Gene expression(GE)classification is a research trend as it has been used to diagnose and prognosis many diseases.Employing machine learning(ML)in the prediction of many diseases based on GE data has been a flourishin...Gene expression(GE)classification is a research trend as it has been used to diagnose and prognosis many diseases.Employing machine learning(ML)in the prediction of many diseases based on GE data has been a flourishing research area.However,some diseases,like Alzheimer’s disease(AD),have not received considerable attention,probably owing to data scarcity obstacles.In this work,we shed light on the prediction of AD from GE data accurately using ML.Our approach consists of four phases:preprocessing,gene selection(GS),classification,and performance validation.In the preprocessing phase,gene columns are preprocessed identically.In the GS phase,a hybrid filtering method and embedded method are used.In the classification phase,three ML models are implemented using the bare minimum of the chosen genes obtained from the previous phase.The final phase is to validate the performance of these classifiers using different metrics.The crux of this article is to select the most informative genes from the hybrid method,and the best ML technique to predict AD using this minimal set of genes.Five different datasets are used to achieve our goal.We predict AD with impressive values forMultiLayer Perceptron(MLP)classifier which has the best performance metrics in four datasets,and the Support Vector Machine(SVM)achieves the highest performance values in only one dataset.We assessed the classifiers using sevenmetrics;and received impressive results,allowing for a credible performance rating.The metrics values we obtain in our study lie in the range[.97,.99]for the accuracy(Acc),[.97,.99]for F1-score,[.94,.98]for kappa index,[.97,.99]for area under curve(AUC),[.95,1]for precision,[.98,.99]for sensitivity(recall),and[.98,1]for specificity.With these results,the proposed approach outperforms recent interesting results.With these results,the proposed approach outperforms recent interesting results.展开更多
目的研究G_(2)/S期应答相关蛋白1(G_(2) and S phase-expressed protein 1,GTSE1)在肝细胞癌(hepatocellular carcinoma,HCC)中的表达、免疫学作用和预后分析,及其潜在作用机制。方法使用公共数据库癌症基因组图谱(The Cancer Genome At...目的研究G_(2)/S期应答相关蛋白1(G_(2) and S phase-expressed protein 1,GTSE1)在肝细胞癌(hepatocellular carcinoma,HCC)中的表达、免疫学作用和预后分析,及其潜在作用机制。方法使用公共数据库癌症基因组图谱(The Cancer Genome Atlas,TCGA)提供的数据,用Kaplan-Meier、肿瘤免疫评估资源(Tumor Immune Estimation Resource,TIMER)数据库和基因表达谱交互分析(Gene Expression Profiling Interactive Analysis,GEPIA)数据库进行GTSE1基因表达、免疫学作用及预后分析,通过免疫组化实验验证GTSE1在临床样本中的表达,应用R软件对GTSE1相关差异基因进行基因本体(gene ontology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析。结果GTSE1在人类癌组织中显著高表达,且与肝细胞癌预后不良显著相关(P<0.05);GTSE1基因表达与HCC中浸润性免疫细胞的丰度显著相关(P<0.001)。GTSE1相关的差异表达基因主要富集于核分裂、细胞器裂变、离子通道活性等基因模块;其参与的信号通路主要包括神经活性配体-受体的相互作用、细胞周期等。结论GTSE1在HCC中的表达显著上调并与患者预后不良显著相关,且在免疫细胞浸润中发挥重要作用,可作为HCC的预后标志物和免疫治疗靶点。展开更多
This paper presents the limiting expression for the gen calized inverse A T.S(2) and itscorresgonding projectors Since comonon imnortors inverses,such as and AT.S(2) etc are all generalized in e e AT.S(2) In fact,we g...This paper presents the limiting expression for the gen calized inverse A T.S(2) and itscorresgonding projectors Since comonon imnortors inverses,such as and AT.S(2) etc are all generalized in e e AT.S(2) In fact,we give a unified limiting formula of computine such imporiant generalined inverses and its corresponding proiectors,Based on this we estalish and imbedling method fire compoting the generalized in verse AT.S(2) The results extend earlier work by various authors.展开更多
To investigate the dynamic change of heat shock protein 90 （Hsp90） in the genesis and development of tumor, we successfully established tumor animal model using Marek’s disease and then determined the location of H...To investigate the dynamic change of heat shock protein 90 （Hsp90） in the genesis and development of tumor, we successfully established tumor animal model using Marek’s disease and then determined the location of Hsp90 in the tumor tissue using immunohistochemistry method, the antibody titer level of Hsp90 in the serum and the expression level in the tissue using enzyme-linked immunosorbent assay （ELISA） method. Our result showed that Hsp90 location in the tumor tissue was signiifcantly associated with the tumor cell and most in the cytoplasm of the tumor cell, and Hsp90 expression level in the tissue and the antibody titer level in the serum was most signiifcantly increased with the development of tumor. This is the ifrst report to show the presence of Hsp90 in tumor tissues induced by the Marek’s disease, with its expression correlated to the tumoral grading. These data may also be valuable for developing new molecular anti-cancer therapies.展开更多
Chilling stress is a production constraint of tomato,a tropical origin,chilling-sensitive horticultural crop.The development of chilling tolerant tomato thus has significant potential to impact tomato production.Gluta...Chilling stress is a production constraint of tomato,a tropical origin,chilling-sensitive horticultural crop.The development of chilling tolerant tomato thus has significant potential to impact tomato production.Glutaredoxins(GRXs)are ubiquitous oxidoreductases,which utilize the reducing power of glutathione to reduce disulfide bonds of substrate proteins and maintain cellular redox homeostasis.Here,we report that tomato expressing Arabidopsis GRX gene AtGRXS17 conferred tolerance to chilling stress without adverse effects on growth and development.AtGRXS17-expressing tomato plants displayed lower ion leakage,higher maximal photochemical efficiency of photosystem II(Fv/Fm)and increased accumulation of soluble sugar compared with wild-type plants after the chilling stress challenge.Furthermore,chilling tolerance was correlated with increased antioxidant enzyme activities and reduced H2O2 accumulation.At the same time,temporal expression patterns of the endogenous C-repeat/DRE-binding factor 1(SlCBF1)and CBF mediated-cold regulated genes were not altered in AtGRXS17-expressing plants when compared with wild-type plants,and proline concentrations remained unchanged relative to wild-type plants under chilling stress.Green fluorescent protein-AtGRXS17 fusion proteins,which were initially localized in the cytoplasm,migrated into the nucleus during chilling stress,reflecting a possible role of AtGRXS17 in nuclear signaling of chilling stress responses.Together,our findings demonstrate that genetically engineered tomato plants expressing AtGRXS17 can enhance chilling tolerance and suggest a genetic engineering strategy to improve chilling tolerance without yield penalty across different crop species.展开更多
[ Objective] This study ~med to investigate the influence of high temperature on the expression of heat shock transcription factor AtHsfAla in different genotypes of Arabidopsis. [ Method ] Arabidopsis plants overexpr...[ Objective] This study ~med to investigate the influence of high temperature on the expression of heat shock transcription factor AtHsfAla in different genotypes of Arabidopsis. [ Method ] Arabidopsis plants overexpressing heat shock transcription factor AtHsfA1 a were used as experimental materials and treated un- der high temperature at 39℃ for 1 rain and 5 min; total RNA of AtI-IsfAla was extracted, and the reverse transcription and amplification were conducted using RT- PCR technology, the amplification products were detected by electrophoresis. [ Result ] The expression levels of AtHsfA1 a in Arabidopsis plants overexpressing heat shock transcription factor AtHsfAla at high temperature and room temperature were higher than wild-type Arabidopsis; the expression levels of AtHsfAla in both wild-type Arab/dops/s and transgenic Arabidopsls plants overexpressing heat shock transcription factor AtHsfAla at high temperature of 39 ~C were higher than that at room temperature of 25 ~C, but the expression levels of AtHsfAla in wild-type Arab/dops/s and transgenic Arab/dops/s plants overexpressing heat shock transcription factor AtHsfAla varied little after high temperature treatment at 39 ~C for 1 rain or 5 rain. [ Conclusion] The expression of AtHsfAla is induced rapidly by high tem- perature, thus regulating the expression of early adversity-resistant genes. This study will lay the foundation demonstrating the mechanism of Arabidopsis heat shock transcription factor AtHsfAla.展开更多
INTRODUCTIONThe increased expression of ICAM-1 on a widerange of cells and in the sera of patients withmalignancies, chronic liver diseases andinflammation diseases has been described since thelate 1980s[1-22]. Recent...INTRODUCTIONThe increased expression of ICAM-1 on a widerange of cells and in the sera of patients withmalignancies, chronic liver diseases andinflammation diseases has been described since thelate 1980s[1-22]. Recently rapid progress in studieson expression of ICAM-1 in patients withhepatocellular carcinoma ( HCC ) have beenachieved, including clinical and experimentalresearches[23-31].展开更多
In this study, an Alzheimer＇s disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus, and the changes of gene expression profile in the hipp...In this study, an Alzheimer＇s disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus, and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis. Results showed that the expression of 50 genes was significantly up-regulated （fold change 〉 2）, while 21 genes were significantly down-regulated in the hippocampus of Alzheimer＇s disease model rats （fold change 〈 0.5） compared with the sham-operation group. The differentially expressed genes are involved in many functions, such as brain nerve system development, neuronal differentiation and functional regulation, cellular growth, differentiation and apoptosis, synaptogenesis and plasticity, inflammatory and immune responses, ion channels/transporters, signal transduction, cell material/energy metabolism. Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1 40-induced rat model of Alzheimer＇s disease, thereby affecting the hippocampal and brain functions.展开更多
On 28 February 2012, under the close judiciary of and diplomatic cooperation between the United States and China for five years, a fossilized nest containing 22 dinosaur eggs, which was smuggled to America, finally ma...On 28 February 2012, under the close judiciary of and diplomatic cooperation between the United States and China for five years, a fossilized nest containing 22 dinosaur eggs, which was smuggled to America, finally made its way home.展开更多
文摘Gene expression(GE)classification is a research trend as it has been used to diagnose and prognosis many diseases.Employing machine learning(ML)in the prediction of many diseases based on GE data has been a flourishing research area.However,some diseases,like Alzheimer’s disease(AD),have not received considerable attention,probably owing to data scarcity obstacles.In this work,we shed light on the prediction of AD from GE data accurately using ML.Our approach consists of four phases:preprocessing,gene selection(GS),classification,and performance validation.In the preprocessing phase,gene columns are preprocessed identically.In the GS phase,a hybrid filtering method and embedded method are used.In the classification phase,three ML models are implemented using the bare minimum of the chosen genes obtained from the previous phase.The final phase is to validate the performance of these classifiers using different metrics.The crux of this article is to select the most informative genes from the hybrid method,and the best ML technique to predict AD using this minimal set of genes.Five different datasets are used to achieve our goal.We predict AD with impressive values forMultiLayer Perceptron(MLP)classifier which has the best performance metrics in four datasets,and the Support Vector Machine(SVM)achieves the highest performance values in only one dataset.We assessed the classifiers using sevenmetrics;and received impressive results,allowing for a credible performance rating.The metrics values we obtain in our study lie in the range[.97,.99]for the accuracy(Acc),[.97,.99]for F1-score,[.94,.98]for kappa index,[.97,.99]for area under curve(AUC),[.95,1]for precision,[.98,.99]for sensitivity(recall),and[.98,1]for specificity.With these results,the proposed approach outperforms recent interesting results.With these results,the proposed approach outperforms recent interesting results.
文摘目的研究G_(2)/S期应答相关蛋白1(G_(2) and S phase-expressed protein 1,GTSE1)在肝细胞癌(hepatocellular carcinoma,HCC)中的表达、免疫学作用和预后分析,及其潜在作用机制。方法使用公共数据库癌症基因组图谱(The Cancer Genome Atlas,TCGA)提供的数据,用Kaplan-Meier、肿瘤免疫评估资源(Tumor Immune Estimation Resource,TIMER)数据库和基因表达谱交互分析(Gene Expression Profiling Interactive Analysis,GEPIA)数据库进行GTSE1基因表达、免疫学作用及预后分析,通过免疫组化实验验证GTSE1在临床样本中的表达,应用R软件对GTSE1相关差异基因进行基因本体(gene ontology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)富集分析。结果GTSE1在人类癌组织中显著高表达,且与肝细胞癌预后不良显著相关(P<0.05);GTSE1基因表达与HCC中浸润性免疫细胞的丰度显著相关(P<0.001)。GTSE1相关的差异表达基因主要富集于核分裂、细胞器裂变、离子通道活性等基因模块;其参与的信号通路主要包括神经活性配体-受体的相互作用、细胞周期等。结论GTSE1在HCC中的表达显著上调并与患者预后不良显著相关,且在免疫细胞浸润中发挥重要作用,可作为HCC的预后标志物和免疫治疗靶点。
基金This project is supported by the National Natural Science Foundation of China.
文摘This paper presents the limiting expression for the gen calized inverse A T.S(2) and itscorresgonding projectors Since comonon imnortors inverses,such as and AT.S(2) etc are all generalized in e e AT.S(2) In fact,we give a unified limiting formula of computine such imporiant generalined inverses and its corresponding proiectors,Based on this we estalish and imbedling method fire compoting the generalized in verse AT.S(2) The results extend earlier work by various authors.
基金supported by the National Natural Science Foundation of China (31101787)the Natural Science Foundation of Shandong Province,China (ZR2010CM035)
文摘To investigate the dynamic change of heat shock protein 90 （Hsp90） in the genesis and development of tumor, we successfully established tumor animal model using Marek’s disease and then determined the location of Hsp90 in the tumor tissue using immunohistochemistry method, the antibody titer level of Hsp90 in the serum and the expression level in the tissue using enzyme-linked immunosorbent assay （ELISA） method. Our result showed that Hsp90 location in the tumor tissue was signiifcantly associated with the tumor cell and most in the cytoplasm of the tumor cell, and Hsp90 expression level in the tissue and the antibody titer level in the serum was most signiifcantly increased with the development of tumor. This is the ifrst report to show the presence of Hsp90 in tumor tissues induced by the Marek’s disease, with its expression correlated to the tumoral grading. These data may also be valuable for developing new molecular anti-cancer therapies.
基金We thank Dr.Barbara Valent for supplying pBV579(35S::mCherry::NLS::Tnos)This research was supported by the Kansas State University AES project NAHF381121(to S.H.P.,Q.W.,S.A.S.)National Science Foundation award IOS-1258028(F.F.W.,Y.H.,J.P.).
文摘Chilling stress is a production constraint of tomato,a tropical origin,chilling-sensitive horticultural crop.The development of chilling tolerant tomato thus has significant potential to impact tomato production.Glutaredoxins(GRXs)are ubiquitous oxidoreductases,which utilize the reducing power of glutathione to reduce disulfide bonds of substrate proteins and maintain cellular redox homeostasis.Here,we report that tomato expressing Arabidopsis GRX gene AtGRXS17 conferred tolerance to chilling stress without adverse effects on growth and development.AtGRXS17-expressing tomato plants displayed lower ion leakage,higher maximal photochemical efficiency of photosystem II(Fv/Fm)and increased accumulation of soluble sugar compared with wild-type plants after the chilling stress challenge.Furthermore,chilling tolerance was correlated with increased antioxidant enzyme activities and reduced H2O2 accumulation.At the same time,temporal expression patterns of the endogenous C-repeat/DRE-binding factor 1(SlCBF1)and CBF mediated-cold regulated genes were not altered in AtGRXS17-expressing plants when compared with wild-type plants,and proline concentrations remained unchanged relative to wild-type plants under chilling stress.Green fluorescent protein-AtGRXS17 fusion proteins,which were initially localized in the cytoplasm,migrated into the nucleus during chilling stress,reflecting a possible role of AtGRXS17 in nuclear signaling of chilling stress responses.Together,our findings demonstrate that genetically engineered tomato plants expressing AtGRXS17 can enhance chilling tolerance and suggest a genetic engineering strategy to improve chilling tolerance without yield penalty across different crop species.
基金Supported by National Natural Science Foundation of China(31060039,31260061)Natural Science Foundation of Yunnan Province(2010ZC163)+1 种基金College-level Project of Kunming University(YJL11025)College-level Project for Key Discipline Construction of Kunming University
文摘[ Objective] This study ~med to investigate the influence of high temperature on the expression of heat shock transcription factor AtHsfAla in different genotypes of Arabidopsis. [ Method ] Arabidopsis plants overexpressing heat shock transcription factor AtHsfA1 a were used as experimental materials and treated un- der high temperature at 39℃ for 1 rain and 5 min; total RNA of AtI-IsfAla was extracted, and the reverse transcription and amplification were conducted using RT- PCR technology, the amplification products were detected by electrophoresis. [ Result ] The expression levels of AtHsfA1 a in Arabidopsis plants overexpressing heat shock transcription factor AtHsfAla at high temperature and room temperature were higher than wild-type Arabidopsis; the expression levels of AtHsfAla in both wild-type Arab/dops/s and transgenic Arabidopsls plants overexpressing heat shock transcription factor AtHsfAla at high temperature of 39 ~C were higher than that at room temperature of 25 ~C, but the expression levels of AtHsfAla in wild-type Arab/dops/s and transgenic Arab/dops/s plants overexpressing heat shock transcription factor AtHsfAla varied little after high temperature treatment at 39 ~C for 1 rain or 5 rain. [ Conclusion] The expression of AtHsfAla is induced rapidly by high tem- perature, thus regulating the expression of early adversity-resistant genes. This study will lay the foundation demonstrating the mechanism of Arabidopsis heat shock transcription factor AtHsfAla.
基金Supported by the grant from the Guangxi ScienceTechnology Committee, No. 9811003
文摘INTRODUCTIONThe increased expression of ICAM-1 on a widerange of cells and in the sera of patients withmalignancies, chronic liver diseases andinflammation diseases has been described since thelate 1980s[1-22]. Recently rapid progress in studieson expression of ICAM-1 in patients withhepatocellular carcinoma ( HCC ) have beenachieved, including clinical and experimentalresearches[23-31].
基金sponsored by the National Natural Science Foundation of China,No. 30973779
文摘In this study, an Alzheimer＇s disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus, and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis. Results showed that the expression of 50 genes was significantly up-regulated （fold change 〉 2）, while 21 genes were significantly down-regulated in the hippocampus of Alzheimer＇s disease model rats （fold change 〈 0.5） compared with the sham-operation group. The differentially expressed genes are involved in many functions, such as brain nerve system development, neuronal differentiation and functional regulation, cellular growth, differentiation and apoptosis, synaptogenesis and plasticity, inflammatory and immune responses, ion channels/transporters, signal transduction, cell material/energy metabolism. Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1 40-induced rat model of Alzheimer＇s disease, thereby affecting the hippocampal and brain functions.
文摘On 28 February 2012, under the close judiciary of and diplomatic cooperation between the United States and China for five years, a fossilized nest containing 22 dinosaur eggs, which was smuggled to America, finally made its way home.
