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Multi-omics analyses provide insights into the evolutionary history and the synthesis of medicinal components of the Chinese wingnut

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Plant Diversity 2024年第3期46卷 309-320页

作者： zi-Yan Zhang He-Xiao Xia Meng-Jie yuan Feng Gao Wen-Hua Bao Lan Jin Min li Yong li College of life Science and Technology Inner Mongolia Normal UniversityHohhot 010020China Key Laboratory of Biodiversity Conservation and Sustainable Utilization in Mongolian Plateau for College and University of Inner Mongolia Autonomous Region Hohhot 010022China College of Landscape and Art Henan Agricultural UniversityZhengzhou 450002China State Key Laboratory of Tree Genetics and Breeding Chinese Academy of ForestryBeijing 100091China

Chinese wingnut(Pterocarya stenoptera)is a medicinally and economically important tree species within the family Juglandaceae.However,the lack of high-quality reference genome has hindered its in-depth research.In this study,we successfully assembled its chromosome-level genome and performed multiomics analyses to address its evolutionary history and synthesis of medicinal components.A thorough examination of genomes has uncovered a significant expansion in the Lateral Organ Boundaries Domain gene family among the winged group in Juglandaceae.This notable increase may be attributed to their frequent exposure to flood-prone environments.After further differentiation between Chinese wingnut and Cyclocarya paliurus,significant positive selection occurred on the genes of NADH dehydrogenase related to mitochondrial aerobic respiration in Chinese wingnut,enhancing its ability to cope with waterlogging stress.Comparative genomic analysis revealed Chinese wingnut evolved more unique genes related to arginine synthesis,potentially endowing it with a higher capacity to purify nutrient-rich water bodies.Expansion of terpene synthase families enables the production of increased quantities of terpenoid volatiles,potentially serving as an evolved defense mechanism against herbivorous insects.Through combined transcriptomic and metabolomic analysis,we identified the candidate genes involved in the synthesis of terpenoid volatiles.Our study offers essential genetic resources for Chinese wingnut,unveiling its evolutionary history and identifying key genes linked to the production of terpenoid volatiles.

关键词： Genome Medicinal components Metabolome Pterocarya stenoptera Transcriptome

UPLC-Q-TOF/MS-Based Serum Metabolomics Reveals Potential Anti-tumor Mechanism of Banxia Xiexin Decoction in Colorectal Cancer Mice

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Chinese Journal of Integrative Medicine 2024年第7期30卷 623-632页

作者： YUE Yin-zi li Ming-xuan WANG Xiao-hui QIN yuan-yuan WANG Ya-hui TAN Jin-hua SU lian-lin YAN Shuai Department of General Surgery Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine School of Pharmacy Nanjing University of Chinese Medicine Department of General Surgery Bayinguoleng Mongolian Autonomous Prefecture People's Hospital Department of Pharmacy Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine Department of Anorectal Surgery Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

Objective: To clarify the potential mechanism of Banxia Xiexin Decoction(BXD) on colorectal cancer(CRC) from the perspective of metabolomics. Methods: Forty male C57BL/6 mice were randomly divided into normal control(NC), azoxymethane/dextran sulfate sodium(AOM/DSS) model, low-dose BXD(L-BXD), high-dose BXD(H-BXD) and mesalamine(MS) groups according to a random number table, 8 mice in each group. Colorectal cancer model was induced by AOM/DSS. BXD was administered daily at doses of 3.915(L-BXD) and 15.66 g/kg(H-BXD) by gavage for consecutive 21 days, and 100 mg/kg MS was used as positive control. Following the entire modeling cycle, colon length of mice was measured and quantity of colorectal tumors were counted. The spleen and thymus index were determined by calculating the spleen/thymus weight to body weight. Inflammatory cytokine and changes of serum metabolites were analyzed by enzyme-linked immunosorbent assay kits and ultra performance liquid chromatography-quadrupole/time-of-flight mass spectrometry(UPLC-Q/TOF-MS), respectively. Results: Notably, BXD supplementation protected against weight loss, mitigated tumor formation, and diminished histologic damage in mice treated with AOM/DSS(Plites were screened in the AOM/DSS group, including 48 potential biomarkers, involving 18 main metabolic pathways. Totally 18 potential biomarkers related to CRC were identified, and the anti-CRC mechanism of BXD was closely related to D-glutamine and D-glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, arginine biosynthesis, nitrogen metabolism and so on. Conclusion: BXD exerts partial protective effects on AOM/DSS-induced CRC by reducing inflammation, protecting organism immunity ability, and regulating amino acid metabolism.

关键词： colorectal cancer metabolomics ultra performance liquid chromatography-quadrupole/time-of-flight mass spectrometry azoxymethane dextran sulfate sodium Banxia Xiexin Decoction Chinese medicine

Boosting Hydrogen Storage Performance of MgH_(2) by Oxygen Vacancy-Rich H-V_(2)O_(5) Nanosheet as an Excited H-Pump

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Nano-Micro Letters 2024年第8期16卷 398-416页

作者： li Ren Yinghui li zi li Xi lin Chong Lu Wenjiang Ding Jianxin Zou National Engineering Research Center of light Alloys Net Forming&State Key Laboratory of Metal Matrix Composites Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China Shanghai Engineering Research Center of Mg Materials and Applications&School of Materials Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China Center of Hydrogen Science Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China Instrumental Analysis Center of SJTU Shanghai Jiao Tong UniversityShanghai 200240People’s Republic of China

MgH_(2) is a promising high-capacity solid-state hydrogen storage material,while its application is greatly hindered by the high desorption temperature and sluggish kinetics.Herein,intertwined 2D oxygen vacancy-rich V_(2)O_(5) nanosheets(H-V_(2)O_(5))are specifically designed and used as catalysts to improve the hydrogen storage properties of MgH_(2).The as-prepared MgH_(2)-H-V_(2)O_(5) composites exhibit low desorption temperatures(Tonset=185℃)with a hydrogen capacity of 6.54 wt%,fast kinetics(Ea=84.55±1.37 kJ mol^(-1) H_(2) for desorption),and long cycling stability.Impressively,hydrogen absorption can be achieved at a temperature as low as 30℃ with a capacity of 2.38 wt%within 60 min.Moreover,the composites maintain a capacity retention rate of~99%after 100 cycles at 275℃.Experimental studies and theoretical calculations demonstrate that the in-situ formed VH_(2)/V catalysts,unique 2D structure of H-V_(2)O_(5) nanosheets,and abundant oxygen vacancies positively contribute to the improved hydrogen sorption properties.Notably,the existence of oxygen vacancies plays a double role,which could not only directly accelerate the hydrogen ab/de-sorption rate of MgH_(2),but also indirectly affect the activity of the catalytic phase VH_(2)/V,thereby further boosting the hydrogen storage performance of MgH_(2).This work highlights an oxygen vacancy excited“hydrogen pump”effect of VH_(2)/V on the hydrogen sorption of Mg/MgH_(2).The strategy developed here may pave a new way toward the development of oxygen vacancy-rich transition metal oxides catalyzed hydride systems.

关键词： Hydrogen storage MgH_(2) V_(2)O_(5)nanosheets Oxygen vacancies VH_(2)

Identification and validation of a new prognostic signature based on cancer-associated fibroblast-driven genes in breast cancer

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World Journal of Clinical Cases 2024年第4期12卷 700-720页

作者： zi-Zheng Wu yuan-Jun Wei Tong li Jie Zheng Yin-Feng liu Meng Han Diagnosis and Treatment Center The First Hospital of QinhuangdaoQinhuangdao 066000Hebei ProvinceChina Department of General Surgery Hebei Medical UniversityShijiazhuang 050000Hebei ProvinceChina Breast Disease Diagnosis and Treatment Center The First Hospital of QinhuangdaoHebei Medical UniversityQinhuangdao 066000Hebei ProvinceChina Breast Disease Diagnosis and Treatment Center Chengde Medical CollegeChengde 067000Hebei ProvinceChina

BACKGROUND Breast cancer(BC),a leading malignant disease,affects women all over the world.Cancer associated fibroblasts(CAFs)stimulate epithelial-mesenchymal transition,and induce chemoresistance and immunosuppression.AIM To establish a CAFs-associated prognostic signature to improve BC patient out-come estimation.METHODS We retrieved the transcript profile and clinical data of 1072 BC samples from The Cancer Genome Atlas(TCGA)databases,and 3661 BC samples from the The Gene Expression Omnibus.CAFs and immune cell infiltrations were quantified using CIBERSORT algorithm.CAF-associated gene identification was done by weighted gene co-expression network analysis.A CAF risk signature was established via univariate,least absolute shrinkage and selection operator regression,and mul-tivariate Cox regression analyses.The receiver operating characteristic(ROC)and Kaplan-Meier curves were employed to evaluate the predictability of the model.Subsequently,a nomogram was developed with the risk score and patient clinical signature.Using Spearman's correlations analysis,the relationship between CAF risk score and gene set enrichment scores were examined.Patient samples were collected to validate gene expression by quantitative real-time polymerase chain reaction(qRT-PCR).RESULTS Employing an 8-gene(IL18,MYD88,GliPR1,TNN,BHLHE41,DNAJB5,FKBP14,and XG)signature,we attemp-ted to estimate BC patient prognosis.Based on our analysis,high-risk patients exhibited worse outcomes than low-risk patients.Multivariate analysis revealed the risk score as an independent indicator of BC patient prognosis.ROC analysis exhibited satisfactory nomogram predictability.The area under the curve showed 0.805 at 3 years,and 0.801 at 5 years in the TCGA cohort.We also demonstrated that a reduced CAF risk score was strongly associated with enhanced chemotherapeutic outcomes.CAF risk score was significantly correlated with most hallmark gene sets.Finally,the prognostic signature were further validated by qRT-PCR.CONCLUSION We introduced a newly-discovered

关键词： Breast cancer Prognosis Gene signature The Cancer Genome Atlas The Gene Expression Omnibus

Semi-supervised remote sensing image scene classification with prototype-based consistency

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Chinese Journal of Aeronautics 2024年第2期37卷 459-470页

作者： Yang li Zhang li zi WANG Kun WANG Qifeng YU College of Aerospace Science and Engineering National University of Defense TechnologyChangsha 410073China

Deep learning significantly improves the accuracy of remote sensing image scene classification,benefiting from the large-scale datasets.However,annotating the remote sensing images is time-consuming and even tough for experts.Deep neural networks trained using a few labeled samples usually generalize less to new unseen images.In this paper,we propose a semi-supervised approach for remote sensing image scene classification based on the prototype-based consistency,by exploring massive unlabeled images.To this end,we,first,propose a feature enhancement module to extract discriminative features.This is achieved by focusing the model on the foreground areas.Then,the prototype-based classifier is introduced to the framework,which is used to acquire consistent feature representations.We conduct a series of experiments on NWPU-RESISC45 and Aerial Image Dataset(AID).Our method improves the State-Of-The-Art(SOTA)method on NWPU-RESISC45 from 92.03%to 93.08%and on AID from 94.25%to 95.24%in terms of accuracy.

关键词： Semi-supervised learning Remote sensing Scene classification Prototype network Deep learning

Influencer identification of dynamical networks based on an information entropy dimension reduction method

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Chinese Physics B 2024年第4期33卷 375-384页

作者：段东立纪思源袁紫薇 School of Information and Control Engineering Xi'an University of Architecture and TechnologyXi'an 710311China School of Mechanical Engineering Northwestern Polytechnical UniversityXi'an 710072China

Identifying critical nodes or sets in large-scale networks is a fundamental scientific problem and one of the key research directions in the fields of data mining and network science when implementing network attacks, defense, repair and control.Traditional methods usually begin from the centrality, node location or the impact on the largest connected component after node destruction, mainly based on the network structure.However, these algorithms do not consider network state changes.We applied a model that combines a random connectivity matrix and minimal low-dimensional structures to represent network connectivity.By using mean field theory and information entropy to calculate node activity,we calculated the overlap between the random parts and fixed low-dimensional parts to quantify the influence of node impact on network state changes and ranked them by importance.We applied this algorithm and the proposed importance algorithm to the overall analysis and stratified analysis of the C.elegans neural network.We observed a change in the critical entropy of the network state and by utilizing the proposed method we can calculate the nodes that indirectly affect muscle cells through neural layers.

关键词： dynamical networks network influencer low-dimensional dynamics network disintegration

Nonreciprocal generation of Schrodinger cat state induced by topology

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Science China(Physics,Mechanics & Astronomy) 2024年第4期67卷 23-30页

作者： zi-Hao li li-li Zheng Ying Wu Xin-You Lü School of Physics and Institute for Quantum Science and Engineering Huazhong University of Science and Technologyand Wuhan Institute of Quantum TechnologyWuhan 430074China Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education Jianghan UniversityWuhan 430074China

The Schrodinger cat state produced differently in two directions is anticipated to be a critical quantum resource in quantum information technologies.By exploring the interplay between quantum nonreciprocity and topology in a one-dimensional microcavity array,we obtain the Schrodinger cat state(a pure quantum state)in a chosen direction at the edge cavity,whereas a classical state in the other direction.This nonreciprocal generation of the cat state originates from the topologically protected chiralitymode excitation in the nontrivial phase,but in the trivial phase,the nonreciprocal generation of cat state vanishes.Thus,our proposal is switchable by tuning the parameters so that a topological phase transition occurs.Moreover,the obtained cat state has nonreciprocal high fidelity,nonclassicality,and quantum coherence,which are sufficient to be used in various one-way quantum technologies,e.g.,invisible quantum sensing,noise-tolerant quantum computing,and chiral quantum networks.Our work provides a general approach to control quantum nonreciprocities with the topological effect,which substantially broadens the fields of nonreciprocal photonics and topological physics.

关键词： Schr?dinger cat state nonreciprocity topology

Protein lipidation in health and disease:molecular basis,physiological function and pathological implication

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Signal Transduction and Targeted Therapy 2024年第4期9卷 1423-1465页

作者： yuan yuan Peiyuan li jianghui li Qiu Zhao Ying Chang Xingxing He Department of Gastroenterology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina Department of Gastroenterology Zhongnan Hospital of Wuhan UniversityWuhanChina Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases WuhanChina

Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes.Among these,protein lipidations which refer to lipid attachment to proteins are prominent,which primarily encompassing five types including S-palmitoylation,N-myristoylation,S-prenylation,glycosylphosphatidylinositol(GPl)anchor and cholesterylation.lipid attachment to proteins plays an essential role in the regulation of protein trafficking,localisation,stability,conformation,interactions and signal transduction by enhancing hydrophobicity.Accumulating evidence from genetic,structural,and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases.Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation,and several agents have been developed and tested in preclinical and clinical studies,some of which,such as asciminib and lonafarnib are FDA-approved for therapeutic use,indicating that targeting protein lipidations represents a promising therapeutic strategy.Here,we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types,outline the impact of protein lipidations on physiology and disease,and highlight potential therapeutic targets and clinical research progress,aiming to provide a comprehensive reference for future protein lipidation research.

关键词： lipid ation primarily

Modulation of d-orbital to realize enriched electronic cobalt sites in cobalt sulfide for enhanced hydrogen evolution in electrocatalytic water/seawater splitting

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Rare Metals 2024年第2期43卷 511-521页

作者： Jian-Peng Sun Yu Zheng zi-Sheng Zhang Xiang-Chao Meng zi-Zhen li Key Laboratory of Marine Chemistry Theory and Technology(Ministry of Education) College of Chemistry and Chemical EngineeringOcean University of ChinaQingdao266100China Shanxi Institute of Energy Taiyuan030600China Department of Chemical and Biological Engineering Faculty of EngineeringUniversity of OttawaOttawaONK1N6 N5Canada

Herein,a novel single-atomic Pt doping and interface-rich CoS/Co(OH)_(2)(Pt-CoS/Co(OH)_(2)/C)electrocatalyst has been successfully prepared.Benefiting from precise regulation of d-orbital electronic structure modulation on Co site,Pt-CoS/Co(OH)_(2)/C exhibited remarkable HER activity and high stability for hydrogen evolution in splitting both water(73 mV@10 mA·cm^(−2)) and seawater(87 mV@10 mA·cm^(−2)).Notably,atomic Pt doping was introduced into CoS/Co(OH)_(2),which could produce local unbalanced Coulombic force and significantly increased the number of S vacancies,and then expose abundant Co sites.Meantime,Co(OH)_(2) in Pt-CoS/Co(OH)_(2)/C could act as the adsorption sites for H_(2)O in hydrogen evolution reaction process.Density functional theory results also proved that atomic Pt doping,S vacancies and Co(OH)_(2) coupling could result in the formation of enriched electronic Co sites and optimize d_(z2) orbital electronic structure,and then realize the depth upward shift of d-band center and enhance the adsorption of H*on Co sites.

关键词： Electrocatalysts Hydrogen evolution reaction Pt-CoS/Co(OH)_(2) d-band center Electronic structure Water/seawater electrolysis