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Unveiling protein corona composition:predicting with resampling embedding and machine learning

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Regenerative Biomaterials 2024年第1期3卷 27-33页

作者： Rong Liao yan zhuang Xiangfeng Li Ke Chen Xingming Wang Cong Feng Guangfu Yin Xiangdong Zhu Jiangli Lin Xingdong Zhang College of Biomedical Engineering National Engineering Research Centre for BiomaterialsSichuan UniversityChengdu610065China

Biomaterials with surface nanostructures effectively enhance protein secretion and stimulate tissue regeneration.When nanoparticles(NPs)enter the living system,they quickly interact with proteins in the body fluid,forming the protein corona(PC).The accurate prediction of the PC composition is critical for analyzing the osteoinductivity of biomaterials and guiding the reverse design of NPs.However,achieving accurate predictions remains a significant challenge.Although several machine learning(ML)models like Random Forest(RF)have been used for PC prediction,they often fail to consider the extreme values in the abundance region of PC absorption and struggle to improve accuracy due to the imbalanced data distribution.In this study,resampling embedding was introduced to resolve the issue of imbalanced distribution in PC data.Various ML models were evaluated,and RF model was finally used for prediction,and good correlation coefficient(R^(2))and root-mean-square deviation(RMSE)values were obtained.Our ablation experiments demonstrated that the proposed method achieved an R^(2) of 0.68,indicating an improvement of approximately 10%,and an RMSE of 0.90,representing a reduction of approximately 10%.Furthermore,through the verification of label-free quantification of four NPs:hydroxyapatite(HA),titanium dioxide(TiO_(2)),silicon dioxide(SiO_(2))and silver(Ag),and we achieved a prediction performance with an R^(2) value>0.70 using Random Oversampling.Additionally,the feature analysis revealed that the composition of the PC is most significantly influenced by the incubation plasma concentration,PDI and surface modification.

关键词： nanoparticles protein corona machine learming resampling technique feature analysis

Boundedness of solutions for a class of semilinear oscillators

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Acta Mathematica Sinica,English Series 2024年

作者： yan zhuang Da Xiong PIAO yan Min NIU Ocean University of China School of Mathematical Sciences

We are concerned with the boundedness for the equation x + f(x, x) + ω2x = p(t), where p is quasi-periodic function. Since the corresponding system is non-Hamiltonian, we transform the original system into a new reversible one, the Poincaré mapping of which satisfies the twist theorem for quasi-periodic reversible mappings of low smoothness, or is close to its linear part by normal form theorem. We then obtain results concerning the boundedness of solutions based on the recently work.The above two cases need some smooth and growth assumptions for f and p, which are precisely the innovations of this paper.

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Existence of multi-hump generalized homoclinic solutions for a class of reversible systems

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Science China Mathematics 2024年

作者： Shengfu Deng yan Zhou Jinsen zhuang School of Mathematical Sciences Huaqiao University

In this paper, we investigate a class of reversible dynamical systems in four dimensions. The spectrums of their linear operators at the equilibria are assumed to have a pair of positive and negative real eigenvalues and a pair of purely imaginary eigenvalues for the small parameterμ> 0, where these two real eigenvalues bifurcate from a double eigenvalue 0 forμ=0. It has been shown that this class of systems owns a generalized homoclinic solution with one hump at the center （a homoclinic solution exponentially approaching a periodic solution with a small amplitude）. This paper gives a rigorous existence proof of two-hump solutions.These two humps are far away and are glued by the small oscillations in the middle if some appropriate free constants are activated. The obtained results are also applied to some classical systems. The ideas here may be used to study the existence of 2k-hump solutions.

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MFG-E8 Alleviates Cognitive Impairments Induced by Chronic Cerebral Hypoperfusion by Phagocytosing Myelin Debris and Promoting Remyelination

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Neuroscience Bulletin 2024年第4期40卷 483-499页

作者： Xiaohong Dong Zhi Zhang Xin Shu Zi zhuang Pinyi Liu Renyuan Liu Shengnan Xia Xinyu Bao Yun Xu yan Chen Department of Neurology Nanjing Drum Tower HospitalAffiliated Hospital of Medical SchoolNanjing UniversityNanjing210008China Department of Neurology Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western MedicineNanjing University of Chinese MedicineNanjing210008China Department of Neurology Drum Tower Hospital of Nanjing Medical UniversityNanjing210008China Jiangsu Key Laboratory for Molecular Medicine Medical School of Nanjing UniversityNanjing210008China Jiangsu Provincial Key Discipline of Neurology Nanjing210008China

Chronic cerebral hypoperfusion is one of the pathophysiological mechanisms contributing to cognitive decline by causing white matter injury.Microglia phagocytosing myelin debris in a timely manner can promote remyelination and contribute to the repair of white matter.However,milk fat globule-epidermal growth factor-factor 8(MFG-E8),a microglial phagocytosis-related protein,has not been well studied in hypoperfusion-related cognitive dysfunction.We found that the expression of MFG-E8 was significantly decreased in the brain of mice after bilateral carotid artery stenosis(BCAS).MFG-E8 knockout mice demonstrated more severe BCAS-induced cognitive impairments in the behavioral tests.In addition,we discovered that the deletion of MFG-E8 aggravated white matter damage and the destruction of myelin microstructure through fluorescent staining and electron microscopy.Meanwhile,MFG-E8 overexpression by AAV improved white matter injury and increased the number of mature oligodendrocytes after BCAS.Moreover,in vitro and in vivo experiments showed that MFG-E8 could enhance the phagocytic function of microglia via theαVβ3/αVβ5/Rac1 pathway and IGF-1 production to promote the differentiation of oligodendrocyte progenitor cells into mature oligodendrocytes.Interestingly,we found that MFG-E8 was mainly derived from astrocytes,not microglia.Our findings suggest that MFG-E8 is a potential therapeutic target for cognitive impairments following cerebral hypoperfusion.

关键词： White matter injury Cognitive dysfunction MFG-E8 Remyelination Microglial phagocytosis

Differential expression profile of circular RNAs in mouse peritoneum with peritoneal fibrosis and the potential regulatory role of novel_circ_0007527

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Genes & Diseases 2024年第3期11卷 59-62页

作者： Yingfeng Shi yan Hu Hui Chen Jinqing Li Min Tao Xun Zhou Qin Zhong Andong Qiu Shougang zhuang Na Liu Department of Nephrology Shanghai East HospitalTongji University School of MedicineShanghai 200120China School of Life Science and Technology Advanced Institute of Translational MedicineTongji UniversityShanghai 200092China Department of Medicine Rhode Island Hospital and Alpert Medical SchoolBrown UniversityProvidenceRI 02912USA

CircRNAs,a novel type of endogenous non-coding RNAs(ncRNAs),are typically produced by back-splicing from exons of protein-coding genes,which are characterized by a covalently closed structure with neither 5'to 3'polarity nor a poly(A)tail.'On the one hand,circRNAs are involved in the regulation of a variety of important biological processes,such as apoptosis,proliferation,migration,and inflammatory responses.'On the other hand,the relationship between circRNAs and several fibrotic diseases has been reported.2 However.

关键词： endogenous peritoneal diseases

Pumping-induced Well Hydraulics and Groundwater Budget in a Leaky Aquifer System with Vertical Heterogeneity in Aquitard Hydraulic Properties

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Acta Geologica Sinica(English Edition) 2024年第2期98卷 477-490页

作者： zhuang Chao LÜChenyang yan Long LI Yabing ZHOU Zhifang WANG Jinguo DOU Zhi Walter A.ILLMAN School of Earth Sciences and Engineering Hohai UniversityNanjing 211100China School of Geography Earth and Environmental SciencesUniversity of BirminghamBirmingham B152TTU.K. Department of Modern Mechanics University of Science and Technology of ChinaHefei 230027China Department of Earth and Environmental Sciences University of WaterlooOntario N2L 3G1Canada

In groundwater hydrology,aquitard heterogeneity is often less considered compared to aquifers,despite its significant impact on groundwater hydraulics and groundwater resources evaluation.A semi-analytical solution is derived for pumping-induced well hydraulics and groundwater budget with consideration of vertical heterogeneity in aquitard hydraulic conductivity(K)and specific storage(S_(s)).The proposed new solution is innovative in its partitioning of the aquitard into multiple homogeneous sub-layers to enable consideration of various forms of vertically heterogeneous K or S_(s).Two scenarios of analytical investigations are explored:one is the presence of aquitard interlayers with distinct K or S_(s) values,a common field-scale occurrence;another is an exponentially depth-decaying aquitard S_(s),a regional-scale phenomenon supported by statistical analysis.Analytical investigations reveal that a low-K interlayer can significantly increase aquifer drawdown and enhance aquifer/aquitard depletion;a high-S_(s) interlayer can noticeably reduce aquifer drawdown and increase aquitard depletion.Locations of low-K or high-S_(s) interlayers also significantly impact well hydraulics and groundwater budget.In the context of an exponentially depth-decaying aquitard S_(s),a larger decay exponent can enhance aquifer drawdown.When using current models with a vertically homogeneous aquitard,half the sum of the geometric and harmonic means of exponentially depth-decaying aquitard S_(s) should be used to calculate aquitard depletion and unconfined aquifer leakage.

关键词： hydrogeology aquitard vertical heterogeneity semi-analytical solution well hydraulics groundwater budget

主跨330 m高速铁路无砟轨道混合梁斜拉桥设计

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铁道工程学报 2024年第4期41卷 42-47,59页

作者：庄严中铁第一勘察设计院集团有限公司西安710043

研究目的:为满足防洪及通航要求,南玉高铁百合郁江特大桥采用(36+40+64+330+64+40+36)m钢箱-混凝土混合梁斜拉桥跨越郁江。该桥为目前国内在建最大跨度的高速铁路无砟轨道钢箱-混凝土混合梁斜拉桥。本文主要基于百合郁江特大桥的设计与... 详细信息

研究目的:为满足防洪及通航要求,南玉高铁百合郁江特大桥采用(36+40+64+330+64+40+36)m钢箱-混凝土混合梁斜拉桥跨越郁江。该桥为目前国内在建最大跨度的高速铁路无砟轨道钢箱-混凝土混合梁斜拉桥。本文主要基于百合郁江特大桥的设计与受力特点,通过多种评价方法,探讨在大跨度钢混斜拉桥上铺设无砟轨道适应性,为后续建造同类型无砟轨道桥梁提供理论参考。研究结论:(1)主桥采用钢箱梁与混凝土箱梁,并在钢箱梁顶板上现浇混凝土桥面板,为无砟轨道铺设创造了良好条件,并且能很好地控制后期主梁的收缩徐变变形,提高大跨桥梁对无砟轨道适应性;(2)百合郁江特大桥具有良好的静力性能和刚度条件;(3)主桥将轨道结构高度由725 mm调整为775 mm,分别为底座板和道床板预留了20 mm和30 mm的纠偏量,为后续无砟轨道分级施工和纠偏提供了基础,能更好地将施工与测量误差逐级消除,提高无砟轨道铺设精度;(4)采用多种无砟轨道适应性评价方法对主桥无砟轨道线形进行分析,结论均满足设计要求;(5)该桥的成功实施,为国内外高速铁路无砟轨道桥梁建设提供了宝贵的经验,将进一步推动高速铁路无砟轨道大跨度桥梁的技术发展。

关键词：无砟轨道大跨度钢箱梁混合梁斜拉桥

Hepatocyte growth factor enhances the ability of dental pulp stem cells to ameliorate atherosclerosis in apolipoprotein E-knockout mice

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World Journal of Stem Cells 2024年第5期16卷 575-590页

作者： Han Duan Ning Tao Lin Lv Kai-Xin yan Yong-Gang You zhuang Mao Chang-Yao Wang Xue Li Jia-yan Jin Chu-Tse Wu Hua Wang School of Life Sciences Hebei UniversityBaoding 071002Hebei ProvinceChina Beijing Institute of Radiation Medicine Beijing 100850China Department of Cardiology The Sixth Medical CentreChinese People’s Liberation Army General HospitalBeijing 100037China Department of Orthopaedics The Fourth Medical CentreChinese People’s Liberation Army General HospitalBeijing 100853China Third Cadet Regiment School of Basic Medical ScienceAir Force Medical UniversityXi’an 710032Shaanxi ProvinceChina

BACKGROUND Atherosclerosis(AS),a chronic inflammatory disease of blood vessels,is a major contributor to cardiovascular disease.Dental pulp stem cells(DPSCs)are capable of exerting immunomodulatory and anti-inflammatory effects by secreting cytokines and exosomes and are widely used to treat autoimmune and inflam-mation-related diseases.Hepatocyte growth factor(HGF)is a pleiotropic cytokine that plays a key role in many inflammatory and autoimmune diseases.AIM To modify DPSCs with HGF(DPSC-HGF)and evaluate the therapeutic effect of DPSC-HGF on AS using an apolipoprotein E-knockout(ApoE-/-)mouse model and an in vitro cellular model.METHODS ApoE-/-mice were fed with a high-fat diet(HFD)for 12 wk and injected with DPSC-HGF or Ad-Null modified DPSCs(DPSC-Null)through tail vein at weeks 4,7,and 11,respectively,and the therapeutic efficacy and mechanisms were analyzed by histopathology,flow cytometry,lipid and glucose measurements,real-time reverse transcription polymerase chain reaction(RT-PCR),and enzyme-linked immunosorbent assay at the different time points of the experiment.An in vitro inflammatory cell model was established by using RAW264.7 cells and human aortic endothelial cells(HAOECs),and indirect co-cultured with supernatant of DPSC-Null(DPSC-Null-CM)or DPSC-HGF-CM,and the effect and mechanisms were analyzed by flow cytometry,RT-PCR and western blot.Nuclear factor-κB(NF-κB)activators and inhibitors were also used to validate the related signaling pathways.RESULTS DPSC-Null and DPSC-HGF treatments decreased the area of atherosclerotic plaques and reduced the expression of inflammatory factors,and the percentage of macrophages in the aorta,and DPSC-HGF treatment had more pronounced effects.DPSCs treatment had no effect on serum lipoprotein levels.The FACS results showed that DPSCs treatment reduced the percentages of monocytes,neutrophils,and M1 macrophages in the peripheral blood and spleen.DPSC-Null-CM and DPSC-HGF-CM reduced adhesion molecule expression in tumor necrosis factor-αstimulated HAOECs and regul

关键词： Atherosclerosis Apolipoprotein E-knockout mice Cell therapy Dental pulp stem cells Hepatocyte growth factor

On the longitudinal shifts of the Agulhas retroflection point

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Acta Oceanologica Sinica 2024年第5期43卷 16-29页

作者： Weiwei Zhang Xiaoyi yang Wei zhuang Xiaohai yan State Key Laboratory of Marine Environmental Science College of Ocean and Earth SciencesXiamen UniversityXiamen 361002China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519082China Center for Remote Sensing College of EarthOcean and EnvironmentUniversity of DelawareNewarkDE 19716USA Joint Center for Remote Sensing University of Delaware-Xiamen UniversityNewarkDE 19716USA and Xiamen 361002China

The Agulhas system is the strongest western boundary current system in the Southern Hemisphere and plays an important role in modulating the Indian-to-Atlantic Ocean water exchange by the Agulhas leakage.It is difficult to measure in situ transport of the Agulhas leakage as well as the Agulhas retroflection position due to their intermittent nature.In this study,an innovative kinematic algorithm was designed and applied to the gridded altimeter observational data,to ascertain the longitudinal position of Agulhas retroflection,the stability of Agulhas jet stream,as well as its strength.The results show that the east-west shift of retroflection is related neither to the strength of Agulhas current nor to its stability.Further analysis uncovers the connection between the westward extension of Agulhas jet stream and an anomalous cyclonic circulation at its northern side,which is likely attributed to the local wind stress curl anomaly.To confirm the effect of local wind forcing on the east-west shift of retroflection,numerical sensitivity experiments were conducted.The results show that the local wind stress can induce a similar longitudinal shift of the retroflection as altimetry observations.Further statistical and case study indicates that whether an Agulhas ring can continuously migrate westward to the Atlantic Ocean or re-merge into the main flow depends on the retroflection position.Therefore,the westward retroflection may contribute to a stronger Agulhas leakage than the eastward retroflection.

关键词： Agulhas system Agulhas leakage retroflection position local wind stress curl