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

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

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Constructing a biofunctionalized 3D-printed gelatin/sodium alginate/chitosan tri-polymer complex scaffold with improvised biological andmechanical properties for bone-tissue engineering

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Bio-Design and Manufacturing 2024年第1期7卷 57-73页

作者： Amit Kumar Singh Krishna Pramanik Amit Biswas centre of Excellence in Tissue engineering Department of Biotechnology and Medical EngineeringNational Institute of TechnologyRourkela 769008India

Sodium alginate(SA)/chitosan(CH)polyelectrolyte scaffold is a suitable substrate for tissue-engineering application.The present study deals with further improvement in the tensile strength and biological properties of this type of scaffold to make it a potential template for bone-tissue regeneration.We experimented with adding 0%–15%(volume fraction)gelatin(GE),a protein-based biopolymer known to promote cell adhesion,proliferation,and differentiation.The resulting tri-polymer complex was used as bioink to fabricate SA/CH/GEmatrices by three-dimensional(3D)printing.Morphological studies using scanning electron microscopy revealed the microfibrous porous architecture of all the structures,which had a pore size range of 383–419μm.X-ray diffraction and Fourier-transform infrared spectroscopy analyses revealed the amorphous nature of the scaffold and the strong electrostatic interactions among the functional groups of the polymers,thereby forming polyelectrolyte complexes which were found to improve mechanical properties and structural stability.The scaffolds exhibited a desirable degradation rate,controlled swelling,and hydrophilic characteristics which are favorable for bone-tissue engineering.The tensile strength improved from(386±15)to(693±15)kPa due to the increased stiffness of SA/CH scaffolds upon addition of gelatin.The enhanced protein adsorption and in vitro bioactivity(forming an apatite layer)confirmed the ability of the SA/CH/GE scaffold to offer higher cellular adhesion and a bone-like environment to cells during the process of tissue regeneration.In vitro biological evaluation including the MTT assay,confocal microscopy analysis,and alizarin red S assay showed a significant increase in cell attachment,cell viability,and cell proliferation,which further improved biomineralization over the scaffold surface.In addition,SA/CH containing 15%gelatin designated as SA/CH/GE15 showed superior performance to the other fabricated 3D structures,demonstrating its potential for use in bone-tissue engineering.

关键词： Scaffold Biomaterial Sodium alginate Chitosan Gelatin 3D printing Tissue engineering

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Plasma-exfoliated g-C_(3)N_(4) with oxygen doping: tailoring photocatalytic properties

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Frontiers of Chemical Science and engineering 2024年第2期18卷 27-39页

作者： Yuxin Li Junxin Guo Rui Han Zhao Wang national engineering Research centre of Industry Crystallization Technology School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China

Heteroatom doping and defect engineering have been proposed as effective ways to modulate the energy band structure and improve the photocatalytic activity of g-C_(3)N_(4). In this work, ultrathin defective g-C_(3)N_(4) was successfully prepared using cold plasma. Plasma exfoliation reduces the thickness of g-C_(3)N_(4) from 10 nm to 3 nm, while simultaneously introducing a large number of nitrogen defects and oxygen atoms into g-C_(3)N_(4). The amount of doped O was regulated by varying the time and power of the plasma treatment. Due to N vacancies, O atoms formed strong bonds with C atoms, resulting in O doping in g-C_(3)N_(4). The mechanism of plasma treatment involves oxygen etching and gas expansion. Photocatalytic experiments demonstrated that appropriate amount of O doping improved the photocatalytic degradation of rhodamine B compared with pure g-C_(3)N_(4). The introduction of O optimized the energy band structure and photoelectric properties of g-C_(3)N_(4). Active species trapping experiments revealed ·O_(2)^(–) as the main active species during the degradation.

关键词： graphitic carbon nitride cold plasma oxygen doping nitrogen defect visible-light photocatalysis

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Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens

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Journal of Animal Science and Biotechnology 2024年第1期15卷 53-67页

作者： Xiaoli Guo Qianqian Zhou Jiaming Jin Fangren Lan Chaoliang Wen Junying Li Ning Yang Congjiao Sun national engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsChina Agricultural UniversityBeijing 100193China

Background Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying hens.Methods Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic steatosis.Results The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins(DEPs) interacted with differentially acetylated proteins(DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group(P < 0.05). Lipidomics detected a variety of sphingolipids(SPs) and glycerophospholipids(GPs) were negatively correlated with hepatic steatosis(r ≤-0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol transport.Conclusions In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of acetylation in hepatic steatosis and depict the ch

关键词： Acetylation Cholesterol metabolism Hepatic steatosis Laying hens Multiomics

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Cobalt-nitrogen co-doped porous carbon sphere as highly efficient catalyst for liquid-phase cyclohexane oxidation with molecular oxygen and the active sites investigation

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Frontiers of Chemical Science and engineering 2024年第3期18卷 101-112页

作者： Lei Chen Yuan Sun Jinshan Chi Wei Xiong Pingle Liu Fang Hao College of Chemical engineering National&Local United Engineering Research Centre for Chemical Process Simulation and IntensificationXiangtan UniversityXiangtan411105China

The selective oxidation of cyclohexane to cyclohexanone and cyclohexanol(KA oil)is a challenging issue in the chemical industry.At present the industrial conversion of cyclohexane to cyclohexanone and cyclohexanol is normally controlled at less than 5%selectivity.Thus,the development of highly active and stable catalysts for the aerobic oxidation of cyclohexane is necessary to overcome this low-efficiency process.Therefore,we have developed a cobalt-nitrogen co-doped porous sphere catalyst,Co-NC-x(x is the Zn/Co molar ratio,where x=0,0.5,1,2,and 4)by pyrolyzing resorcinol-formaldehyde resin microspheres.It achieved 88.28%cyclohexanone and cyclohexanol selectivity and a cyclohexane conversion of 8.88%under Co-NC-2.The results showed that the introduction of zinc effectively alleviated the aggregation of Co nanoparticles and optimized the structural properties of the material.In addition,Co0 and pyridinic-N are proposed to be the possible active species,and their proportion efficiently increased in the presence of Zn^(2+)species.In this study,we developed a novel strategy to design highly active catalysts for cyclohexane oxidation.

关键词： KA oil production cyclohexane selective oxidation cobalt-nitrogen co-doped porous carbon spheres metal-organic framework

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Role of microbiota-gut-brain axis in neurodegenerative diseases and the potential of microbiome-targeted d ietary strategies: A review of current evidence and future perspective

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Food Science and Human Wellness 2024年

作者： Shuqing Zhang Wenjing Chen Chen Ma Yinghua Luo Li Dong Xiaosong Hu Fang Chen Daotong Li College of Food Science and Nutritional engineering national engineering Research centre for Fruit and Vegetable Processing Key Laboratory of Fruits and Vegetables Processing Ministry of agriculture engineering Research centre for Fruits and Vegetables Processing Ministry of Education China Agricultural University

Neurodegenerative diseases (NDs)， mainly including Alzheimer’s disease， Parkinson’s disease， and Multiple sclerosis， represent a major public health challenge with the steady increase of aging population worldwide. Emerging evidence has revealed the key role of the microbiota-gut-brain axis in the pathogenesis of NDs. Diet is one of the most important environmental factors shaping the structure and function of gut microbiota. Manipulating the gut microbiota through specific diet patterns may represent a promising approach for NDs prevention. In this review， we highlight gut microbiota variations in NDs， outline several crucial signaling pathways of the gut-brain communication， and discuss the interplay of nutrients-microbes and biological effect of diet-derived microbial metabolites on neural physiology. In particular， we summarized the current knowledge about the application of dietary patterns in NDs to prevent disease progression via the modulation of the gut microbiota. Our study provides novel insights on the diet-microbiota-gut-brain axis in neurodegenerative disorders and highlights the potential of developing microbiome-targeted personalized dietary intervention for NDs management.

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Progress of gaseous arsenic removal from flue gas by adsorption:Experimental and theoretical calculations

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Journal of Environmental Sciences 2024年第2期136卷 470-485页

作者： Xuelei Yan Qingzhu Li Xiaowei Huang Bensheng Li Shengtu Li Qingwei Wang School of Metallurgy and Environment Central South UniversityChangsha 410083China national engineering Research centre for Control and Treatment of Heavy Metal Pollution Central South UniversityChangsha 410083China national engineering Research Center for Rare Earth Materials General Research Institute for Non-Ferrous MetalsBeijing 100088China

Because of its high mobility and difficult capture,gaseous arsenic pollution control has become the focus of arsenic pollution control.It mainly exists in the form of highly toxic As_(2)O_(3)in the flue gas.Therefore,removing gaseous As_(2)O_(3)from flue gas is of great practical significance for arsenic pollution control.Stabilizing gaseous As_(2)O_(3)on the surface of adsorbents by physical or chemical adsorption is an effective way to reduce the content of arsenic in the flue gas and alleviate arsenic pollution.Over the past few decades,various adsorbents have been developed to capture gaseous As_(2)O_(3)in the flue gas,and their adsorption mechanisms have been studied in detail.Thus,it is necessary to review the strategies of arsenic removal from flue gas by adsorption,which can inspire further research.Based on summarizing the morphological distribution of gaseous As_(2)O_(3)in the flue gas,this review further summarizes the removal of gaseous As_(2)O_(3)by several adsorbents and the effect of temperature and the main components of the flue gas on arsenic adsorption.In addition,the mechanism of arsenic removal based on adsorption in the flue gas is discussed in depth through theoretical calculations,which is the particular focus of this review.Finally,prospects based on the present research state of arsenic removal by adsorption are proposed to provide ideas for developing effective and stable adsorbents for arsenic removal from flue gas.

关键词： Gaseous arsenic Flue gas Adsorption Theoretical calculation Mechanism

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Simulation and forecasting of fishery weather based on statistical machine learning

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Information Processing in agriculture 2024年第1期11卷 127-142页

作者： Xueqian Fu Chunyu Zhang Fuhao Chang Lingling Han Xiaolong Zhao Zhengjie Wang Qiaoyu Ma national Innovation Center for Digital Fishery China Agricultural UniversityBeijingChina Key Laboratory of Smart Farming Technologies for Aquatic Animal and Livestock Ministry of Agriculture and Rural AffairsBeijingChina Beijing engineering and Technology Research Center for Internet of Things in agriculture BeijingChina College of Information and Electrical engineering China Agricultural UniversityBeijingChina

As the new generation of artificial intelligence(AI)continues to evolve,weather big data and statistical machine learning(SML)technologies complement each other and are deeply integrated to significantly improve the processing and forecasting accuracy of fishery weather.Accurate fishery weather services play a crucial role in fishery production,serving as a great safeguard for economic benefits and personal safety,enabling fishermen to carry out fishery production better,and contributing to the sustainable development of the fishery industry.The objective of this paper is to offer an understanding of the present state of research and development in SML technology for simulating and forecasting fishery weather.Specifically,we analyze the current state of research and technical features of SML in weather and summarize the applications of SML in simulation and forecasting of fishery weather,which mainly include three aspects:fishery weather scenario generation,fishery weather forecasting,and fishery extreme weather warning.We also illustrate the main technical means and principles of SML technology.Finally,we summarize the most advanced SML fields and provide an outlook on their application value in the field of fishery weather.

关键词： Fishery weather Statistical machine learning Weather generation Weather forecasting Extreme weather warning

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Estimating wheat spike-leaf composite indicator(SLI)dynamics by coupling spectral indices and machine learning

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The Crop Journal 2024年第3期12卷 927-937页

作者： Haiyu Tao Ruiheng Zhou Yining Tang Wanyu Li Xia Yao Tao Cheng Yan Zhu Weixing Cao Yongchao Tian national engineering and Technology Center for Information agriculture Key Laboratory of Crop System Analysis and Decision MakingMinistry of Agriculture and Rural AffairsJiangsu Key Laboratory for Information AgricultureNanjing Agricultural UniversityNanjing 210095JiangsuChina

The contribution of spike photosynthesis to grain yield(GY)has been overlooked in the accurate spectral prediction of yield.Thus,it’s essential to construct and estimate a yield-related phenotypic trait considering spike photosynthesis.Based on field and spectral reflectance data from 19 wheat cultivars under two nitrogen fertilization conditions in two years,our objectives were to(i)construct a yield-related phenotypic trait(spike–leaf composite indicator,SLI)accounting for the contribution of the spike to photosynthesis,(ii)develop a novel spectral index(enhanced triangle vegetation index,ETVI3)sensitive to SLI,and(iii)establish and evaluate SLI estimation models by integrating spectral indices and machine learning algorithms.The results showed that SLI was sensitive to nitrogen fertilizer and wheat cultivar variation as well as a better predictor of yield than the leaf area index.ETVI3 maintained a strong correlation with SLI throughout the growth stage,whereas the correlations of other spectral indices with SLI were poor after spike emergence.Integrating spectral indices and machine learning algorithms improved the estimation accuracy of SLI,with the most accurate estimates of SLI showing coefficient of determination,root mean square error(RMSE),and relative RMSE values of 0.71,0.047,and 26.93%,respectively.These results provide new insights into the role of fruiting organs for the accurate spectral prediction of GY.This high-throughput SLI estimation approach can be applied for wheat yield prediction at whole growth stages and may be assisted with agronomical practices and variety selection.

关键词： Wheat spike photosynthesis Yield-related phenotypic trait Spectral indices Machine learning Estimation

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Lactiplantibacillus plantarum FRT4 attenuates high-energy low-protein dietinduced fatty liver hemorrhage syndrome in laying hens through regulating gut-liver axis

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1292-1311页

作者： Daojie Li Hongying Cai Guohua Liu Yunsheng Han Kai Qiu Weiwei Liu Kun Meng Peilong Yang Key Laboratory of Feed Biotechnology of Ministry of agriculture and Rural Affairs Institute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081China national engineering Research Center of Biological Feed Beijing 100081China

Background Fatty liver hemorrhage syndrome(FLHS)becomes one of the most major factors resulting in the laying hen death for caged egg production.This study aimed to investigate the therapeutic effects of Lactiplantibacillus plan-tarum(Lp.plantarum)FRT4 on FLHS model in laying hen with a focus on liver lipid metabolism,and gut microbiota.Results The FLHS model of laying hens was established by feeding a high-energy low-protein(HELP)diet,and the treatment groups were fed a HELP diet supplemented with differential proportions of Lp.plantarum FRT4.The results indicated that Lp.plantarum FRT4 increased laying rate,and reduced the liver lipid accumulation by regulating lipid metabolism(lipid synthesis and transport)and improving the gut microbiota composition.Moreover,Lp.plan-tarum FRT4 regulated the liver glycerophospholipid metabolism.Meanwhile,“gut-liver”axis analysis showed that there was a correlation between gut microbiota and lipid metabolites.Conclusions The results indicated that Lp.plantarum FRT4 improved the laying performance and alleviated FLHS in HELP diet-induced laying hens through regulating“gut-liver”axis.Our findings reveal that glycerophospholipid metabolism could be the underlying mechanism for the anti-FLHS effect of Lp.plantarum FRT4 and for future use of Lp.plantarum FRT4 as an excellent additive for the prevention and mitigation of FLHS in laying hens.

关键词： Fatty liver hemorrhage syndrome Gut microbiota Lactiplantibacillus plantarum FRT4 Laying hens Lipid metabolism

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