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A prognostic four-gene signature and a therapeutic strategy for hepatocellular carcinoma:Construction and analysis of a circRNA-mediated competing endogenous RNA network

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Hepatobiliary & Pancreatic Diseases International 2024年第3期23卷 272-287页

作者： Hai-Yan zhang Jia-Jie Zhu Zong-ming Liu Yu-xuan zhang Jia-Jia Chen Ke-Da Chen Zhejiang Chinese Medical University Hangzhou 310053China Shulan International Medical College Zhejiang Shuren UniversityHangzhou 310015China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious DiseasesNational Medical Center for Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhou 310009China

Background:Hepatocellular carcinoma(HCC)has a poor long-term prognosis.The competition of circular RNAs(circRNAs)with endogenous RNA is a novel tool for predicting HCC prognosis.Based on the alterations of circRNA regulatory networks,the analysis of gene modules related to HCC is feasible.Methods:Multiple expression datasets and RNA element targeting prediction tools were used to construct a circRNA-microRNA-mRNA network in HCC.Gene function,pathway,and protein interaction analyses were performed for the differentially expressed genes(DEGs)in this regulatory network.In the proteinprotein interaction network,hub genes were identified and subjected to regression analysis,producing an optimized four-gene signature for prognostic risk stratification in HCC patients.Anti-HCC drugs were excavated by assessing the DEGs between the low-and high-risk groups.A circRNA-microRNA-hub gene subnetwork was constructed,in which three hallmark genes,KIF4A,CCNA2,and PBK,were subjected to functional enrichment analysis.Results:A four-gene signature(KIF4A,CCNA2,PBK,and ZWINT)that effectively estimated the overall survival and aided in prognostic risk assessment in the The Cancer Genome Atlas(TCGA)cohort and International Cancer Genome Consortium(ICGC)cohort was developed.CDK inhibitors,PI3K inhibitors,HDAC inhibitors,and EGFR inhibitors were predicted as four potential mechanisms of drug action(MOA)in high-risk HCC patients.Subsequent analysis has revealed that PBK,CCNA2,and KIF4A play a crucial role in regulating the tumor microenvironment by promoting immune cell invasion,regulating microsatellite instability(MSI),and exerting an impact on HCC progression.Conclusions:The present study highlights the role of the circRNA-related regulatory network,identifies a four-gene prognostic signature and biomarkers,and further identifies novel therapy for HCC.

关键词： Hepatocellular carcinoma circRNA-related ceRNA network Biomarker Least absolute shrinkage and selection operator Bioinformatics

Benefit-Risk Assessment of Chinese Medicine Injections for Primary Liver Cancer Based on Multi-criteria Decision Analysis

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Chinese Journal of Integrative Medicine 2024年第6期30卷 559-564页

作者： zhang Rong-rong SHAO ming-yi FU Yu ZHAO Rui-xia WANG Jing-wen FANG Yu-xuan The First Clinical Medical College of Henan University of Traditional Chinese Medicine Zhengzhou450046China Personal Department the First Affiliated Hospital of Henan University of Chinese MedicineZhengzhou450000China Scientific Research Department the First Affiliated Hospital of Henan University of Chinese MedicineZhengzhou450000China Digestive Department the First Affiliated Hospital of Henan University of Chinese MedicineZhengzhou450000China

ObjectiveTo evaluate the benefit-risk of 3 commonly used Chinese medicine injections, Aidi Injection (ADI), Cinobufagin Injection (CINI) and Compound Kushen Injection (CKI), in the treatment of primary liver cancer (PLC), so as to provide a reference for clinical decision-making.MethodsRandomized controlled trials (RCTs) of ADI, CINI and CKI in the treatment of PLC published in the databases of China National Knowledge Infrastructure, Wanfang, China Science and Technology Journal Database, SinoMed, PubMed, Cochrane Library, and Web of Science were retrieved from January 2020 to October 2022. The data of benefit and risk indicators were combined to obtain the effect value. The multi-criteria decision analysis (MCDA) model was applied to build the decision tree. The benefit value, risk value and benefit risk value of the 3 injections in PLC treatment were calculated. Monte Carlo simulation was carried out to calculate the 95% confidence interval and probability of differences among the 3 injections, so as to optimize the evaluation results.ResultsA total of 71 RCTs were included. The benefit values of ADI, CINI and CKI combined with transcatheter arterial chemoembolization (TACE) were 42, 38 and 36, respectively. The risk values were 42, 25 and 37, respectively. The benefit risk values were 42, 31 and 37, respectively. The benefit risk differences of ADI vs. CINI, ADI vs. CKI, and CKI vs. CINI were 11 (−0.86, 17.75), 5 (−5.01, 11.09), and 6 (−1.87, 12.63), respectively. The probability that ADI superior to CINI, ADI superior to CKI, and CKI superior to CINI was 96.26%, 77.27%, and 92.62%, respectively.ConclusionBased on the results of MCDA model, CINI combined with TACE has the greatest risk in the treatment of the PLC. Considering the efficacy and safety, the possible priority of the 3 Chinese medicine injections combined with TACE in the treatment of PLC is ADI, CKI and CINI.

关键词： multi-criteria decision analysis benefit-risk assessment Chinese medicine injections primary livercancer

Integrating machine learning and CALPHAD method for exploring low-modulus near-β-Ti alloys

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Rare Metals 2024年第1期43卷 309-323页

作者： Hao Zou Yue-Yan Tian Li-Gang zhang Ren-Hao Xue Zi-xuan Deng ming-ming Lu Jian-Xin Wang Li-Bin Liu School of Computer Science and Engineering Central South UniversityChangsha 410083China School of Materials Science and Engineering Central South UniversityChangsha 410083China State Key Laboratory of Powder Metallurgy Central South UniversityChangsha 410083China

Traditional theoretical and empirical calculation methods can guide the design of β-and metastable β-alloys for bio-titanium. However, it is still difficult to obtain novel near-β-Ti alloys with low modulus. This study developed a method that combines machine learning with calculation of phase diagrams(CALPHAD) to facilitate the design of near-β-Ti alloys. An elastic modulus database of Ti–Nb–Zr–Mo–Ta–Sn system was constructed first, and then three features(the electron to atom ratio, mean absolute deviation of atom mass, and mean electronegativity) were selected as the key factors of modulus by performing a three-step feature selection. With these features, a highly accurate model was built for predicting the modulus of near-β-Ti alloys. To further ensure the accuracy of modulus prediction, machine learning with the elastic constants calculated was leveraged by CALPHAD database. The root mean square error of the well-trained model can be as low as 6.75 GPa. Guided by the prediction of machine learning and CALPHAD, three novel near-β-Ti alloys with elastic modulus below 50 GPa were successfully designed in this study. The best candidate alloy(Ti–26Nb–4Zr–4Sn–1Mo–Ta) exhibits an ultra-low modulus(36.6 GPa) after cold rolling with a thickness reduction of 20%. Our method can greatly save time and resources in the development of novel Ti alloys, and experimental verifications have demonstrated the reliability of this method.

关键词： Near-β-Ti alloy Machine learning Calculation of phase diagram Low-modulus alloy Feature selection

Synthesis and Modulation of Low-Dimensional Transition Metal Chalcogenide Materials via Atomic Substitution

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Nano-Micro Letters 2024年第9期16卷 49-94页

作者： xuan Wang Akang Chen XinLei Wu Jiatao zhang Jichen Dong Leining zhang Key Laboratory of Cluster Science Ministry of Education of ChinaBeijing Key Laboratory of Photoelectronic and Electrophonic Conversion MaterialsSchool of Chemistry and Chemical EngineeringBeijing Institute of TechnologyBeijing 100081People’s Republic of China Beijing National Laboratory for Molecular Sciences Key Laboratory of Organic SolidsInstitute of Chemistry Chinese Academy of SciencesBeijing 100190People’s Republic of China

In recent years,low-dimensional transition metal chalcogenide(TMC)materials have garnered growing research attention due to their superior electronic,optical,and catalytic properties compared to their bulk counterparts.The controllable synthesis and manipulation of these materials are crucial for tailoring their properties and unlocking their full potential in various applications.In this context,the atomic substitution method has emerged as a favorable approach.It involves the replacement of specific atoms within TMC structures with other elements and possesses the capability to regulate the compositions finely,crystal structures,and inherent properties of the resulting materials.In this review,we present a comprehensive overview on various strategies of atomic substitution employed in the synthesis of zero-dimensional,one-dimensional and two-dimensional TMC materials.The effects of substituting elements,substitution ratios,and substitution positions on the structures and morphologies of resulting material are discussed.The enhanced electrocatalytic performance and photovoltaic properties of the obtained materials are also provided,emphasizing the role of atomic substitution in achieving these advancements.Finally,challenges and future prospects in the field of atomic substitution for fabricating low-dimensional TMC materials are summarized.

关键词： Transition metal chalcogenides Atomic substitution Ion exchange Low-dimensional materials Controllable synthesis

Optimising multi-vent module-based adaptive ventilation using a novel parameter for improved indoor air quality and health protection

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Building Simulation 2024年第1期17卷 113-130页

作者： Haotian zhang Xiaoxiao Ding Weirong zhang Weijia zhang Yingli xuan Key Laboratory of Green Built Environment and Energy Efficient Technology Beijing University of TechnologyBeijing 100124China Department ofArchitecture TokyoPolytechnic UniversityTokyoJapan

As infectious respiratory diseases are highly transmissible through the air,researchers have improved traditional total volume air distribution systems to reduce infection risk.Multi-vent module-based adaptive ventilation(MAV)is a novel ventilation type that facilitates the switching of inlets and outlets to suit different indoor scenarios without changing ductwork layout.However,little research has evaluated MAV module sizing and air velocity selection,both related to MAV system efficiency in removing contaminants and the corresponding level of protection for occupants in the ventilated room.Therefore,the module-source offset ratio(MSOR)is proposed,based on the MAV module size and its distance from an infected occupant,to inform selection of optimal MAV module parameters.Computational fluid dynamics simulations illustrated contaminant distribution in a two-person MAV equipped office.Discrete phase particles modelled respiratory contaminants from the infected occupant,and contaminant concentration distributions were compared under four MAV air distribution layouts,three air velocities,and three module sizes considered using the MsOR.Results indicate that lower air velocities favour rising contaminant levels,provided the ventilation rate is met.Optimal contaminant discharge can be achieved when the line of outlets is located directly above the infected occupant.Using this parameter to guide MAV system design,85.7% of contaminants may be rendered harmless to the human body within 120 s using the default air vent layout.A more appropriate supply air velocity and air vent layout increases this value to 91.4%.These results are expected to inform the deployment of MAV systems to reduce airborne infection risk.

关键词： multi-vent module-based adaptive ventilation computational fluid dynamics indoor air quality infection control

Significant contribution of carbonyls to atmospheric oxidation capacity(AOC)during the winter haze pollution over North China Plain

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Journal of Environmental Sciences 2024年第5期139卷 377-388页

作者： Xue Yang Gen zhang Guang Pan Guolan Fan Houyong zhang xuan Ge mingyue Du School of Municipal and Environmental Engineering Shandong Jianzhu UniversityJi’nan 250101China State Key Laboratory of Severe Weather&Key Laboratory of Atmospheric Chemistry of China Meteorological Administration Chinese Academy of Meteorological SciencesBeijing 100081China Shandong Jinan Ecological Environment Monitoring Center Ji’nan 250101China

Atmospheric carbonyl compounds play significant roles in the cycling of radicals and have exhibited surprisingly high levels in winter that were well correlated to particulate matter,for which the reason have not been clearly elucidated.Here we measured carbonyl compounds and other trace gasses together with PM_(2.5)over urban Jinan in North China Plain during the winter.Markedly higher carbonyl concentrations(average:14.63±4.21 ppbv)were found during wintertime haze pollution,about one to three-times relative to those on nonhaze days,with slight difference in chemical composition except formaldehyde(HCHO).HCHO(3.68 ppbv),acetone(3.17 ppbv),and acetaldehyde(CH_3CHO)(2.83 ppbv)were the three most abundant species,accounting for~75% of the total carbonylson both haze and non-haze days.Results from observational-based model(OBM)with atmospheric oxidation capacity(AOC)indicated that AOC significantly increased with the increasing carbonyls during the winter haze events.Carbonyl photolysis have supplied key oxidants such as RO_(2) and HO_(2),and thereby enhancing the formation of fine particles and secondary organic aerosols,elucidating the observed haze-carbonyls inter-correlation.Diurnal variation with carbonyls exhibiting peak values at early-noon and night highlighted the combined contribution of both secondary formation and primary diesel-fuel sources.1-butene was further confirmed to be the major precursor for HCHO.This study confirms the great contribution of carbonyls to AOC,and also suggests that reducing the emissions of carbonyls would be an effective way to mitigate haze pollution in urban area of the NCP region.

关键词： Carbonyls Haze Observation-based model Source apportionment Atmospheric oxidation capacity

Influence of ecological function protection zone on the water conservation in Gansu-Qinghai Contiguous Region of the upper Yellow River

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Journal of Mountain Science 2024年第4期21卷 1345-1357页

作者： TONG Huali CHEN Qingbo zhang xuan College of Geography and Environmental Science Northwest Normal UniversityLanzhou 730070China Gansu Province Land Use and Comprehensive Improvement Engineering Research Center Lanzhou 730070China

The implementation of Ecological Function Protection Zone(EFPZ)policy is significant for the ecological restoration and conservation of soil and water in the territory space.This manuscript analyzed and quantified the impact of EFPZ on the regional water conservation function,based on land use data from 2005,2008,2010,2015 and 2020,by conducting a counterfactual simulation along with the GeoSOS-FLUS model and the InVEST model.The results demonstrate that the delineation of EFPZ can significantly influence the water conservation.(1)From 2010 to 2020,as the EFPZ was implemented,the water conservation in the study area was increasing year by year,with a growth rate of 0.03×10^(8) m^(3)∙a^(-1).On the other hand,the simulated water conservation capacity without the implementation of EFPZ decreased year by year,with a decrease rate of 0.01×10^(8) m^(3)∙a^(-1).(2)The EFPZ accounts for only 23%of the total area,but the contribution rate of water conservation reaches 80%.The actual values of water conservation and average water yield per unit pixel in the EFPZ show an increasing trend both internally and externally,while the counterfactual simulation values exhibit a decreasing trend.(3)The water conservation is much higher within the EFPZ than without EFPZ.The implementation of EFPZ has a significant effect on the improvement of the water conservation capacity in Maqu EFPZ and Yellow River Source EFPZ.The protection effectiveness should be enhanced in Qilian Mountain EFPZ and afforestation activities need to be carefully considered in Loess Plateau EFPZ.

关键词： Water conservation function Ecological Function Protection Zone Counterfactual simulation Geo SOS-FLUS model InVEST model

Endochondral ossification of hindlimbs in embryonic development of Japanese Quail(Coturnix japonica)

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Avian Research 2024年第1期15卷 123-132页

作者： xuan Li Yuxin zhang Hongfeng Zhao College of Life Sciences Shaanxi Normal UniversityXi’an710119China

The endochondral ossification of hindlimb is essential to a bird’s ability to stand,walk and fly.Most hindlimb is ossified in the embryos before hatching in precocial birds.However,the molecular mechanisms of hindlimb ossification in birds is still unclear.Therefore,we tried to examine the process of hindlimb ossification and its molecular regulation by using an animal model—Japanese Quail(Coturnix japonica).We selected four critical stages(Embryo Day:E6,E8,E12 and E16) of skeletal development of embryonic quails for hindlimb skeleton staining to show the process of endochondral ossification and to examine the molecular regulation of endochondral osteogenesis by RNA-Seq analysis.The results showed that ossification became increased with embryonic development and most hindlimb was ossified before hatching.RNA-Seq analysis revealed that various signaling pathways were involved with endochondral ossification with thyroid hormone signaling and WNT signaling pathway particularly enriched.Moreover,the expression levels of 42 genes were continuously upregulated and 14 genes were continuously downregulated from E6 to E16.The present study might provide new insights into complex molecular mechanisms in regulation of endochondral ossification.

关键词： Embryos Hindlimb Ossification Precocial Transcriptomics

Design and tailoring of patterned ZnO nanostructures for perovskite light absorption modulation

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International Journal of Minerals,Metallurgy and Materials 2024年第5期31卷 855-861页

作者： Haonan Si xuan Zhao Qingliang Liao Yue zhang Academy for Advanced Interdisciplinary Science and Technology Beijing Advanced Innovation Center for Materials Genome EngineeringUniversity of Science and Technology BeijingBeijing 100083China Key Laboratory of Advanced Materials and Devices for Post-Moore Chips Ministry of EducationBeijing Key Laboratory for Advanced Energy Materials and TechnologiesSchool of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing 100083China

Lithography is a pivotal micro/nanomanufacturing technique,facilitating performance enhancements in an extensive array of devices,encompassing sensors,transistors,and photovoltaic devices.The key to creating highly precise,multiscale-distributed patterned structures is the precise control of the lithography process.Herein,high-quality patterned ZnO nanostructures are constructed by systematically tuning the exposure and development times during lithography.By optimizing these parameters,ZnO nanorod arrays with line/hole arrangements are successfully prepared.Patterned ZnO nanostructures with highly controllable morphology and structure possess discrete three-dimensional space structure,enlarged surface area,and improved light capture ability,which achieve highly efficient energy conversion in perovskite solar cells.The lithography process management for these patterned ZnO nanostructures provides important guidance for the design and construction of complex nanostructures and devices with excellent performance.

关键词： lithography patterned ZnO nanorod arrays light absorption perovskite solar cell