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iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 593-600页

作者： Md.Mehedi Hasan Mst.Shamima Khatun Hiroyuki Kurata department of Bioscience and Bioinformatics Kyushu Institute of TechnologyIizukaFukuoka 820-8502Japan biomedical informatics r&d center Kyushu Institute of TechnologyIizukaFukuoka 820-8502Japan

Linear B-cell epitopes are critically important for immunological applications,such as vaccine design,immunodiagnostic test,and antibody production,as well as disease diagnosis and *** accurate identification of linear B-cell epitopes remains challenging despite several decades of *** this work,we have developed a novel predictor,Identification of Linear B-cell Epitope(i LBE),by integrating evolutionary and sequence-based *** successive feature vectors were optimized by a Wilcoxon-rank sum *** the random forest(rF)algorithm using the optimal consecutive feature vectors was applied to predict linear B-cell *** combined the rF scores by the logistic regression to enhance the prediction *** yielded an area under curve score of 0.809 on the training dataset and outperformed other prediction models on a comprehensive independent *** is a powerful computational tool to identify the linear B-cell epitopes and would help to develop penetrating diagnostic tests.A web application with curated datasets for iLBE is freely accessible at http://***/iLBE/.

关键词： Linear B-cell epitope BLAST Feature encoding Feature selection random forest

Storage time affects the level and diagnostic efficacy of plasma biomarkers for neurodegenerative diseases

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Neural regeneration research 2025年第8期20卷 2373-2381页

作者： Lifang Zhao Mingkai Zhang Qimeng Li Xuemin Wang Jie Lu Ying Han Yanning Cai department of Clinical Biobank Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Geriatric Medical research center BeijingChina department of Neurology Xuanwu HospitalCapital Medical UniversityBeijingChina department of radiology and Nuclear Medicine Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Key Laboratory of Magnetic resonance Imaging and Brain informatics BeijingChina Key Laboratory of Neurodegenerative diseases Ministry of EducationBeijingChina School of biomedical Engineering Hainan UniversityHaikouHainan ProvinceChina center of Alzheimer’s disease Beijing Institute for Brain DisordersBeijingChina National Clinical research center for Geriatric diseases BeijingChina Institute of biomedical Engineering Shenzhen Bay LaboratoryGaoke Innovation CenterShenzhenGuangdong ProvinceChina department of Neurobiology Xuanwu HospitalCapital Medical UniversityBeijingChina

Several promising plasma biomarker proteins,such as amyloid-β(Aβ),tau,neurofilament light chain,and glial fibrillary acidic protein,are widely used for the diagnosis of neurodegenerative ***,little is known about the long-term stability of these biomarker proteins in plasma samples stored at-80°*** aimed to explore how storage time would affect the diagnostic accuracy of these biomarkers using a large *** samples from 229 cognitively unimpaired individuals,encompassing healthy controls and those experiencing subjective cognitive decline,as well as 99 patients with cognitive impairment,comprising those with mild cognitive impairment and dementia,were acquired from the Sino Longitudinal Study on Cognitive decline *** samples were stored at-80°C for up to 6 years before being used in this *** results showed that plasma levels of Aβ42,Aβ40,neurofilament light chain,and glial fibrillary acidic protein were not significantly correlated with sample storage ***,the level of total tau showed a negative correlation with sample storage ***,in individuals without cognitive impairment,plasma levels of total protein and tau phosphorylated protein threonine 181(p-tau181)also showed a negative correlation with sample storage *** was not observed in individuals with cognitive ***,we speculate that the diagnostic accuracy of plasma p-tau181 and the p-tau181 to total tau ratio may be influenced by sample storage ***,caution is advised when using these plasma biomarkers for the identification of neurodegenerative diseases,such as Alzheimer's ***,in cohort studies,it is important to consider the impact of storage time on the overall results.

关键词： Alzheimer’s disease amyloid-β diagnostic ability glial fibrillary acidic protein neurodegeneration neurofilament light chain plasma biomarkers single molecule array storage time tau

Molecular design, synthesis strategies and recent advances of hydrogels for wound dressing applications

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Chinese Journal of Chemical Engineering 2021年第2期34卷 308-320页

作者： dan Zeng Shihong Shen daidi Fan Shaanxi Key Laboratory of degradable biomedical Materials Shaanxi R&D Center of Biomaterials and Fermentation EngineeringSchool of Chemical EngineeringNorthwest UniversityXi’an 710069China

With the changes in the modern disease spectrum,pressure ulcers,diabetic feet,and vascular-derived diseases caused refractory wounds is increasing *** development of wound dressings has partly improved the effect of wound ***,traditional wound dressings can only cover the wound and block bacteria,but are generally powerless to recurrent wound infection and tissue *** is an urgent need to develop a new type of wound dressing with comprehensive performance to achieve multiple effects such as protecting the wound site from the external environment,absorbing wound exudate,anti-inflammatory,antibacterial,and accelerating wound healing *** wound dressings have the aforementioned characteristics,and can keep the wound in a moist environment because of the high water content,which is an ideal choice for wound *** review introduces the wound healing process and the development and performance advantages of hydrogel wound *** choice of different preparation materials gives the particularities of different hydrogel wound *** also systematically explains the main physical and chemical crosslinking methods for hydrogel ***,in-depth discussion of four typical hydrogel wound dressings including double network hydrogels,nanocomposite hydrogels,drug-loaded hydrogels and smart hydrogels fully demonstrates the feasibility of developing hydrogels as wound dressing products and their future development trends.

关键词： Hydrogels Wound dressing Molecular design Crosslinked networks biomedical applications

Hemoglobin integrated red blood cell membrane-coated metalorganic framework nano-platform for improving the self-adaptive blood glucose management

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Nano research 2025年第1期18卷 618-627页

作者： Shuai Wu Li Zhu Sheng Ni Xiong Zhao Meng Yan Yuan Zhong Karissa Kusuma Yi Liang Kaiwen Bao Kai Qu Xian Qin Kun Zhang Wuquan deng da Sun Wei Wu Key Laboratory of Biorheological Science and Technology Ministry of EducationCollege of BioengineeringChongqing UniversityChongqing 400044China Chongqing University Three Gorges Hospital Chongqing Municipality Clinical Research Center for Endocrinology and Metabolic DiseasesChongqing 404000China Institute of Life Sciences&biomedical Collaborative Innovation center of Zhejiang Province Wenzhou UniversityWenzhou 325035China department of Endocrinology School of MedicineChongqing Emergency Medical CenterChongqing University Central HospitalChongqing 400014China

diabetes,a prevalent chronic metabolic disorder,often leads to severe ***,existing treatment methods may pose life-threatening risks due to poor patient compliance and inaccurate dosing of subcutaneous insulin ***,a biomimetic red blood cell(rBC)membrane-coated glucose-responsive nanoplatform is developed for controlling insulin *** nanoplatforms with rBC membrane can prolong the half-life of nano-formulation in vivo mediated by the biomimetic immune ***,the cascade catalytic effect of glucose oxidase(GOx)encapsulated in metal-organic frameworks(MOFs)and hemoglobin(Hb)in the rBC membrane are able to not only facilitate glucose-responsive insulin release,but also eliminate the detrimental by-product hydrogen peroxide(H_(2)O_(2))resulting from the Hb mediated H_(2)O_(2)*** in vitro and in vivo studies have demonstrated the favorable glucose-responsive performances of this advanced nano-platform with a single intravenous injection maintaining blood glucose balance in Type 1 diabetes(T1d)mice for an extended duration without the hypoglycemia ***,this biomimetic insulin delivery system is poised to function as a strategy for the intravenous insulin administration,offering a promising drug candidate for the self-adaptive long-term T1d treatment.

关键词： glucose-responsive metal-organic frameworks red blood cell membrane insulin delivery glucose oxidase hemoglobin

Eu^(3+)/Tb^(3+)-doped whitlockite nanocrystals:Controllable synthesis,cell imaging,and the degradation process in the bone reconstruction

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Nano research 2022年第2期15卷 1303-1309页

作者： Zichen Yang Tianyu Yao Xiaoyan Zheng Junfeng Hui daidi Fan Shaanxi Key Laboratory of degradable biomedical Materials and Shaanxi r&d center of Biomaterials and Fermentation Engineering School of Chemical EngineeringNorthwest UniversityXian 710069China College of Life Sciences Northwest UniversityXian 710069China

Whitlockite(WH,Ca_(18)Mg_(2)(HPO_(4))_(2)(PO_(4))_(12))is an important inorganic phase in human bones and has positive significance for participating in the bone reconstruction *** this paper,we report different doping strategies to prepare WH and WH-Ln(Eu/Tb)nanocrystals,and have successfully synthesized WH-Ln(Eu/Tb)nanoparticles(NPs)with bright red or green fluorescence based on ions exchange doping by two-step hydrothermal ***-5%Ln(Eu/Tb)NPs with the best fluorescence properties were successfully applied to live cell imaging,and WH-5%Eu NPs were implanted into the bone defect site in rabbit femoral condyles to visually observe its degradation *** related results would help us understand WH nanocrystals and further expand their potential applications in tissue engineering and related fields.

关键词： whitlockite ions doping controllable synthesis cell imaging degradation process

Biaxial stretching of polytetrafluoroethylene in industrial scale to fabricate medical ePTFE membrane with node-fibril microstructure

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regenerative Biomaterials 2023年第1期10卷 1161-1177页

作者： Gang Wang Yusheng Feng Caiyun Gao Xu Zhang Qunsong Wang Jie Zhang Hongjie Zhang YongqiangWu Xin Li Lin Wang Ye Fu Xiaoye Yu deyuan Zhang Jianxiong Liu Jiandong ding State Key Laboratory of Molecular Engineering of Polymers Department of Macromolecular ScienceFudan UniversityShanghai 200438China r&d center Lifetech Scientific(Shenzhen)Co.Ltd.Shenzhen 518057China r&d center Lifevalve Medical Scientific Co.Ltd.Shenzhen 518057China

Expanded polytetrafluoroethylene(ePTFE)is promising in biomedical fields such as covered stents and plastic surgery owing to its excellent biocompatibility and mechanical ***,ePTFE material prepared by the traditional biaxial stretching process is with thicker middle and thinner sides due to the bowing effect,which poses a major problem in industrial-scale *** solve this problem,we design an olive-shaped winding roller to provide the middle part of the ePTFE tape with a greater longitudinal stretching amplitude than the two sides,so as to make up for the excessive longitudinal retraction tendency of the middle part when it is transversely *** as-fabricated ePTFE membrane has,as designed,uniform thickness and node-fibril *** addition,we examine the effects of mass ratio of lubricant to PTFE powder,biaxial stretching ratio and sintering temperature on the performance of the resultant ePTFE ***,the relation between the internal microstructure of the ePTFE membrane and its mechanical properties is *** stable mechanical properties,the sintered ePTFE membrane exhibits satisfactory biological *** make a series of biological assessments including in vitro hemolysis,coagulation,bacterial reverse mutation and in vivo thrombosis,intracutaneous reactivity test,pyrogen test and subchronic systemic toxicity test;all of the results meet the relevant international *** muscle implantation of the sintered ePTFE membrane into rabbits indicates acceptable inflammatory reactions of our sintered ePTFE membrane fabricated on industrial *** a medical-grade raw material with the unique physical form and condensed-state microstructure is expected to afford an inert biomaterial potentially for stent-graft membrane.

关键词： biomedical polymer medical-grade raw material expanded polytetrafluoroethylene olive roller polymer processing biaxial stretching

NetBCE: An Interpretable deep Neural Network for Accurate Prediction of Linear B-cell Epitopes

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 1002-1012页

作者： Haodong Xu Zhongming Zhao center for Precision Health School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTX 77030USA Human Genetics center School of Public HealthThe University of Texas Health Science Center at HoustonHoustonTX 77030USA The University of Texas Md Anderson Cancer center UTHealth Houston Graduate School of biomedical Sciences HoustonTX 77030USA department of biomedical informatics Vanderbilt University Medical CenterNashvilleTN 37203USA

Identification of B-cell epitopes(BCEs)plays an essential role in the development of peptide vaccines and immuno-diagnostic reagents,as well as antibody design and *** this work,we generated a large benchmark dataset comprising 124,879 experimentally supported linear epitope-containing regions in 3567 protein clusters from over 1.3 million B cell *** of this curated dataset showed large pathogen diversity covering 176 different *** accuracy in linear BCE prediction was found to strongly vary with different features,while all sequencederived and structural features were *** search more efficient and interpretive feature representations,a ten-layer deep learning framework for linear BCE prediction,namely Net BCE,was *** BCE achieved high accuracy and robust performance with the average area under the curve(AUC)value of 0.8455 in five-fold cross-validation through automatically learning the informative classification *** BCE substantially outperformed the conventional machine learning algorithms and other tools,with more than 22.06%improvement of AUC value compared to other tools using an independent *** investigating the output of important network modules in Net BCE,epitopes and non-epitopes tended to be presented in distinct regions with efficient feature representation along the network layer *** Net BCE is freely available at https://***/bsml320/Net BCE.

关键词： prediction network value

Knowledge representation in Patient Safety reporting: An Ontological Approach

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Journal of data and Information Science 2016年第2期1卷 75-91页

作者： Liang Chen Yang Gong School of biomedical informatics The University of Texas Health Science Center at Houston

Purpose： The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. design/methodology/approach： We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our design, implementation,and evaluation of the ontology at its initial stage. Findings： We describe the design and initial outcomes of the ontology implementation. The evaluation results demonstrate the clinical validity of the ontology by a self-developed survey measurement. research limitations： The proposed ontology was developed and evaluated using a small number of information sources. Presently, US data are used, but they are not essential for the ultimate structure of the *** implications： The goal of improving patient safety can be aided through investigating patient safety reports and providing actionable knowledge to clinical *** such, constructing a domain specific ontology for patient safety reports serves as a cornerstone in information collection and text mining ***/value： The use of ontologies provides abstracted representation of semantic information and enables a wealth of applications in a reporting system. Therefore, constructing such a knowledge base is recognized as a high priority in health care.

关键词： Patient safety Medical error Knowledge representation Health information technology Ontology

High efficiency production of ginsenoside compound K by catalyzing ginsenoside rb1 using snailase

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Chinese Journal of Chemical Engineering 2018年第7期26卷 1591-1597页

作者： Zhiguang duan Chenhui Zhu Jingjing Shi daidi Fan Jianjun deng rongzhan Fu rong Huang Cuiying Fan Shaanxi Key Laboratory of degradable biomedical Materials School of Chemical EngineeringNorthwest UniversityTaibai North Road 229Xi'an 710069China Shanxi r&d center of Biomaterials and Fermentation Engineering School of Chemical Engineering Northwest University Taibai North Road 229Xi'an 710069China

The rare ginsenoside Compound K （C-K） is attracting more attention because of its good physiological activity and urgent need. There are many pathways to obtain ginsenoside C-K, including chemical and biological methods. Among these, the conversion of PPd-type ginsenosides by enzymatic hydrolysis is a trend due to its high efficiency and mild conditions. For effectively extracting from the other panaxadiol saponins, the conversion process for ginsenoside C-K was investigated using snailases in this study. The univariate experimental design and response surface methodology were used to determine the optimal hydrolysis conditions for the conversion of ginsenoside rbl into ginsenoside C-K by snailases. The optimum conditions were as follows： pH 5,12, temperature 51 ℃, ratio of snailase/substrate 0.21, and reaction time 48 h. On the basis of these parameters, the addition of 1.0 mmol· L- 1 ferric ion was found to significantly improve the enzymolysis ofsnailases for the first time. With the above conditions, the maximum conversion rate reached 89.7%, suggesting that the process can obviously increase the yield of ginsenoside C-K. The bioassay tests indicated that the ginsenoside C-K showed anti-tumor activity in a series of tumor cell lines. Based on these results, we can conclude that the process of rare ginsenoside C- K production by enzymolysis with snailase is feasible, efficient, and suitable for the industrial production and application.

关键词： Ginsenoside rb1 Ginsenoside Compound K Snailase Enzymolysis