Objective： To establish and optimize the two-dimensional gel electrophoresis （2-DE） maps of squamous carcinoma of the cervix and to study the protein difference between squamous carcinoma of the cervix （SCC） and ...Objective： To establish and optimize the two-dimensional gel electrophoresis （2-DE） maps of squamous carcinoma of the cervix and to study the protein difference between squamous carcinoma of the cervix （SCC） and normal cervical tissue. Methods： Using Two-dimensional gel electrophoresis followed by computer-assisted image analysis, the differential proteins between squamous carcinoma of the cervical tissue and normal cervical tissue were compared. Then using matrix-assisted laser desorption/ionization-time of flight mass spectrometry, the differential proteins were identified. Results： The well-resolved and reproducible two-dimensional gel electrophoresis patterns of squamous carcinoma of the cervix tissue and normal cervical tissue were obtained. After silver staining, the average matching ratio of squamous carcinoma of the cervix was 86.1%. There was a good reproducibility of spot position in 2-DE map, with average deviation in IEF direction of 0.95±0.13 mm, while in SDS-PAGE direction it was 1.20±0.18 mm. Ten protein spots were identified by mass spectrometry, some of which were involved in cell proliferation, cell apoptosis, intracellular enzymes, structural proteins, cycle regulation, and tumor occurrence. Conclusion： The differentially expressed proteins provide a fundamental basis for further study of human squamous carcinoma of the cervix and screening of its specific markers.展开更多
The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using t...The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product （gil55628）, gfyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylgfutathione lyase, adenyfate kinase isozyme 1, two unnamed proteins products （gil55628 and gi11334163）, and poly（rC）-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.展开更多
Cells are highly sensitive to their geometrical and mechanical microenvironment that directly regulate cell shape,cytoskeleton and organelle,as well as the nucleus morphology and genetic expression.The emerging two-di...Cells are highly sensitive to their geometrical and mechanical microenvironment that directly regulate cell shape,cytoskeleton and organelle,as well as the nucleus morphology and genetic expression.The emerging two-dimensional micropatterning techniques offer powerful tools to construct controllable and well-organized microenvironment for single-cell level investigations with qualitative analysis,cellular standardization,and in vivo environment mimicking.Here,we provide an overview of the basic principle and characteristics of the two most widely-used micropatterning techniques,including photolithographic micropatterning and soft lithography micropatterning.Moreover,we summarize the application of micropatterning technique in controlling cytoskeleton,cell migration,nucleus and gene expression,as well as intercellular communication.展开更多
The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a ch...The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.展开更多
Objective： To establish and optimize the two-demensional electrophoresis maps of uterine leiomyoma and to study the difference of global protein patterns between uterine leiomyoma and normal myometrium. Methods： Usi...Objective： To establish and optimize the two-demensional electrophoresis maps of uterine leiomyoma and to study the difference of global protein patterns between uterine leiomyoma and normal myometrium. Methods： Using Two-dimensional electrophoresis followed by computer-assisted image analysis, the differential proteins between uterine leiomyoma and normal myometrium were compared. Results： The well-resolved and reproducible two-dimensional gel electrophoresis patterns of uterine leiomyoma and normal myometrium were established. Totally 1085±108 and 1103±151 protein spots were obtained by using the pH 4-7 IPG strips in uterine leiomyoma and normal myometrium map, respectively, of which 7 spots increased and 15 spots decreased in quantity in uterine leiomyoma compared with normal myometrium. Conclusion： The differentially expressed proteins are useful for studying the mechanism of the cause of uterine leiomyoma.展开更多
With the rapid development of information technology,the electronifi-cation of medical records has gradually become a trend.In China,the population base is huge and the supporting medical institutions are numerous,so ...With the rapid development of information technology,the electronifi-cation of medical records has gradually become a trend.In China,the population base is huge and the supporting medical institutions are numerous,so this reality drives the conversion of paper medical records to electronic medical records.Electronic medical records are the basis for establishing a smart hospital and an important guarantee for achieving medical intelligence,and the massive amount of electronic medical record data is also an important data set for conducting research in the medical field.However,electronic medical records contain a large amount of private patient information,which must be desensitized before they are used as open resources.Therefore,to solve the above problems,data masking for Chinese electronic medical records with named entity recognition is proposed in this paper.Firstly,the text is vectorized to satisfy the required format of the model input.Secondly,since the input sentences may have a long or short length and the relationship between sentences in context is not negligible.To this end,a neural network model for named entity recognition based on bidirectional long short-term memory(BiLSTM)with conditional random fields(CRF)is constructed.Finally,the data masking operation is performed based on the named entity recog-nition results,mainly using regular expression filtering encryption and principal component analysis(PCA)word vector compression and replacement.In addi-tion,comparison experiments with the hidden markov model(HMM)model,LSTM-CRF model,and BiLSTM model are conducted in this paper.The experi-mental results show that the method used in this paper achieves 92.72%Accuracy,92.30%Recall,and 92.51%F1_score,which has higher accuracy compared with other models.展开更多
Proteome analysis technology has been used extensively in conducting discovery research of biology and has become one of the most essential technologies in functional genomics. The proteomes of the human hepatoma cell...Proteome analysis technology has been used extensively in conducting discovery research of biology and has become one of the most essential technologies in functional genomics. The proteomes of the human hepatoma cell line BEL-7404 and the normal human liver cell line L-02 have been separated by high resolution two-dimensional gel electrophoresis (2-DE) with immobilized pH gradient isoelectric focusing (IPG-IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension (IPG-DALT). The resulting images have been analyzed using 2-D analysis software. Quantitative analysis reveals that 7 protein spots are detected only in hepatoma BEL-7404 cells, 14 only in L-02 cells, and 78 protein spots show significant fluctuation in quantity in both cell lines (P【0.01). These protein spots have been displayed on a proteome differential expression map. Analysis for the reproducibility of 2-DE indicates that the positional variability in the IEF dimension展开更多
To obtain comparable high query performance with relational databases,diverse database technologies have to be adapted to confront the complexity posed by both Resource Description Framework(RDF) data and SPARQL query...To obtain comparable high query performance with relational databases,diverse database technologies have to be adapted to confront the complexity posed by both Resource Description Framework(RDF) data and SPARQL query.Database caching is one of such technologies that improves the performance of database with reasonable space expense based on the spatial/temporal/semantic locality principle.However,existing caching schemes exploited in RDF stores are found to be dysfunctional for complex query semantics.Although semantic caching approaches work effectively in this case,little work has been done in this area.In this paper,we try to improve SPARQL query performance with semantic caching approaches,i.e.,SPARQL algebraic expression tree(AET) based caching and entity caching.Successive queries with multiple identical sub-queries and star-shaped joins can be efficiently evaluated with these two approaches.The approaches are implemented on a two-level-storage structure.The main memory stores the most frequently accessed cache items,and items swapped out are stored on the disk for future possible reuse.Evaluation results on three mainstream RDF benchmarks illustrate the effectiveness and efficiency of our approaches.Comparisons with previous research are also provided.展开更多
基金the National Natural Science Foundation of China (No.30700195)grant from Science and Technology Project of Wenzhou (No.Y2005A038)
文摘Objective： To establish and optimize the two-dimensional gel electrophoresis （2-DE） maps of squamous carcinoma of the cervix and to study the protein difference between squamous carcinoma of the cervix （SCC） and normal cervical tissue. Methods： Using Two-dimensional gel electrophoresis followed by computer-assisted image analysis, the differential proteins between squamous carcinoma of the cervical tissue and normal cervical tissue were compared. Then using matrix-assisted laser desorption/ionization-time of flight mass spectrometry, the differential proteins were identified. Results： The well-resolved and reproducible two-dimensional gel electrophoresis patterns of squamous carcinoma of the cervix tissue and normal cervical tissue were obtained. After silver staining, the average matching ratio of squamous carcinoma of the cervix was 86.1%. There was a good reproducibility of spot position in 2-DE map, with average deviation in IEF direction of 0.95±0.13 mm, while in SDS-PAGE direction it was 1.20±0.18 mm. Ten protein spots were identified by mass spectrometry, some of which were involved in cell proliferation, cell apoptosis, intracellular enzymes, structural proteins, cycle regulation, and tumor occurrence. Conclusion： The differentially expressed proteins provide a fundamental basis for further study of human squamous carcinoma of the cervix and screening of its specific markers.
基金supported by the Key Projects in the National Science & Technology Pillar Program, No.2009BAI87B02the National Natural Science Foundation of China, No. 31100696the National Basic Research Program of China (973 Program), No. 2012CB518106
文摘The present study utilized samples from bilateral motor branches of the femoral nerve, as well as saphenous nerves, ventral roots, and dorsal roots of the spinal cord, to detect differential protein expression using two-dimensional gel electrophoresis and nano ultra-high performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry techniques. A mass spectrum was identified using the Mascot search. Results revealed differential expression of 11 proteins, including transgelin, Ig kappa chain precursor, plasma glutathione peroxidase precursor, an unnamed protein product （gil55628）, gfyceraldehyde-3-phosphate dehydrogenase-like protein, lactoylgfutathione lyase, adenyfate kinase isozyme 1, two unnamed proteins products （gil55628 and gi11334163）, and poly（rC）-binding protein 1 in motor and sensory nerves. Results suggested that these proteins played roles in specific nerve regeneration following peripheral nerve injury and served as specific markers for motor and sensory nerves.
基金supported by the National Natural Science Foundation of China(Nos.12174208,32227802)National Key Research and Development Program of China(No.2022YFC3400600)+3 种基金Guangdong Major Project of Basic and Applied Basic Research(No.2020B0301030009)China Postdoctoral Science Foundation(No.2020 M680032)Fundamental Research Funds for the Central Universities(Nos.2122021337,2122021405)the 111 Project(No.B23045).
文摘Cells are highly sensitive to their geometrical and mechanical microenvironment that directly regulate cell shape,cytoskeleton and organelle,as well as the nucleus morphology and genetic expression.The emerging two-dimensional micropatterning techniques offer powerful tools to construct controllable and well-organized microenvironment for single-cell level investigations with qualitative analysis,cellular standardization,and in vivo environment mimicking.Here,we provide an overview of the basic principle and characteristics of the two most widely-used micropatterning techniques,including photolithographic micropatterning and soft lithography micropatterning.Moreover,we summarize the application of micropatterning technique in controlling cytoskeleton,cell migration,nucleus and gene expression,as well as intercellular communication.
文摘The events of cell death and the expression of nuclear matrix protein (NMP) have been investigated in a promyelocytic leukemic cell line HL-60 induced with etoposide. By means of TUNEL assay, the nuclei displayed a characteristic morphology change, and the amount of apoptotic cells increased early and reached maximun about 39% after treatment with etoposide for 2 h. Nucleosomal DNA fragmentation was observed after treatment for 4 h. The morphological change of HL-60 cells, thus, occurred earlier than the appearance of DNA ladder. Total nuclear matrix proteins were analyzed by 2-dimensional gel electrophoresis. Differential expression of 59 nuclear matrix proteins was found in 4 h etoposide treated cells. Western blotting was then performed on three nuclear matrix acssociated proteins, PML, HSC70 and NuMA. The expression of the suppressor PML protein and heat shock protein HSC70 were significantly upregulated after etoposide treatment, while NuMA, a nuclear mitotic apparatus protein, was down regulated. These results demonstrate that significant biochemical alterations in nuclear matrix proteins take place during the apoptotic process.
基金This work was supported byTechnological Developing Committee of Wenzhou(No.Y2004A044).
文摘Objective： To establish and optimize the two-demensional electrophoresis maps of uterine leiomyoma and to study the difference of global protein patterns between uterine leiomyoma and normal myometrium. Methods： Using Two-dimensional electrophoresis followed by computer-assisted image analysis, the differential proteins between uterine leiomyoma and normal myometrium were compared. Results： The well-resolved and reproducible two-dimensional gel electrophoresis patterns of uterine leiomyoma and normal myometrium were established. Totally 1085±108 and 1103±151 protein spots were obtained by using the pH 4-7 IPG strips in uterine leiomyoma and normal myometrium map, respectively, of which 7 spots increased and 15 spots decreased in quantity in uterine leiomyoma compared with normal myometrium. Conclusion： The differentially expressed proteins are useful for studying the mechanism of the cause of uterine leiomyoma.
基金This research was supported by the National Natural Science Foundation of China under Grant(No.42050102)the Postgraduate Education Reform Project of Jiangsu Province under Grant(No.SJCX22_0343)Also,this research was supported by Dou Wanchun Expert Workstation of Yunnan Province(No.202205AF150013).
文摘With the rapid development of information technology,the electronifi-cation of medical records has gradually become a trend.In China,the population base is huge and the supporting medical institutions are numerous,so this reality drives the conversion of paper medical records to electronic medical records.Electronic medical records are the basis for establishing a smart hospital and an important guarantee for achieving medical intelligence,and the massive amount of electronic medical record data is also an important data set for conducting research in the medical field.However,electronic medical records contain a large amount of private patient information,which must be desensitized before they are used as open resources.Therefore,to solve the above problems,data masking for Chinese electronic medical records with named entity recognition is proposed in this paper.Firstly,the text is vectorized to satisfy the required format of the model input.Secondly,since the input sentences may have a long or short length and the relationship between sentences in context is not negligible.To this end,a neural network model for named entity recognition based on bidirectional long short-term memory(BiLSTM)with conditional random fields(CRF)is constructed.Finally,the data masking operation is performed based on the named entity recog-nition results,mainly using regular expression filtering encryption and principal component analysis(PCA)word vector compression and replacement.In addi-tion,comparison experiments with the hidden markov model(HMM)model,LSTM-CRF model,and BiLSTM model are conducted in this paper.The experi-mental results show that the method used in this paper achieves 92.72%Accuracy,92.30%Recall,and 92.51%F1_score,which has higher accuracy compared with other models.
文摘Proteome analysis technology has been used extensively in conducting discovery research of biology and has become one of the most essential technologies in functional genomics. The proteomes of the human hepatoma cell line BEL-7404 and the normal human liver cell line L-02 have been separated by high resolution two-dimensional gel electrophoresis (2-DE) with immobilized pH gradient isoelectric focusing (IPG-IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension (IPG-DALT). The resulting images have been analyzed using 2-D analysis software. Quantitative analysis reveals that 7 protein spots are detected only in hepatoma BEL-7404 cells, 14 only in L-02 cells, and 78 protein spots show significant fluctuation in quantity in both cell lines (P【0.01). These protein spots have been displayed on a proteome differential expression map. Analysis for the reproducibility of 2-DE indicates that the positional variability in the IEF dimension
基金supported by the National Natural Science Foundation of China (Nos.60903010,61025007,and 60933001)the National Basic Research Program (973) of China (No.2011CB302206)+2 种基金the Natural Science Foundation of Jiangsu Province,China (No.BK2009268)the Fundamental Research Funds for the Central Universities (No.N110404013)the Key Laboratory of Advanced Information Science and Network Technology of Beijing (No.XDXX1011)
文摘To obtain comparable high query performance with relational databases,diverse database technologies have to be adapted to confront the complexity posed by both Resource Description Framework(RDF) data and SPARQL query.Database caching is one of such technologies that improves the performance of database with reasonable space expense based on the spatial/temporal/semantic locality principle.However,existing caching schemes exploited in RDF stores are found to be dysfunctional for complex query semantics.Although semantic caching approaches work effectively in this case,little work has been done in this area.In this paper,we try to improve SPARQL query performance with semantic caching approaches,i.e.,SPARQL algebraic expression tree(AET) based caching and entity caching.Successive queries with multiple identical sub-queries and star-shaped joins can be efficiently evaluated with these two approaches.The approaches are implemented on a two-level-storage structure.The main memory stores the most frequently accessed cache items,and items swapped out are stored on the disk for future possible reuse.Evaluation results on three mainstream RDF benchmarks illustrate the effectiveness and efficiency of our approaches.Comparisons with previous research are also provided.
