Multi-label learning is an active research area which plays an important role in machine learning. Traditional learning algorithms, however, have to depend on samples with complete labels. The existing learning algori...Multi-label learning is an active research area which plays an important role in machine learning. Traditional learning algorithms, however, have to depend on samples with complete labels. The existing learning algorithms with missing labels do not consider the relevance of labels, resulting in label estimation errors of new samples. A new multi-label learning algorithm with support vector machine(SVM) based association(SVMA) is proposed to estimate missing labels by constructing the association between different labels. SVMA will establish a mapping function to minimize the number of samples in the margin while ensuring the margin large enough as well as minimizing the misclassification probability. To evaluate the performance of SVMA in the condition of missing labels, four typical data sets are adopted with the integrity of the labels being handled manually. Simulation results show the superiority of SVMA in dealing with the samples with missing labels compared with other models in image classification.展开更多
Single nucletide polymorphism(SNP)is an important factor for the study of genetic variation in human families and animal and plant strains.Therefore,it is widely used in the study of population genetics and disease re...Single nucletide polymorphism(SNP)is an important factor for the study of genetic variation in human families and animal and plant strains.Therefore,it is widely used in the study of population genetics and disease related gene.In pharmacogenomics research,identifying the association between SNP site and drug is the key to clinical precision medication,therefore,a predictive model of SNP site and drug association based on denoising variational auto-encoder(DVAE-SVM)is proposed.Firstly,k-mer algorithm is used to construct the initial SNP site feature vector,meanwhile,MACCS molecular fingerprint is introduced to generate the feature vector of the drug module.Then,we use the DVAE to extract the effective features of the initial feature vector of the SNP site.Finally,the effective feature vector of the SNP site and the feature vector of the drug module are fused input to the support vector machines(SVM)to predict the relationship of SNP site and drug module.The results of five-fold cross-validation experiments indicate that the proposed algorithm performs better than random forest(RF)and logistic regression(LR)classification.Further experiments show that compared with the feature extraction algorithms of principal component analysis(PCA),denoising auto-encoder(DAE)and variational auto-encode(VAE),the proposed algorithm has better prediction results.展开更多
Common neurodegenerative diseases of the central nervous system are characterized by progressive damage to the function of neurons, even leading to the permanent loss of function. Gene therapy via gene replacement or ...Common neurodegenerative diseases of the central nervous system are characterized by progressive damage to the function of neurons, even leading to the permanent loss of function. Gene therapy via gene replacement or gene correction provides the potential for transformative therapies to delay or possibly stop further progression of the neurodegenerative disease in affected patients. Adeno-associated virus has been the vector of choice in recent clinical trials of therapies for neurodegenerative diseases due to its safety and efficiency in mediating gene transfer to the central nervous system. This review aims to discuss and summarize the progress and clinical applications of adeno-associated virus in neurodegenerative disease in central nervous system. Results from some clinical trials and successful cases of central neurodegenerative diseases deserve further study and exploration.展开更多
The quasi-geostrophic Q vector is an important rainfall associated with large-scale weather systems diagnostic tool for studying development of surface and is calculated using data at single vertical level. When ageos...The quasi-geostrophic Q vector is an important rainfall associated with large-scale weather systems diagnostic tool for studying development of surface and is calculated using data at single vertical level. When ageostrophic Q vector was introduced, it required data at two vertical levels. In this study, moist ageostrophic Q vector is modified so that it can be calculated using data at a single vertical level. The comparison study between the original and modified moist ageostrophic Q vectors is conducted using the data from 5 to 6 July 1991 during the torrential rainfall event associated with the Changjiang-Huaihe mei-yu front in China. The results reveal that divergences of original and modified moist ageostrophic Q vectors have similar horizontal distributions and their centers are almost located in the precipitation centers. This indicates that modified moist ageostrophic Q vector can be used to diagnose convective development with reasonable accuracy.展开更多
Human hepatocellular carcinoma(HCC)heavily endangers human heath worldwide.HCC is one of most frequent cancers in China because patients with liver disease,such as chronic hepatitis,have the highest cancer susceptibil...Human hepatocellular carcinoma(HCC)heavily endangers human heath worldwide.HCC is one of most frequent cancers in China because patients with liver disease,such as chronic hepatitis,have the highest cancer susceptibility.Traditional therapeutic approaches have limited efficacy in advanced liver cancer,and novel strategies are urgently needed to improve the limited treatment options for HCC.This review summarizes the basic knowledge,current advances,and future challenges and prospects of adeno-associated virus(AAV)and adenoviruses as vectors for gene therapy of HCC.This paper also reviews the clinical trials of gene therapy using adenovirus vectors,immunotherapy,toxicity and immunological barriers for AAV and adenoviruses,and proposes several alternative strategies to overcome the therapeutic barriers to using AAV and adenoviruses as vectors.展开更多
BACKGROUND: Melanoma differentiation associated gene-7 (mda-7) is a novel tumor suppressor gene, which has suppressor activity in a broad spectrum of human cancer cells both in vitro and in vivo through activation of ...BACKGROUND: Melanoma differentiation associated gene-7 (mda-7) is a novel tumor suppressor gene, which has suppressor activity in a broad spectrum of human cancer cells both in vitro and in vivo through activation of various intracellular signaling pathways. In this study, we investigated the potential effect of mda-7 on human hepatocellular carcinoma (HCC) in vitro. METHODS: Cells from the human HCC cell line Hep3B and the human liver cell line L-02 were assigned to three groups. One was cultured in Dulbecco's modified Eagle's medium without serum (control). The others were transfected with adenovirus expressing the mda-7 gene (Ad.mda-7) or adenovirus vector serving as negative control (Ad.vec). The expression of MDA-7 and Bcl-2 proteins in Hep3B and L-02 cells was confirmed by the reverse transcriptase-polymerase chain reaction and enzyme-linked immunosorbent assay. The methyl thiazolyl tetrazolium colorimetric assay and flow cytometry were used to assess tumor cell proliferation and the cell cycle. Hoechst and Annexin-V/propidium iodide staining were used to study mda-7 gene expression in Hep3B and L-02 cells. The expression of MDA-7, Bcl-2 and Bax proteins were detected by Western blotting. RESULT S: The mda-7 gene was expressed in Hep3B and L-02 cells. The protein concentrations of MDA-7 in supernatants were 790 and 810 pg/ml, respectively. mda-7 induced Hep3B growth suppression and apoptosis, compared with Ad.mda-7 and control (P<0.01). In addition, cell block in G2/M was identified by exposure of HCC cells to secreted MDA-7 protein, but this was not found in L-02. The gene expression of Bcl-2 was markedly decreased in Hep3B but not in L-02. CONCLUSIONS: mda-7 selectively induces growth inhibition and apoptosis in the HCC cell line Hep3B but not in the normal liver cell line L-02 via downregulating the antiapoptosis protein Bcl-2. It could be an ideal gene for gene therapy in HCC.展开更多
Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem...Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem. Methods Human neurotrophin-3(hNT3)genes were inserted into AAV vectors. Then the recombinat AAV plas- mids were encapsidated as recombinant virions. PCl2 cells were transfected with the virions and the positive cells were selected by G418. The transfection positive (hNT3 modified)PC12 cells were cultured for several generations and the cellular genomic DNA and total RNA were extracted. We investigated the integration locus or AAV vectors by South- ern blot and transcript situation or foreign genes by dot blot. Results The hybridization tests showed that AAV in- troduced foreign genes were stably integrated, but at random locus, and robustly transcribed in hNT3 modified PCl2 cells. Conclusion AAV vectors can serve as high efficiency vectors or target genes in neuronal PC12 cells.展开更多
Safe and effective gene therapy approaches require targeted tissue-specific transfer of a therapeutic transgene.Besides traditional approaches, such as transcriptional and transductional targeting, micro RNA-dependent...Safe and effective gene therapy approaches require targeted tissue-specific transfer of a therapeutic transgene.Besides traditional approaches, such as transcriptional and transductional targeting, micro RNA-dependent posttranscriptional suppression of transgene expression has been emerging as powerful new technology to increase the specificity of vector-mediated transgene expression. Micro RNAs are small non-coding RNAs and often expressed in a tissue-, lineage-, activation- or differentiation-specific pattern. They typically regulate gene expression by binding to imperfectly complementary sequences in the 3' untranslated region(UTR) of the m RNA. To control exogenous transgene expression, tandem repeats of artificial micro RNA target sites are usually incorporated into the 3' UTR of the transgene expression cassette, leading to subsequent degradation of transgene m RNA in cel s expressing the corresponding micro RNA. This targeting strategy, first shown for lentiviral vectors in antigen presenting cells, has now been used for tissue-specific expression of vector-encoded therapeutic transgenes, to reduce immune response against the transgene, to control virus tropism for oncolytic virotherapy, to increase safety of live attenuated virus vaccines and to identify and select cell subsets for pluripotent stem cell therapies, respectively. This review provides an introduction into the technical mechanism underlying micro RNA-regulation, highlights new developments in this field and gives an overview of applications of micro RNA-regulated viral vectors for cardiac, suicide gene cancer and hematopoietic stem cell therapy, as well as for treatment of neurological and eye diseases.展开更多
Dominant intermediate Charcot-Marie-Tooth disease type C(DI-CMTC) is a dominantly inherited neuropathy that has been classified primarily based on motor conduction velocity tests but is now known to involve axonal a...Dominant intermediate Charcot-Marie-Tooth disease type C(DI-CMTC) is a dominantly inherited neuropathy that has been classified primarily based on motor conduction velocity tests but is now known to involve axonal and demyelination features.DI-CMTC is linked to tyrosyl-t RNA synthetase(YARS)-associated neuropathies,which are caused by E196 K and G41 R missense mutations and a single de novo deletion(153-156 del VKQV).It is well-established that these YARS mutations induce neuronal dysfunction,morphological symptoms involving axonal degeneration,and impaired motor performance.The present study is the first to describe a novel mouse model of YARS-mutation-induced neuropathy involving a neuron-specific promoter with a deleted mitochondrial targeting sequence that inhibits the expression of YARS protein in the mitochondria.An adenovirus vector system and in vivo techniques were utilized to express YARS fusion proteins with a Flag-tag in the spinal cord,peripheral axons,and dorsal root ganglia.Following transfection of YARS-expressing viruses,the distributions of wild-type(WT) YARS and E196 K mutant proteins were compared in all expressed regions; G41 R was not expressed.The proportion of Flag/green fluorescent protein(GFP) double-positive signaling in the E196 K mutant-type mice did not significantly differ from that of WT mice in dorsal root ganglion neurons.All adenovirus genes,and even the empty vector without the YARS gene,exhibited GFP-positive signaling in the ventral horn of the spinal cord because GFP in an adenovirus vector is driven by a cytomegalovirus promoter.The present study demonstrated that anatomical differences in tissue can lead to dissimilar expressions of YARS genes.Thus,use of this novel animal model will provide data regarding distributional defects between mutant and WT genes in neurons,the DICMTC phenotype,and potential treatment approaches for this disease.展开更多
成簇规则间隔的短回文重复序列及其相关蛋白9(clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9,CRISPR/Cas9)技术目前广泛应用于生命医学领域的基础研究及临床应用研究。由于载体在CRISPR/Cas9...成簇规则间隔的短回文重复序列及其相关蛋白9(clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9,CRISPR/Cas9)技术目前广泛应用于生命医学领域的基础研究及临床应用研究。由于载体在CRISPR/Cas9技术中发挥了重要的作用,如何进一步开发和优化载体系统具有重要的意义。传统的载体大多以病毒载体为主,其递送的效率高,但亦存在插入片段的大小有限、免疫反应、致癌、难以大规模生产甚至脱靶等缺陷;而非病毒纳米载体在一定程度上可解决基因编辑过程中由病毒载体所带来的潜在毒性和容量限制等问题,可能具有更广阔的应用前景。本文主要综述了目前用于CRISPR/Cas9系统递送的非病毒纳米载体,探讨了非病毒纳米载体在递送CRISPR/Cas9系统时可能遇到的主要困难,提出了相应的解决方案和策略,以期为基因治疗和药物研发提供新的参考依据。展开更多
基金Support by the National High Technology Research and Development Program of China(No.2012AA120802)National Natural Science Foundation of China(No.61771186)+1 种基金Postdoctoral Research Project of Heilongjiang Province(No.LBH-Q15121)Undergraduate University Project of Young Scientist Creative Talent of Heilongjiang Province(No.UNPYSCT-2017125)
文摘Multi-label learning is an active research area which plays an important role in machine learning. Traditional learning algorithms, however, have to depend on samples with complete labels. The existing learning algorithms with missing labels do not consider the relevance of labels, resulting in label estimation errors of new samples. A new multi-label learning algorithm with support vector machine(SVM) based association(SVMA) is proposed to estimate missing labels by constructing the association between different labels. SVMA will establish a mapping function to minimize the number of samples in the margin while ensuring the margin large enough as well as minimizing the misclassification probability. To evaluate the performance of SVMA in the condition of missing labels, four typical data sets are adopted with the integrity of the labels being handled manually. Simulation results show the superiority of SVMA in dealing with the samples with missing labels compared with other models in image classification.
基金Lanzhou Talent Innovation and Entrepreneurship Project(No.2020-RC-14)。
文摘Single nucletide polymorphism(SNP)is an important factor for the study of genetic variation in human families and animal and plant strains.Therefore,it is widely used in the study of population genetics and disease related gene.In pharmacogenomics research,identifying the association between SNP site and drug is the key to clinical precision medication,therefore,a predictive model of SNP site and drug association based on denoising variational auto-encoder(DVAE-SVM)is proposed.Firstly,k-mer algorithm is used to construct the initial SNP site feature vector,meanwhile,MACCS molecular fingerprint is introduced to generate the feature vector of the drug module.Then,we use the DVAE to extract the effective features of the initial feature vector of the SNP site.Finally,the effective feature vector of the SNP site and the feature vector of the drug module are fused input to the support vector machines(SVM)to predict the relationship of SNP site and drug module.The results of five-fold cross-validation experiments indicate that the proposed algorithm performs better than random forest(RF)and logistic regression(LR)classification.Further experiments show that compared with the feature extraction algorithms of principal component analysis(PCA),denoising auto-encoder(DAE)and variational auto-encode(VAE),the proposed algorithm has better prediction results.
文摘Common neurodegenerative diseases of the central nervous system are characterized by progressive damage to the function of neurons, even leading to the permanent loss of function. Gene therapy via gene replacement or gene correction provides the potential for transformative therapies to delay or possibly stop further progression of the neurodegenerative disease in affected patients. Adeno-associated virus has been the vector of choice in recent clinical trials of therapies for neurodegenerative diseases due to its safety and efficiency in mediating gene transfer to the central nervous system. This review aims to discuss and summarize the progress and clinical applications of adeno-associated virus in neurodegenerative disease in central nervous system. Results from some clinical trials and successful cases of central neurodegenerative diseases deserve further study and exploration.
基金National Natural Science Foundation of China (Grant Nos. 40405009, 40075009, 40205008)Shanghai Typhoon Research Funding (Grant No. 2003ST005)+1 种基金Shanghai Weather Bureau Research Funding (No. 04A06)Jiangsu Key Laboratory of Meteorological Disaster Fund- ing (No. KJS0602)
文摘The quasi-geostrophic Q vector is an important rainfall associated with large-scale weather systems diagnostic tool for studying development of surface and is calculated using data at single vertical level. When ageostrophic Q vector was introduced, it required data at two vertical levels. In this study, moist ageostrophic Q vector is modified so that it can be calculated using data at a single vertical level. The comparison study between the original and modified moist ageostrophic Q vectors is conducted using the data from 5 to 6 July 1991 during the torrential rainfall event associated with the Changjiang-Huaihe mei-yu front in China. The results reveal that divergences of original and modified moist ageostrophic Q vectors have similar horizontal distributions and their centers are almost located in the precipitation centers. This indicates that modified moist ageostrophic Q vector can be used to diagnose convective development with reasonable accuracy.
基金Supported by National Natural Science Foundation of China.No.81272687Zhejiang Provincial Public Welfare Technology Application Research Projects,No.2014C33275+1 种基金Zhejiang Provincial Natural Science Foundation of China,No.LZ13H160004the Grant for 521 Talent Project of Zhejiang Sci-Tech University,Hangzhou,China
文摘Human hepatocellular carcinoma(HCC)heavily endangers human heath worldwide.HCC is one of most frequent cancers in China because patients with liver disease,such as chronic hepatitis,have the highest cancer susceptibility.Traditional therapeutic approaches have limited efficacy in advanced liver cancer,and novel strategies are urgently needed to improve the limited treatment options for HCC.This review summarizes the basic knowledge,current advances,and future challenges and prospects of adeno-associated virus(AAV)and adenoviruses as vectors for gene therapy of HCC.This paper also reviews the clinical trials of gene therapy using adenovirus vectors,immunotherapy,toxicity and immunological barriers for AAV and adenoviruses,and proposes several alternative strategies to overcome the therapeutic barriers to using AAV and adenoviruses as vectors.
基金a grant from the KeyProject of the China Hubei Provincial Science and Technology Department(2006AA304B52-4).
文摘BACKGROUND: Melanoma differentiation associated gene-7 (mda-7) is a novel tumor suppressor gene, which has suppressor activity in a broad spectrum of human cancer cells both in vitro and in vivo through activation of various intracellular signaling pathways. In this study, we investigated the potential effect of mda-7 on human hepatocellular carcinoma (HCC) in vitro. METHODS: Cells from the human HCC cell line Hep3B and the human liver cell line L-02 were assigned to three groups. One was cultured in Dulbecco's modified Eagle's medium without serum (control). The others were transfected with adenovirus expressing the mda-7 gene (Ad.mda-7) or adenovirus vector serving as negative control (Ad.vec). The expression of MDA-7 and Bcl-2 proteins in Hep3B and L-02 cells was confirmed by the reverse transcriptase-polymerase chain reaction and enzyme-linked immunosorbent assay. The methyl thiazolyl tetrazolium colorimetric assay and flow cytometry were used to assess tumor cell proliferation and the cell cycle. Hoechst and Annexin-V/propidium iodide staining were used to study mda-7 gene expression in Hep3B and L-02 cells. The expression of MDA-7, Bcl-2 and Bax proteins were detected by Western blotting. RESULT S: The mda-7 gene was expressed in Hep3B and L-02 cells. The protein concentrations of MDA-7 in supernatants were 790 and 810 pg/ml, respectively. mda-7 induced Hep3B growth suppression and apoptosis, compared with Ad.mda-7 and control (P<0.01). In addition, cell block in G2/M was identified by exposure of HCC cells to secreted MDA-7 protein, but this was not found in L-02. The gene expression of Bcl-2 was markedly decreased in Hep3B but not in L-02. CONCLUSIONS: mda-7 selectively induces growth inhibition and apoptosis in the HCC cell line Hep3B but not in the normal liver cell line L-02 via downregulating the antiapoptosis protein Bcl-2. It could be an ideal gene for gene therapy in HCC.
文摘Objective To investigate integration and expression of adeno-associated virus (AAV) vectors in neuronal PC12 cells,the result of which can be applied in further gene therapy of diseases of the central nervous sys- tem. Methods Human neurotrophin-3(hNT3)genes were inserted into AAV vectors. Then the recombinat AAV plas- mids were encapsidated as recombinant virions. PCl2 cells were transfected with the virions and the positive cells were selected by G418. The transfection positive (hNT3 modified)PC12 cells were cultured for several generations and the cellular genomic DNA and total RNA were extracted. We investigated the integration locus or AAV vectors by South- ern blot and transcript situation or foreign genes by dot blot. Results The hybridization tests showed that AAV in- troduced foreign genes were stably integrated, but at random locus, and robustly transcribed in hNT3 modified PCl2 cells. Conclusion AAV vectors can serve as high efficiency vectors or target genes in neuronal PC12 cells.
基金Supported by The Deutsche Forschungsgemeinschaft,Nos.FE785/2-2 and FE785/4-1the Bundesministerium für Bildung und Entwicklung,No.031A331
文摘Safe and effective gene therapy approaches require targeted tissue-specific transfer of a therapeutic transgene.Besides traditional approaches, such as transcriptional and transductional targeting, micro RNA-dependent posttranscriptional suppression of transgene expression has been emerging as powerful new technology to increase the specificity of vector-mediated transgene expression. Micro RNAs are small non-coding RNAs and often expressed in a tissue-, lineage-, activation- or differentiation-specific pattern. They typically regulate gene expression by binding to imperfectly complementary sequences in the 3' untranslated region(UTR) of the m RNA. To control exogenous transgene expression, tandem repeats of artificial micro RNA target sites are usually incorporated into the 3' UTR of the transgene expression cassette, leading to subsequent degradation of transgene m RNA in cel s expressing the corresponding micro RNA. This targeting strategy, first shown for lentiviral vectors in antigen presenting cells, has now been used for tissue-specific expression of vector-encoded therapeutic transgenes, to reduce immune response against the transgene, to control virus tropism for oncolytic virotherapy, to increase safety of live attenuated virus vaccines and to identify and select cell subsets for pluripotent stem cell therapies, respectively. This review provides an introduction into the technical mechanism underlying micro RNA-regulation, highlights new developments in this field and gives an overview of applications of micro RNA-regulated viral vectors for cardiac, suicide gene cancer and hematopoietic stem cell therapy, as well as for treatment of neurological and eye diseases.
基金supported by the National Research Foundation(NRF)of Korea grant funded by Korean Government(MEST)(No.2011-0030072)
文摘Dominant intermediate Charcot-Marie-Tooth disease type C(DI-CMTC) is a dominantly inherited neuropathy that has been classified primarily based on motor conduction velocity tests but is now known to involve axonal and demyelination features.DI-CMTC is linked to tyrosyl-t RNA synthetase(YARS)-associated neuropathies,which are caused by E196 K and G41 R missense mutations and a single de novo deletion(153-156 del VKQV).It is well-established that these YARS mutations induce neuronal dysfunction,morphological symptoms involving axonal degeneration,and impaired motor performance.The present study is the first to describe a novel mouse model of YARS-mutation-induced neuropathy involving a neuron-specific promoter with a deleted mitochondrial targeting sequence that inhibits the expression of YARS protein in the mitochondria.An adenovirus vector system and in vivo techniques were utilized to express YARS fusion proteins with a Flag-tag in the spinal cord,peripheral axons,and dorsal root ganglia.Following transfection of YARS-expressing viruses,the distributions of wild-type(WT) YARS and E196 K mutant proteins were compared in all expressed regions; G41 R was not expressed.The proportion of Flag/green fluorescent protein(GFP) double-positive signaling in the E196 K mutant-type mice did not significantly differ from that of WT mice in dorsal root ganglion neurons.All adenovirus genes,and even the empty vector without the YARS gene,exhibited GFP-positive signaling in the ventral horn of the spinal cord because GFP in an adenovirus vector is driven by a cytomegalovirus promoter.The present study demonstrated that anatomical differences in tissue can lead to dissimilar expressions of YARS genes.Thus,use of this novel animal model will provide data regarding distributional defects between mutant and WT genes in neurons,the DICMTC phenotype,and potential treatment approaches for this disease.
文摘成簇规则间隔的短回文重复序列及其相关蛋白9(clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9,CRISPR/Cas9)技术目前广泛应用于生命医学领域的基础研究及临床应用研究。由于载体在CRISPR/Cas9技术中发挥了重要的作用,如何进一步开发和优化载体系统具有重要的意义。传统的载体大多以病毒载体为主,其递送的效率高,但亦存在插入片段的大小有限、免疫反应、致癌、难以大规模生产甚至脱靶等缺陷;而非病毒纳米载体在一定程度上可解决基因编辑过程中由病毒载体所带来的潜在毒性和容量限制等问题,可能具有更广阔的应用前景。本文主要综述了目前用于CRISPR/Cas9系统递送的非病毒纳米载体,探讨了非病毒纳米载体在递送CRISPR/Cas9系统时可能遇到的主要困难,提出了相应的解决方案和策略,以期为基因治疗和药物研发提供新的参考依据。