growth and promoting apoptosis in cancer cells. Additionally, their immunomodulatory properties have been investigated for potential applications in autoimmune disorders. Despite the immense promise shown by growth factor-derived peptides, some challenges need to be addressed. Nevertheless, ongoing research and advancements in biotechnology offer promising avenues to overcome these obstacles. The review summarizes the foundational biology of growth factors and the intricate signaling pathways in various physiological processes as well as diseases such as cancer, neurodegenerative disorders, cardiovascular ailments, and metabolic syndromes.
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- 2024
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164. Moisture-Stable FAPbI3 Perovskite Achieved by Atomic Structure Negotiation
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Wang, Ryan Taoran, primary, Xu, Alex Fan, additional, Li, Wuqi, additional, Li, Yuning, additional, and Xu, Gu, additional
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- 2021
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165. Effect of shock wave processing on the properties of ZnS and ZnS-based phosphors
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Bakhmetyev, V. V., Ogurtsov, K. A., Sychov, M. M., Kotomin, A. A., Dushenok, S. A., Kozlov, A. S., and Xu, Gu
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- 2012
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166. Effect of shock-wave treatment of zinc sulfide on properties of ZnS:Cu,Mn phosphor
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Bakhmet’ev, V. V., Ogurtsov, K. A., Sychov, M. M., Kotomin, A. A., Dushenok, S. A., Kozlov, A. S., and Xu, Gu
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- 2012
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167. Early Analysis and Detection of Compressed Traffic
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Xu Gu, Jiujin Wang, and Xiangzhan Yu
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Matching (graph theory) ,Computer science ,Packet analyzer ,String (computer science) ,Data_CODINGANDINFORMATIONTHEORY ,Filter (signal processing) ,String searching algorithm ,Regular expression ,Algorithm ,Blossom algorithm ,Data transmission - Abstract
The amount of compressed data in network traffic is gradually increasing. Such traffic effectively reduces the transmission time and improves the data transmission efficiency in the network, but it poses a challenge to the existing network traffic identification mechanism. At present, the identification method used for the compression traffic is often used to recover the complete compressed data for content identification. However, this method takes a lot of time to restore the complete compressed data and subsequent content matching.This paper analyzes the specific compressed data format (gz, zip) and proposes an algorithm for decompressing compressed file fragments: decompresses the compressed file fragments and restores some of the original data. Because only the fragments of the compressed file need to be restored, the algorithm effectively improves the efficiency of network data restoration. The structure of regular expression and the string matching algorithm based on suffix search are studied. According to the distribution of target data in the actual traffic monitoring system, a regular expression matching algorithm based on preprocessing is proposed: extract the exact string of the regular expression, use the exact string as the pattern string to filter the suspicious data in the data using the suffix-based string matching algorithm, and then use the regular expression for matching verification. As a result of filtering many unrelated data during the process of searching for suspicious data, the efficiency of the algorithm is improved. In the end, the paper designs a packet capture system, which compresses compressed traffic transmitted through partial recombination of FTP and HTTP protocols, combines compressed file fragment decompression algorithm with preprocessed regular expression matching method, and realizes early detection and identification of compressed traffic.In summary, this paper proposes and implements an early analysis and detection system for compressed flow, which plays a certain role in the identification and detection of compressed data traffic.
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- 2020
168. High electron mobility triazine for lower driving voltage and higher efficiency organic light emitting devices
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Klenkler, Richard A., Aziz, Hany, Tran, An, Popovic, Zoran D., and Xu, Gu
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- 2008
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169. Electronic structure and spin–orbit coupling in ternary transition metal chalcogenides Cu2TlX 2 (X = Se, Te)
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Yulin Chen, Qinqin Zhang, Yan-Feng Chen, Yang-Yang Lv, Lexian Yang, Lu Kang, Na Qin, Zhongxu Yin, Zhongkai Liu, Shu-Hua Yao, Xu Gu, Xian Du, Jingsong Zhou, Wenxuan Zhao, Runzhe Xu, and Yidian Li
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Materials science ,Condensed matter physics ,Transition metal ,General Physics and Astronomy ,Electronic structure ,Spin–orbit interaction ,Ternary operation - Abstract
Ternary transition metal chalcogenides provide a rich platform to search and study intriguing electronic properties. Using angle-resolved photoemission spectroscopy and ab initio calculation, we investigate the electronic structure of Cu2TlX 2 (X = Se, Te), ternary transition metal chalcogenides with quasi-two-dimensional crystal structure. The band dispersions near the Fermi level are mainly contributed by the Te/Se p orbitals. According to our ab-initio calculation, the electronic structure changes from a semiconductor with indirect band gap in Cu2TlSe2 to a semimetal in Cu2TlTe2, suggesting a band-gap tunability with the composition of Se and Te. By comparing ARPES experimental data with the calculated results, we identify strong modulation of the band structure by spin–orbit coupling in the compounds. Our results provide a ternary platform to study and engineer the electronic properties of transition metal chalcogenides related to large spin–orbit coupling.
- Published
- 2022
170. Defect-engineering of Zr(IV)-based metal-organic frameworks for regulating CO2 photoreduction
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Xiao-Yao Dao, Xinzhu Wang, Wei-Yin Sun, Xiao-Mei Cheng, Xu Gu, Jing Ma, Xiao-Yu Zhang, and Shi-Qing Wang
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Materials science ,General Chemical Engineering ,Energy transfer ,Defect engineering ,Quantum yield ,General Chemistry ,Redox ,Industrial and Manufacturing Engineering ,Chemical engineering ,Yield (chemistry) ,Elementary reaction ,Photocatalysis ,Environmental Chemistry ,Metal-organic framework - Abstract
Defects in MOFs can benefit light absorption and charge transfer for photocatalytic application, nevertheless, studies on interplay between structural defects and photocatalytic properties of MOFs are in infancy. Herein, a series of UiO-66-NH2 with different kinds of defects were created for regulating CO2 photocatalytic reduction. Theoretical calculations in combination with experimental data verified that the sample with ligand-vacant (UiO-66-NH2-LV) defect performed better than non-defect, missing-cluster and monocarboxylate compensated ones in the photocatalytic CO2 reduction reactions. UiO-66-NH2-LV shows superior photocatalytic activity with the highest CO yield of 30.5 μmol g−1h−1, which is 9.2 times higher than that of the sample with missing-cluster (UiO-66-NH2-MC), as well as the highest quantum yield (QY) of 0.90%. DFT calculations further demonstrate the correlation between discriminative photocatalytic activities in defect structures and tunable electronic properties characterized by absorption energy, Eabs, and charge transfer energy, ELMCT, in the photocatalytic process. The ligand-vacant defect with the lowest sum of Eabs and ELMCT will lower photocatalytic reaction energy barrier in the rate-limiting step among the elementary reaction step during CO2 photoreduction. The insights gained from this study will guide the MOFs defect-engineering for enhancing CO2 photocatalytic capacity.
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- 2022
171. Temperature dependence of photoluminescence efficiency in doped and blended organic thin films
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Luo, Yichun, Aziz, Hany, Klenkler, Richard, Xu, Gu, and Popovic, Zoran D.
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- 2008
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172. Meta-analysis of the correlation between high expression of lncRNA NEAT1 in rectal cancer and pathological features and prognosis
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Lin Qiyi, Pan Jianpeng, Wang Huaishuai, Li Yinlin, Zhuang Yixiang, Cai Zhicong, Lin Gaofeng, Liu Weibo, and Xu Guoxi
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lncrna neat1 ,prognosis ,rectal cancer ,meta analysis ,Biochemistry ,QD415-436 - Abstract
Background: To systematically evaluate the relationship between the expression level of long noncoding RNA NEAT1 and the clinical characteristics and prognostic value of rectal cancer patients. Methods: PubMed, EMBASE, Cochrane library database and case-control studies on the correlation between abnormal expression of lncRNA NEAT1 and prognosis of rectal cancer patients published by the American clinical trials registry before May 1, 2023 were searched. The search time was from the establishment of the database to May 30, 2023. Results: A total of 7 case-control studies were included, including 1063 cancer patients. The results of meta-analysis showed that the high expression of lncRNA NEAT1 was significantly correlated with the degree of differentiation [or=0.45, 95%CI=0.32-0.63, P
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- 2024
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173. Annual Report 2023
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Xu Guo
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Chemical engineering ,TP155-156 ,Biotechnology ,TP248.13-248.65 ,Medical technology ,R855-855.5 - Published
- 2024
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174. Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types
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Zehui Feng, Fan Peng, Fanfan Xie, Yang Liu, Huanqin Zhang, Jing Ma, Jinliang Xing, and Xu Guo
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DNBSEQ-T7 ,NovaSeq 6000 ,Sequencing platform ,Capture-Based mtDNA Sequencing ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Mitochondrial genome abnormalities can lead to mitochondrial dysfunction, which in turn affects cellular biology and is closely associated with the development of various diseases. The demand for mitochondrial DNA (mtDNA) sequencing has been increasing, and Illumina and MGI are two commonly used sequencing platforms for capture-based mtDNA sequencing. However, there is currently no systematic comparison of mtDNA sequencing performance between these two platforms. To address this gap, we compared the performance of capture-based mtDNA sequencing between Illumina's NovaSeq 6000 and MGI's DNBSEQ-T7 using tissue, peripheral blood mononuclear cell (PBMC), formalin-fixed paraffin-embedded (FFPE) tissue, plasma, and urine samples. Results Our analysis indicated a high degree of consistency between the two platforms in terms of sequencing quality, GC content, and coverage. In terms of data output, DNBSEQ-T7 showed higher rates of clean data and duplication compared to NovaSeq 6000. Conversely, the amount of mtDNA data obtained by per gigabyte sequencing data was significantly lower in DNBSEQ-T7 compared to NovaSeq 6000. In terms of detection mtDNA copy number, both platforms exhibited good consistency in all sample types. When it comes to detection of mtDNA mutations in tissue, FFPE, and PBMC samples, the two platforms also showed good consistency. However, when detecting mtDNA mutations in plasma and urine samples, significant differenceof themutation number detected was observed between the two platforms. For mtDNA sequencing of plasma and urine samples, a wider range of DNA fragment size distribution was found in NovaSeq 6000 when compared to DNBSEQ-T7. Additionally, two platforms exhibited different characteristics of mtDNA fragment end preference. Conclusions In summary, the two platforms generally showed good consistency in capture-based mtDNA sequencing. However, it is necessary to consider the data preferences generated by two sequencing platforms when plasma and urine samples were analyzed.
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- 2024
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175. Clinical study on the necessity and feasibility of routine MRCP in patients with cholecystolithiasis before LC
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Xu Guo, Qing Fan, Yiman Guo, Xinming Li, Jili Hu, Zhuoyin Wang, Jing Wang, Kai Li, Nengwei Zhang, Buhe Amin, and Bin Zhu
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Cholecystolithiasis ,Magnetic resonance cholangiopancreatography (MRCP) ,Laparoscopic cholecystectomy (LC) ,Preoperative routine MRCP ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Abstract Background In the past quite a long time, intraoperative cholangiography(IOC)was necessary during laparoscopic cholecystectomy (LC). Now magnetic resonance cholangiopancreatography (MRCP) is the main method for diagnosing common bile duct stones (CBDS). Whether MRCP can replace IOC as routine examination before LC is still inconclusive. The aim of this study was to analyze the clinical data of patients undergoing LC for cholecystolithiasis, and to explore the necessity and feasibility of preoperative routine MRCP in patients with cholecystolithiasis. Methods According to whether MRCP was performed before operation, 184 patients undergoing LC for cholecystolithiasis in the Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University from January 1, 2017 to December 31, 2018 were divided into non-MRCP group and MRCP group for this retrospective study. The results of preoperative laboratory test, abdominal ultrasound and MRCP, biliary related comorbidities, surgical complications, hospital stay and hospitalization expenses were compared between the two groups. Results Among the 184 patients, there were 83 patients in non-MRCP group and 101 patients in MRCP group. In MRCP group, the detection rates of cholecystolithiasis combined with CBDS and common bile duct dilatation by MRCP were higher than those by abdominal ultrasound (P 0.05), but there was significant difference in hospitalization expenses (P 0.05). Conclusions The preoperative MRCP can detect CBDS, cystic duct stones and anatomical variants of biliary tract that cannot be diagnosed by abdominal ultrasound, which is helpful to plan the surgical methods and reduce the surgical complications. From the perspective of health economics, routine MRCP in patients with cholecystolithiasis before LC does not increase hospitalization costs, and is necessary and feasible.
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- 2024
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176. Optimal analgesic regimen for total shoulder arthroplasty: a randomized controlled trial and network meta-analysis
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Shiye Li, Wenjie Chen, Liang’en Feng, and Xu Guo
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Total shoulder replacement ,Liposomal bupivacaine ,Local infiltration analgesia ,Single-shot interscalene block ,Continuous interscalene block ,Network meta-analysis ,Orthopedic surgery ,RD701-811 ,Diseases of the musculoskeletal system ,RC925-935 - Abstract
Abstract Objective Clinical approaches to analgesia following total shoulder arthroplasty include liposomal bupivacaine, local infiltration analgesia, single-shot interscalene block, and continuous interscalene block. However, the best method remains contentious. This study conducts a network meta-analysis comparing these four methods, aiming to identify the most effective analgesic approach. Methods Randomized controlled trials on analgesic regimens for total shoulder arthroplasty were identified through searches of PUBMED, Cochrane Central Register of Controlled Trials, EMBASE, Web of Science, and Scopus databases, covering their inception through November 2023. Network meta-analysis was performed using STATA 15.1, and the Cochrane Handbook version 5.1.0 risk of bias tool was employed for quality assessment of the literature. Results Twelve randomized controlled trials were included, comprising 1537 patients undergoing total shoulder arthroplasty. The interventions compared were ssISB, cISB, LIA, and LB. Regarding the quality of the literature, four studies were deemed low risk, one high risk, and seven moderate risk. The network meta-analysis revealed that in terms of VAS scores in the PACU, the ssISB group was the most effective, followed by cISB and LB, with LIA being the least effective. This pattern continued in VAS scores on the first and second postoperative days. Regarding morphine consumption, the cISB group showed the most significant reduction in the PACU and on the first postoperative day, while the LIA group performed best in total postoperative morphine consumption. The shortest average hospital stay was noted in the cISB group. Conclusion The ssISB method excels in controlling early postoperative pain, particularly during the PACU stage and early postoperative period. Additionally, the cISB method is notable for reducing postoperative morphine consumption and shortening average hospital stays. While the LIA method ranks first in reducing total morphine consumption, it is weaker in pain control. The LB method is underwhelming across most assessment parameters. These findings underscore the importance of selecting appropriate analgesic strategies for different postoperative recovery phases and provide valuable insights for clinicians to optimize postoperative pain management. Furthermore, they suggest a need for future research to explore the specific application and effectiveness of these methods in varying clinical contexts.
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- 2024
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177. Identification of potential antioxidant peptides from protein hydrolysates of pearl oil apricot almonds: Combination of in vitro and molecular docking studies
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Mo Chen, Xu Guo, Ning‐yang Li, Ying‐ying Chen, Paula Garcia‐Oliveira, Jin‐yue Sun, Miguel A. Prieto, Qing‐lin Niu, and Chao Liu
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antioxidant peptide ,identification ,Keap1–Nrf2 interaction ,molecular docking ,pearl oil apricot almond ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
Abstract Pearl oil apricot almonds are rich in proteins, being a valuable raw material for preparing antioxidant peptides. In this study, almond protein hydrolysates (APHs) were obtained by enzymatic hydrolysis and divided into APHs‐1 (10 kDa). APHs‐1‐c, purified from APHs‐1, was proved to show the strongest antioxidant effect through activity tracking experiments. APHs‐1‐c also can protect HepG2 cells against oxidative damage by reducing intracellular reactive oxygen species and MDA levels, elevating glutathione levels as well as increasing superoxide dismutase and catalase activities, and its protective effect is related to the Keap1–Nrf2 signaling pathway. Forty bioactive peptide sequences were identified from APHs‐1‐c, and Thr‐Glu‐Asp‐Asp‐Trp‐Arg‐Trp‐His (TEDDWRWH; P1), Trp‐Tyr‐Asp‐Asn‐Glu‐Trp‐Gly‐Tyr‐Arg (WYDNEWGYR; P2), and Ala‐Glu‐Asp‐His‐Glu‐Trp‐Trp‐Arg (AEDHEWWWR; P3) had the most potential for antioxidant activity by molecular docking studies. P1, P2, and P3 showed desirable 1,1‐diphenyl‐2‐picrylhydrazyl radical scavenging activity (IC50 = 0.634–3.381 mmol/L), 2,2′‐azino‐bis (3‐ethylbenzothiazoline‐6‐sulfonic acid) diammonium salt radical scavenging activity (IC50 = 0.221–0.309 mmol/L), and ferric‐reducing antioxidant power. These results suggested that almonds protein hydrolysates and its derived antioxidant peptides could serve as potential ingredients applied in functional foods.
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- 2024
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178. Bridging Interpretability and Performance: Enhanced Machine Learning-Based Prediction of Hematoma Expansion Post-Stroke via Comprehensive Feature Selection
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Beigeng Zhao, Rui Song, Xu Guo, and Lizhi Yu
- Subjects
Hematoma expansion ,post-stroke ,machine learning ,feature selection ,model interpretability ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
Monitoring and controlling the occurrence of hematoma expansion events after a stroke is a primary clinical focus. The introduction of machine learning (ML) techniques offers intelligent decision support for physicians in this domain. However, for doctors without an ML background, the behavior of a hematoma expansion predictor seems opaque, similar to a “black box.” Moreover, the vast and diverse set of features typically present in medical data acts as a double-edged sword: while encapsulating rich information with potential value, it also includes redundant details that offer little to predictive utility. Comprehensive feature selection is crucial, but many current state-of-the-art hematoma expansion prediction studies based on ML often overlook this step. In this paper, we propose a methodology tailored for comprehensive feature selection across diverse and abundant medical data features and rigorously evaluate ML models. Through experiments on a real-world post-stroke hematoma expansion prediction dataset, we demonstrate the efficacy of our approach in enhancing the performance of ML predictors. Visualization of the associated feature selection process and results further bolsters physicians’ understanding of the model’s decision-making basis, thereby strengthening its interpretability.
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- 2024
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179. Metallic micronutrients are associated with the structure and function of the soil microbiome
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Zhongmin Dai, Xu Guo, Jiahui Lin, Xiu Wang, Dan He, Rujiong Zeng, Jun Meng, Jipeng Luo, Manuel Delgado-Baquerizo, Eduardo Moreno-Jiménez, Philip C. Brookes, and Jianming Xu
- Subjects
Science - Abstract
Abstract The relationship between metallic micronutrients and soil microorganisms, and thereby soil functioning, has been little explored. Here, we investigate the relationship between metallic micronutrients (Fe, Mn, Cu, Zn, Mo and Ni) and the abundance, diversity and function of soil microbiomes. In a survey across 180 sites in China, covering a wide range of soil conditions the structure and function of the soil microbiome are highly correlated with metallic micronutrients, especially Fe, followed by Mn, Cu and Zn. These results are robust to controlling for soil pH, which is often reported as the most important predictor of the soil microbiome. An incubation experiment with Fe and Zn additions for five different soil types also shows that increased micronutrient concentration affects microbial community composition and functional genes. In addition, structural equation models indicate that micronutrients positively contribute to the ecosystem productivity, both directly (micronutrient availability to plants) and, to a lesser extent, indirectly (via affecting the microbiome). Our findings highlight the importance of micronutrients in explaining soil microbiome structure and ecosystem functioning.
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- 2023
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180. Computing Power Service System of China and Its Development Path
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Chen Xiaohong, Xu Guanying, Xu Xuesong, Tian Zhiping, Huo Yangjie, and Yi Guodong
- Subjects
computing power service ,system construction ,top-level design ,construction path ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Computing power services are a key factor for strengthening the digital capabilities and core competitiveness of China. In the context of the Digital China initiative, the computing power service system of China needs to adapt to the computing power demands of different fields, levels, and scenarios, and the reasonable allocation and efficient utilization of computing resources should be realized, thereby guiding the development and innovation of the digital economy. Based on a global perspective and China’s current situation, this study clarifies the implications of computing power services and analyzes the problems regarding the development of China’s computing power services, including prominent contradictions between supply and demand, uneven distribution of basic computing resources, lack of circulation channels for resources, non-unified technical service standards. An overall architecture for the construction of China’s computing power service system is proposed from the aspects of computing power service form basis, evolution model, and top-level design, and key strategies and development paths are explored. Furthermore, the following suggestions are proposed: (1) strengthening top-level design of computing power to promote the integrated development of computing networks; (2) optimizing computing power resource layout while lowering the threshold for using computing power; (3) building computing power sharing platforms to revitalize social computing values; (4) improving computing power utilization mechanisms and establishing computing power leasing systems; and (5) stimulating potentials in scientific and technological research by exploiting computing power talent advantages.
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- 2023
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181. VELOCITY MEASUREMENT OF SIMULATED CONTINUOUS CASTING MOULD BY LORENTZ FORCE VELOCIMETRY
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Anmin Li, Chang Wang, Zhang Min, Xu Guodong, Guo Shengrong, and Wang Xiaodong
- Subjects
molten metal ,continuous casting ,flow measurement ,electromagnetic induction ,lorentz force velocimetry ,ultrasonic doppler velocimetry ,Clay industries. Ceramics. Glass ,TP785-869 - Abstract
The real-time monitoring of the molten steel flow in a mould during continuous casting holds significant importance in enhancing a product`s quality. The variation in the meniscus velocity of molten steel during actual production directly correlates with numerous critical defects in continuous casting products. Consequently, monitoring the speed, flow direction, and meniscus velocity variation becomes crucial to adjusting the process parameters and ensuring product quality control. This study utilises the open flow test section of a liquid metal loop platform to simulate the flow field of a mould`s liquid level. The investigation focuses on assessing the accuracy and reliability of Lorentz force velocimetry (LFV) to measure the liquid metal velocity. The electromagnetic sensitive area of LFV is explored through numerical simulation, and multiple sets of measurement experiments are conducted under various flow conditions. The study examines the influence of the measurement position and flow structure on the magnetic field action area and measurement results of LFV. To validate the velocity measurements obtained in this area, Ultrasonic Doppler Velocimetry (UDV) is employed for comparison and verification. The results demonstrate that LFV can accurately measure the horizontal velocity component within a depth range of 0 to 4 mm near the surface of the open flow. The relative error compared to UDV remains below 8%, and the fixed-point measurement can be sustained for over 20 minutes. These findings affirm the reliability and industrial applicability of LFV in measuring the horizontal velocity component near the surface of molten metal.
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- 2023
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182. Effect of high temperature on interfacial microstructure and properties of Ti/Al composite plate
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ZHANG Tao, XU Jiujian, LI Yong, CAO Furong, and XU Guangming
- Subjects
casting and rolling process ,ti/al clad sheet ,high temperature annealing ,interfacial bond strength ,intermetallic compound ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
The effects of high temperature annealing on the interface microstructure and mechanical properties of cast-rolled Ti/Al composite plates were investigated by means of SEM, EBSD, XRD, microhardness, tensile test at room temperature and T-shaped peeling test, etc. The results show that the microstructure of Ti matrix hardly changes during annealing at 550 ℃, while the Al matrix recrystallizes and begins to grow after annealing for 1 h. During the annealing process, the diffusion layer at the interface gradually thickens, and the second phase TiAl3 is generated at 15 min, and the second phase TiAl3 is connected into flakes at 1 h, and the bonding strength of the Ti/Al composite plate interface is decreased rapidly. The bonding strength of Ti/Al composite plate reaches the maximum value of 23.6 N/mm after annealing for 30 min. At 1 h annealing, the tensile strength and elongation of the cast-rolled Ti/Al composite plate reach the peak values of 236 MPa and 27.6%, respectively, which are higher than those of the cast-rolled Ti/Al composite plate.
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- 2023
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183. Annual Report 2023
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Hongyue Jin and Xu Guo
- Subjects
Energy industries. Energy policy. Fuel trade ,HD9502-9502.5 ,Energy conservation ,TJ163.26-163.5 ,Renewable energy sources ,TJ807-830 ,Environmental technology. Sanitary engineering ,TD1-1066 - Published
- 2023
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184. New Awareness of the Interplay Between the Gut Microbiota and Circadian Rhythms
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Pang Xiaoxiao, Chen Long, and Xu Guoxin
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circadian rhythm ,the gut microbiota ,metabolism ,gut-brain-microbiota interaction ,fecal microbiota transplantation ,Genetics ,QH426-470 ,Microbiology ,QR1-502 - Abstract
Circadian rhythms influence various aspects of the biology and physiology of the host, such as food intake and sleep/wake cycles. In recent years, an increasing amount of genetic and epidemiological data has shown that the light/dark cycle is the main cue that regulates circadian rhythms. Other factors, including sleep/wake cycles and food intake, have necessary effects on the composition and rhythms of the gut microbiota. Interestingly, the gut microbiota can affect the circadian rhythm of hosts in turn through contact-dependent and contact-independent mechanisms. Furthermore, the gut microbiota has been shown to regulate the sleep/wake cycles through gut-brain-microbiota interaction. In addition to diabetes, the gut microbiota can also intervene in the progression of neuro- degenerative diseases through the gut-brain-microbiota interaction, and also in other diseases such as hypertension and rheumatoid arthritis, where it is thought to have a spare therapeutic potential. Even though fecal microbiota transplantation has good potential for treating many diseases, the risk of spreading intestinal pathogens should not be ignored.
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- 2023
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185. The nutritional and bio‐active constituents, functional activities, and industrial applications of cashew (Anacardium occidentale): A review
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Ying‐Ying Chen, Ning‐yang Li, Xu Guo, Hai‐jie Huang, P. Garcia‐Oliveira, Jin‐yue Sun, Jian‐dong Zhang, M. A. Prieto, Zhi‐qing Guo, and Chao Liu
- Subjects
Anacardium occidentale ,applications ,bioactive compounds ,bioactivities ,cashew nut ,Nutrition. Foods and food supply ,TX341-641 ,Food processing and manufacture ,TP368-456 - Abstract
Abstract Cashew nut is a globally popular nut not only for its delicious and crunchy flavor but also for bioactive compounds, which present positive benefits to human health. Different parts of cashew have characteristic compounds. The kernel of cashew nut is rich in fatty acids, the testa is rich in polyphenols, cashew apple is rich in polyphenols and carotenoids, and phenols with aliphatic long chain are present in the cashew nutshell liquid. Therefore, the edible part of cashew possesses a wide range of bioactive compounds, with reported biological properties, including anti‐tumor, brain health, cardiovascular and cerebrovascular protection, anti‐diabetic, gastroprotection, pathophysiological disorders protection, and antioxidant. On the other hand, the inedible part of cashew, the cashew nutshell liquid, could play an important role in the industry as surface coatings, insulating formulations and so on. Hence, there are considerable demands to increase the added value of cashew, thereby exploring greater economic value. Thus, this review summarizes nutrients, bioactive compounds, biological functions, and applications of Anacardium occidentale to provide a theoretical basis and inspiration for further in‐depth studies and utilization.
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- 2023
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186. Optimal control method of frequency in diesel generator based islanded microgrid
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HONG Haohao, WANG Chen, XU Guangfu, HOU Wei, LOU Guannan, and WU Renze
- Subjects
islanded microgrid ,diesel generator (dg) ,droop control ,inertial control ,frequency response ,stability analysis ,Applications of electric power ,TK4001-4102 - Abstract
In order to solve the problems such as significant frequency fluctuation and slow dynamic response under load disturbance in islanded microgrid which has a diesel generator (DG) as the primary source, an auxiliary frequency regulation method is proposed to improve the dynamic response process of the system. Firstly, the model of diesel generator system is established to analyze the impact on transient state due to main parameters, including inertia and response delay. Secondly, the energy storage system (ESS) with auxiliary frequency regulation based on droop control is proposed, and the engineering parameter and ESS′s power margin design method are given. In addition, a small signal model of the DG-ESS system is established to prove the stability of the system. Finally, the experimental platform of DG-ESS microgrid is built, and the results verify that the proposed control strategy effectively reduces the transient frequency fluctuation under the change of static or motor load.
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- 2023
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187. Research Progress on Generative Adversarial Network in Cross-modal Medical Image Reconstruction
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LI Zhuoyuan, XU Guohao, WANG Junchen, WANG Saishuo, WANG Chuantao, and ZHAI Jiliang
- Subjects
cross-modal reconstruction ,radiological images ,generative adversarial network ,Medicine - Abstract
Single-modal medical images contain limited disease-specific information. To analyze and diagnose patients, clinicians often need to integrate multiple modal images. However, due to limited medical resources and treatment time, it may be difficult to obtain multi-modal images. Cross-modal image reconstruction can generate medical images for clinical needs, thus assisting clinicians in accurately diagnosing and treating diseases. Traditional cross-modal reconstruction techniques have been applied in some clinical scenarios, but the quality of the reconstructed images needs further improvement. Generative adversarial network (GAN) can recover high-quality and complete image data from low-quality or incomplete medical image data, maximally savings medical equipment resources and accelerating medical treatment speed. This article summarizes the applications of GAN technology in cross-modal image reconstruction across X-ray imaging, computed tomography imaging, magnetic resonance imaging, and positron emission tomography imaging, to provide reference for the development of more advanced cross-modal reconstruction techniques.
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- 2023
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188. Development of planarizing spin-on carbon material for high-temperature processes
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Huang, Runhui, primary, Zhong, Xing-Fu, additional, Koza, Jakub, additional, Xu, Gu, additional, Zhang, Boyu, additional, and Simmons, Sean, additional
- Published
- 2021
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189. Identification of Sub-Synchronous Oscillation Mode Based on HO-VMD and SVD-Regularized TLS-Prony Methods
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Yuzhe Chen, Feng Wu, Linjun Shi, Yang Li, Peng Qi, and Xu Guo
- Subjects
sub-synchronous oscillations (SSOs) ,hippopotamus optimization (HO) ,variational mode decomposition (VMD) ,singular value decomposition (SVD) ,regularized total least squares (RTLS) ,energy ratio ,Technology - Abstract
To reduce errors in sub-synchronous oscillation (SSO) modal identification and improve the accuracy and noise resistance of the traditional Prony algorithm, this paper focuses on SSOs caused by the integration of doubly fed induction generators (DFIGs) with series compensation into the grid. A novel SSO modal identification method based on the hippopotamus optimization–variational mode decomposition (HO-VMD) and singular value decomposition–regularized total least squares–Prony (SVD-RTLS-Prony) algorithms is proposed. First, the energy ratio function is used for real-time monitoring of the system to identify oscillation signals. Then, to address the limitations of the VMD algorithm, the HO algorithm’s excellent optimization capabilities were utilized to improve the VMD algorithm, leading to preliminary denoising. Finally, the SVD-RTLS-improved Prony algorithm was employed to further suppress noise interference and extract oscillation characteristics, allowing for the accurate identification of SSO modes. The performance of the proposed method was evaluated using theoretical and practical models on the Matlab and PSCAD simulation platforms. The results indicate that the algorithms effectively perform denoising and accurately identify the characteristics of SSO signals, confirming its effectiveness, accuracy, superiority, and robustness against interference.
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- 2024
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190. Impact of Phase Angle Jump on a Doubly Fed Induction Generator under Low-Voltage Ride-Through Based on Transfer Function Decomposition
- Author
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Peiru Feng, Jiayin Xu, Zhuang Wang, Shenghu Li, Yuming Shen, and Xu Gui
- Subjects
voltage drop ,phase angle jump ,doubly fed induction generator (DFIG) ,transfer function ,Schur decomposition ,low-voltage ride-through (LVRT) ,Technology - Abstract
During the fault period, a phase angle jump may occur at the stator or the point of common coupling, which will deteriorate the low-voltage ride-through (LVRT) characteristics of a doubly fed induction generator (DFIG). The existing LVRT studies focus on the impact of a voltage drop on DFIGs but often ignore that of a phase angle jump. The time-domain simulation is accurate in describing the response of a DFIG during the LVRT process, but it is time-consuming for a DFIG with the full-order model. In this paper, by using the voltage magnitude and phase angle of the stator or the point of common coupling as the inputs, and the state variables as the outputs, the transfer function of a DFIG is derived to analyze its response and find the LVRT measures against the voltage drop and, especially, the phase angle jump. Firstly, the differential-algebraic equations of the DFIG are linearized to propose their transfer function model. Secondly, considering its high-order characteristic, a model reduction method for the transfer function of the DFIG using the Schur decomposition is proposed, and the analytical expression of the output variables of the DFIG with the phase angle jump is derived by the inverse Laplace transformation to judge the necessity of the LVRT measures. Finally, the simulation results of the DFIG are provided to verify the accuracy of the transfer function model and its reduced-order form and validate the feasibility of the LVRT against the phase angle jump with the proposed models.
- Published
- 2024
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191. Global Analysis of Natural Products Biosynthetic Diversity Encoded in Fungal Genomes
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Shu Zhang, Guohui Shi, Xinran Xu, Xu Guo, Sijia Li, Zhiyuan Li, Qi Wu, and Wen-Bing Yin
- Subjects
fungi ,gene cluster families ,biosynthetic potential ,biosynthetic diversity ,natural products ,Biology (General) ,QH301-705.5 - Abstract
Fungal secondary metabolites (SMs) represent an invaluable source of therapeutic drugs. Genomics-based approaches to SM discovery have revealed a vast and largely untapped biosynthetic potential within fungal genomes. Here, we used the publicly available fungal genome sequences from the NCBI public database, as well as tools such as antiSMASH, BIG-SLiCE, etc., to analyze a total of 11,598 fungal genomes, identifying 293,926 biosynthetic gene clusters (BGCs), which were subsequently categorized into 26,825 gene cluster families (GCFs). It was discovered that only a tiny fraction, less than 1%, of these GCFs could be mapped to known natural products (NPs). Some GCFs that only contain a single BGC internally are crucial for the biodiversity of fungal biosynthesis. Evident patterns emerged from our analysis, revealing popular taxa as prominent sources of both actual and potential biosynthetic diversity. Our study also suggests that the genus rank distribution of GCF is generally consistent with NP diversity. It is noteworthy that genera Xylaria, Hypoxylon, Colletotrichum, Diaporthe, Nemania, and Calonectria appear to possess a higher potential for SM synthesis. In addition, 7213 BGCs match possible known compound structures, and homologous gene clusters of well-known drugs can be located in different genera, facilitating the development of derivatives that share structural similarity to these drugs and may potentially possess similar biological activity. Our study demonstrated the various types of fungi with mining potential, assisting researchers in prioritizing their research efforts and avoiding duplicate mining of known resources to further explore fungal NP producers.
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- 2024
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192. The Value of Small Dense Low-Density Lipoprotein Cholesterol in Predicting the Risk and Severity of Coronary Heart Disease in Patients with Type 2 Diabetes Mellitus
- Author
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Juan Huang, Jun-Xu Gu, Hui-Zhang Bao, Shan-Shan Li, Xiao-Qin Yao, Ming Yang, Yang Li, Ai-Min Zhang, Yue Yin, Na Zhang, and Mei Jia
- Abstract
Background: Elevated small density low – density lipoprotein cholesterol (sdLDL-C) particles are hallmarks of atherogenic dyslipidemia in patients with type 2 diabetes mellitus (T2DM), which is hypothesized to drive atherosclerotic risk. The present study aims to investigate the association between serum sdLDL-C level and the presence and severity of coronary heart disease (CHD). Method: A total of 3684 consecutive patients with T2DM who received selective coronary angiography (CAG) were enrolled. The patients were subsequently divided into CHD and non-CHD groups according to results of CAG. The severity of CHD was evaluated by the number of stenotic, and the Gensini Score (GS).The patients were subsequently divided into four groups by the quartiles of sdLDL-C and evaluate the risk and severity of sdLDL-C and CHD.Results: The sdLDL-C levels in CHD group were significantly higher than non-CHD group [0.80 (0.49) mmol/L vs 0.70 (0.30) mmol/L, P < 0.001]. The results from CHD subgroup analysis indicated that the patients with multiple-vessel disease and high GS had higher sdLDL-C levels compared with those in their matched subgroups (P < 0.05). By adjusting the confounding factors and analyzing by the multiple logistic regression, sdLDL-C had independent correlation with the presence and severity of CHD [CHD: OR = 2.757, 95%, CI = 1.662 - 5.364, P = 0.023; multiple-vessel disease: OR = 3.788, 95%, CI = 1.866 - 7.685, P = 0.026; High GS: OR = 3.054, 95%, CI = 1.944 - 5.699, P = 0.022].Conclusion: In T2DM patients, the increase of sdLDL-C is related to the increase the prevalence and the severity of CHD. After adjustment for other risk factors, sdLDL-C was found to be an independent risk factor for CHD. Therefore, measuring sdLDL-C may allow for T2DM patients to predict the presence and severity of CHD.
- Published
- 2020
193. Lipid-protein interactions modulate the conformational equilibrium of a potassium channel
- Author
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Bert L. de Groot and Ruo-Xu Gu
- Subjects
Potassium Channels ,Protein Conformation ,Science ,Lipid Bilayers ,Biophysics ,General Physics and Astronomy ,Gating ,Molecular dynamics ,Molecular Dynamics Simulation ,Article ,Protein Structure, Secondary ,General Biochemistry, Genetics and Molecular Biology ,Protein–protein interaction ,Computational biophysics ,Protein structure ,Animals ,Humans ,lcsh:Science ,Multidisciplinary ,Chemistry ,General Chemistry ,Lipids ,Potassium channel ,Crosstalk (biology) ,Transmembrane domain ,Membrane ,Membrane protein ,Permeation and transport ,lcsh:Q ,Protein Binding - Abstract
Cell membranes actively participate in the regulation of protein structure and function. In this work, we conduct molecular dynamics simulations to investigate how different membrane environments affect protein structure and function in the case of MthK, a potassium channel. We observe different ion permeation rates of MthK in membranes with different properties, and ascribe them to a shift of the conformational equilibrium between two states of the channel that differ according to whether a transmembrane helix has a kink. Further investigations indicate that two key residues in the kink region mediate a crosstalk between two gates at the selectivity filter and the central cavity, respectively. Opening of one gate eventually leads to closure of the other. Our simulations provide an atomistic model of how lipid-protein interactions affect the conformational equilibrium of a membrane protein. The gating mechanism revealed for MthK may also apply to other potassium channels., Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.
- Published
- 2020
194. Suppression of histone deacetylases by SAHA relieves bone cancer pain in rats via inhibiting activation of glial cells in spinal dorsal horn and dorsal root ganglia
- Author
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Fa Ming Chen, Ze Xu Gu, Chen Zhang, Jian Ping Deng, Wei Wang, Yan Yan Wei, Kai Xiang Zhou, Chang Le Wu, Xiao Tao He, Wen Jun Zhao, Yu Lin Dong, Chao Zhu, Xiao Han, and Xiao Fan Hu
- Subjects
Spinal dorsal horn ,Spinal Cord Dorsal Horn ,Immunology ,H&E stain ,Bone Neoplasms ,Pharmacology ,lcsh:RC346-429 ,Proinflammatory cytokine ,Rats, Sprague-Dawley ,Pathogenesis ,Cellular and Molecular Neuroscience ,Neuroinflammation ,Downregulation and upregulation ,Western blot ,Ganglia, Spinal ,Glial cells ,medicine ,Animals ,Bone cancer pain ,lcsh:Neurology. Diseases of the nervous system ,Analgesics ,Vorinostat ,medicine.diagnostic_test ,Chemistry ,Histone deacetylase 2 ,Research ,General Neuroscience ,HDACs ,Cancer Pain ,HDAC1 ,Rats ,Histone Deacetylase Inhibitors ,Neurology ,Female ,Neuroglia - Abstract
Background Robust activation of glial cells has been reported to occur particularly during the pathogenesis of bone cancer pain (BCP). Researchers from our group and others have shown that histone deacetylases (HDACs) play a significant role in modulating glia-mediated immune responses; however, it still remains unclear whether HDACs are involved in the activation of glial cells during the development of BCP. Methods BCP model was established by intra-tibia tumor cell inoculation (TCI). The expression levels and distribution sites of histone deacetylases (HDACs) in the spinal dorsal horn and dorsal root ganglia were evaluated by Western blot and immunofluorescent staining, respectively. Suberoylanilide hydroxamic acid (SAHA), a clinically used HDAC inhibitor, was then intraperitoneally and intrathecally injected to rescue the increased expression levels of HDAC1 and HDAC2. The analgesic effects of SAHA administration on BCP were then evaluated by measuring the paw withdrawal thresholds (PWTs). The effects of SAHA on activation of glial cells and expression of proinflammatory cytokines (TNF-α, IL-1β, and IL-6) in the spinal dorsal horn and dorsal root ganglia of TCI rats were further evaluated by immunofluorescent staining and Western blot analysis. Subsequently, the effects of SAHA administration on tumor growth and cancer cell-induced bone destruction were analyzed by hematoxylin and eosin (HE) staining and micro-CT scanning. Results TCI caused rapid and long-lasting increased expression of HDAC1/HDAC2 in glial cells of the spinal dorsal horn and dorsal root ganglia. Inhibiting HDACs by SAHA not only reversed TCI-induced upregulation of HDACs but also inhibited the activation of glial cells in the spinal dorsal horn and dorsal root ganglia, and relieved TCI-induced mechanical allodynia. Further, we found that SAHA administration could not prevent cancer infiltration or bone destruction in the tibia, which indicated that the analgesic effects of SAHA were not due to its anti-tumor effects. Moreover, we found that SAHA administration could inhibit GSK3β activity in the spinal dorsal horn and dorsal root ganglia, which might contributed to the relief of BCP. Conclusion Our findings suggest that HDAC1 and HDAC2 are involved in the glia-mediated neuroinflammation in the spinal dorsal horn and dorsal root ganglia underlying the pathogenesis of BCP, which indicated that inhibiting HDACs by SAHA might be a potential strategy for pain relief of BCP.
- Published
- 2020
195. Visualization of the mechanosensitive ion channel MscS under membrane tension
- Author
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Yixiao, Zhang, Csaba, Daday, Ruo-Xu, Gu, Charles D, Cox, Boris, Martinac, Bert L, de Groot, and Thomas, Walz
- Subjects
Models, Molecular ,Protein Conformation ,Escherichia coli Proteins ,Cryoelectron Microscopy ,Detergents ,Lipid Bilayers ,beta-Cyclodextrins ,Membranes, Artificial ,Mechanotransduction, Cellular ,Ion Channels ,Nanostructures ,Mutation ,Escherichia coli ,Phosphatidylcholines ,Hydrophobic and Hydrophilic Interactions - Abstract
Mechanosensitive channels sense mechanical forces in cell membranes and underlie many biological sensing processes
- Published
- 2020
196. Additional file 4 of Suppression of histone deacetylases by SAHA relieves bone cancer pain in rats via inhibiting activation of glial cells in spinal dorsal horn and dorsal root ganglia
- Author
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He, Xiao-Tao, Hu, Xiao-Fan, Zhu, Chao, Kai-Xiang Zhou, Zhao, Wen-Jun, Zhang, Chen, Han, Xiao, Chang-Le Wu, Wei, Yan-Yan, Wang, Wei, Deng, Jian-Ping, Chen, Fa-Ming, Ze-Xu Gu, and Dong, Yu-Lin
- Abstract
Additional file 4. Table S1. Primer sequences used in this study.
- Published
- 2020
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197. Gamete/Embryo-Fetal Origins of Cardiovascular Diseases
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Sheng, Jian-Zhong, primary, Zhang, Li, additional, Xu, Gu-Feng, additional, and Jiang, Ying, additional
- Published
- 2013
- Full Text
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198. Regulation of Shigella Effector Kinase OspG through Modulation of Its Dynamic Properties
- Author
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Andrey M. Grishin, Kathryn R. Barber, Gary S. Shaw, Ruo-Xu Gu, Miroslaw Cygler, and D. Peter Tieleman
- Subjects
Models, Molecular ,0301 basic medicine ,Protein Folding ,Protein Conformation ,Virulence Factors ,Ubiquitin-Protein Ligases ,Chromosomal translocation ,Molecular Dynamics Simulation ,Body Temperature ,Shigella flexneri ,03 medical and health sciences ,Bacterial Proteins ,Ubiquitin ,Structural Biology ,Catalytic Domain ,Humans ,Secretion ,Kinase activity ,Molecular Biology ,Binding Sites ,biology ,Protein Stability ,Kinase ,Chemistry ,Effector ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Cell biology ,030104 developmental biology ,biology.protein ,Thermodynamics ,Protein Binding ,Conjugate - Abstract
Gram-negative pathogens secrete effector proteins into human cells to modulate normal cellular processes and establish a bacterial replication niche. Shigella and pathogenic Escherichia coli possess homologous effector kinases, OspG and NleH1/2, respectively. Upon translocation, OspG but not NleH binds to ubiquitin and a subset of E2 ~ Ub conjugates, which was shown to activate its kinase activity. Here we show that OspG, having a minimal kinase fold, acquired a novel mechanism of regulation of its activity. Binding of the E2 ~ Ub conjugate to OspG not only stimulates its kinase activity but also increases its optimal temperature for activity to match the human body temperature and stabilizes its labile C-terminal domain. The melting temperature ( T m ) of OspG alone is only 31 °C, as compared to 41 °C to NleH1/2 homologs. In the presence of E2 ~ Ub, the T m of OspG increases to ~ 42 °C, while Ub by itself increases the T m to 39 °C. Moreover, OspG alone displays maximal activity at 26 °C, while in the presence of E2 ~ Ub, maximal activity occurs at ~ 42 °C. Using NMR and molecular dynamics calculations, we have identified the C-terminal lobe and, in particular, the C-terminal helix, as the key elements responsible for lower thermal stability of OspG as compared to homologous effector kinases.
- Published
- 2018
199. Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein
- Author
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Ruo-Xu Gu, Estefania Barreto-Ojeda, D. Peter Tieleman, and Valentina Corradi
- Subjects
0301 basic medicine ,Physiology ,Lipid Bilayers ,Static Electricity ,ATP-binding cassette transporter ,Plasma protein binding ,Glycerophospholipids ,Molecular Dynamics Simulation ,01 natural sciences ,Molecular Docking Simulation ,03 medical and health sciences ,Molecular dynamics ,chemistry.chemical_compound ,Mice ,Phosphatidylcholine ,0103 physical sciences ,Static electricity ,Animals ,ATP Binding Cassette Transporter, Subfamily B, Member 1 ,Research Articles ,P-glycoprotein ,Phosphatidylethanolamine ,Binding Sites ,010304 chemical physics ,biology ,030104 developmental biology ,chemistry ,biology.protein ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Research Article ,Protein Binding - Abstract
P-glycoprotein contributes to multidrug resistance by exporting a broad range of substrates across the cell membrane. Using molecular dynamics simulations, Barreto-Ojeda et al. identify key lipid-binding sites and reveal lipid access pathways toward the cavity of the transporter., P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.
- Published
- 2018
200. The application of lead-free solder to optical fiber packaging
- Author
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Ou, Shengquan, Xu, Gu, Xu, Yuhuan, and Tu, K. N.
- Published
- 2004
- Full Text
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