35 results on '"Yao, Ting"'
Search Results
2. Functional connectivity analysis on electroencephalography signals reveals potential biomarkers for treatment response in major depression
- Author
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Huang, Shiau-Shian, Yu, Yu-Hsiang, Chen, His-Han, Hung, Chia-Chun, Wang, Yao-Ting, Chang, Chieh Hsin, Peng, Syu-Jyun, and Kuo, Po-Hsiu
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- 2023
- Full Text
- View/download PDF
3. Adhesive cryogel particles for bridging confined and irregular tissue defects
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Xue, Yao-Ting, Chen, Ming-Yu, Cao, Jia-Sheng, Wang, Lei, Hu, Jia-Hao, Li, Si-Yang, Shen, Ji-Liang, Li, Xin-Ge, Zhang, Kai-Hang, Hao, Shu-Qiang, Juengpanich, Sarun, Cheng, Si-Bo, Wong, Tuck-Whye, Yang, Xu-Xu, Li, Tie-Feng, Cai, Xiu-Jun, and Yang, Wei
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- 2023
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- View/download PDF
4. Therapeutic advantage of teriparatide in very elderly patients with proximal femoral fractures: a functional and BMD analysis
- Author
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Sheng, Ooi Chin, Wu, Wen-Tien, Peng, Cheng-Huan, Yao, Ting-Kuo, Chen, Ing-Ho, Wang, Jen-Hung, and Yeh, Kuang-Ting
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- 2024
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- View/download PDF
5. Exosome lncRNA IFNG-AS1 derived from mesenchymal stem cells of human adipose ameliorates neurogenesis and ASD-like behavior in BTBR mice
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Fu, Yu, Zhang, Yuan-lin, Liu, Rong-qi, Xu, Meng-meng, Xie, Jun-ling, Zhang, Xing-liao, Xie, Guang-ming, Han, Yao-ting, Zhang, Xin-Min, Zhang, Wan-ting, Zhang, Jing, and Zhang, Jun
- Published
- 2024
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6. Femoral neck system versus multiple cannulated screws for the fixation of Pauwels classification type II femoral neck fractures in older female patients with low bone mass
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Yeoh, Soon-Chin, Wu, Wen-Tien, Peng, Cheng-Huan, Yao, Ting-Kuo, Chang, Chia-Ming, Liu, Kuan-Lin, Yu, Tzai-Chiu, Chen, Ing-Ho, Wang, Jen-Hung, and Yeh, Kuang-Ting
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- 2024
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7. The role of preserved bowel and mesentery fixation in apple-peel intestinal atresia
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Han, Jinbao, Hao, Zenghui, Wang, Long, Yao, Ting, Fan, Wei, Zhao, Zheng, Huang, Liuming, and Xu, Zhilin
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- 2022
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8. Ubiquitin-like modifier 1 ligating enzyme 1 relieves cisplatin-induced premature ovarian failure by reducing endoplasmic reticulum stress in granulosa cells
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Tang, Xiangting, Dong, Hao, Fang, Zhi, Li, Jingyi, Yang, Qi, Yao, Ting, and Pan, Zezheng
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- 2022
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9. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing
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Huang, Yao-Ting, Liu, Po-Yu, and Shih, Pei-Wen
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- 2021
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10. Influence of humor expression on suicidal ideation among adolescents: mediating effects of depressive emotion and positive emotion
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Lee, Chun-Yang, Chiang, Yi-Chen, Li, An, Li, Xian, Wu, Yao-Ting, Lin, Yu-Jung, Zhao, Yuchen, and Zhang, Xiaoke
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- 2020
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- View/download PDF
11. Molecular epidemiology and clinical characteristics of hepatitis delta virus (HDV) infected patients with elevated transaminases in Shanghai, China
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Wu, Shanshan, Zhang, Yi, Tang, Yuyan, Yao, Ting, Lv, Mengjiao, Tang, Zhenghao, Zang, Guoqing, Yu, Yongsheng, and Chen, Xiaohua
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- 2020
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12. The subject-dependent, cumulative, and recency association of aerobic fitness with academic performance in Taiwanese junior high school students
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Hsieh, Shu-Shih, Tsai, Jia-Ren, Chang, Shao-Hsi, Ho, Jen-Yu, Chen, Jui-Fu, Chen, Po-Hsi, Sung, Yao-Ting, and Hung, Tsung-Min
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- 2019
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13. Genome characterization of bile-isolated Shewanella algae ACCC
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Tseng, Shu-Ying, Tung, Kwong-Chung, Cheng, Jan-Fang, Lee, Yi-Hsuan, Wu, Zong-Yen, Hong, Yu-Kai, Chen, Shi-Yu, Huang, Yao-Ting, and Liu, Po-Yu
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- 2018
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14. Wentong decoction cures allergic bronchial asthma by regulating the apoptosis imbalance of EOS
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Yan, Yue, Bao, Hai-Peng, Li, Chun-Lei, Shi, Qi, Kong, Yan-Hua, Yao, Ting, and Li, You-Lin
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- 2018
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15. Factors associated with emergency services use in Taiwanese advanced cancer patients receiving palliative home care services during out-of-hours periods: a retrospective medical record study
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Kao, Yee-Hsin, Liu, Yao-Ting, Koo, Malcolm, and Chiang, Jui-Kun
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- 2018
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16. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing
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Po-Yu Liu, Pei-Wen Shih, and Yao-Ting Huang
- Subjects
Systematic error ,Microbial Genomes ,lcsh:QH426-470 ,Method ,Computational biology ,Biology ,Genome ,Homologous Sequences ,03 medical and health sciences ,0302 clinical medicine ,Genome polishing ,lcsh:QH301-705.5 ,030304 developmental biology ,0303 health sciences ,Bacteria ,fungi ,Fungi ,Computational Biology ,Genomics ,Sequence Analysis, DNA ,Nanopore ,lcsh:Genetics ,Nanopore Sequencing ,lcsh:Biology (General) ,Metagenomics ,Viruses ,Metagenome ,Nanopore sequencing ,030217 neurology & neurosurgery - Abstract
Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors. The developed program, Homopolish, outperforms Medaka and HELEN in bacteria, viruses, fungi, and metagenomic datasets. When combined with Medaka/HELEN, the genome quality can exceed Q50 on R9.4 flow cells. We show that Nanopore-only sequencing can produce high-quality microbial genomes sufficient for downstream analysis. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-021-02282-6).
- Published
- 2021
17. Influence of humor expression on suicidal ideation among adolescents: mediating effects of depressive emotion and positive emotion
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Yao-Ting Wu, Yu-Jung Lin, Yuchen Zhao, Yi-Chen Chiang, Xian Li, Chun-Yang Lee, Xiaoke Zhang, and An Li
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Adolescent ,lcsh:RC435-571 ,Emotions ,Adolescents ,Structural equation modeling ,Humor expression ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Psychiatry ,Suicidal ideation ,Surveys and Questionnaires ,medicine ,Humans ,030212 general & internal medicine ,Students ,030227 psychiatry ,Psychiatry and Mental health ,Expression (architecture) ,Mediating effects ,Positive emotion ,medicine.symptom ,Psychology ,Depressive emotion ,Clinical psychology ,Research Article - Abstract
Background The occurrence and degree of suicidal ideation during the past month in adolescents should be regarded seriously. Several studies have noted that humor expression style and depressive emotion may influence adolescents’ suicidal ideation. However, there is insufficient evidence concerning whether positive emotion reduces such suicidal ideation in adolescents. In addition, the relationships among humor expression, depressive emotion, positive emotion and suicidal ideation remain to be confirmed. Therefore, in this study, we aimed to test the mediating roles of depressive emotion and positive emotion in the relationship between humor expression and recent adolescent’s suicidal ideation. Methods A total of 1551 students in junior high school completed questionnaires. The collected data were analyzed using structural equation modeling (SEM) with LISREL 8.80 and Monte Carlo resampling with R. Results The results indicate that suicidal ideation in adolescents during the past month was related not only to humor expression but also to depressive emotion and positive emotion. The stronger the depressive emotion felt, the stronger the suicidal ideation; in contrast, the stronger the positive emotion, the weaker the suicidal ideation. Moreover, depressive emotion and positive emotion were found to mediate the relationship between humor expression and suicidal ideation; additionally, positive emotion was found to mediate the relationship between depressive emotion and suicidal ideation. Conclusion These results highlight that depressive emotion and positive emotion may mediate the influence of humor expression on suicidal ideation among adolescents, and positive emotion may mediate the influence of depressive emotion on suicidal ideation. More attention should be paid to decreasing adolescents’ self-deprecating humor expression and depressive emotion, whereas more witty response humor expression and positive emotion should be encouraged to prevent their suicidal ideation.
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- 2020
18. An efficient error correction algorithm using FM-index.
- Author
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Yao-Ting Huang and Yu-Wen Huang
- Subjects
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NUCLEOTIDE sequencing , *GENOMES , *CORRECTION factors , *ACCURACY , *COMPUTER algorithms - Abstract
Background: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent de novo assembly, error correction is necessary prior to assembly. However, existing correction methods still face trade-offs among correction power, accuracy, and speed. Results: We develop a novel overlap-based error correction algorithm using FM-index (called FMOE). FMOE first identifies overlapping reads by aligning a query read simultaneously against multiple reads compressed by FM-index. Subsequently, sequencing errors are corrected by k-mer voting from overlapping reads only. The experimental results indicate that FMOE has highest correction power with comparable accuracy and speed. Our algorithm performs better in long-read than short-read datasets when compared with others. The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads. Conclusions: FMOE is freely available at https://github.com/ythuang0522/FMOC. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
19. BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development
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Yao-Ting Huang, Wan-Jung Chang, Jin-Ling Yuan, Cheng-Tran Hsu, Jin-Jun Yue, Jeremy J.W. Chen, Choun-Sea Lin, Ming-Lun Chou, Swee-Suak Ko, Xiao-Ping Gu, De-Chih Liao, and Ming-Che Shih
- Subjects
Sequence analysis ,Recombinant Fusion Proteins ,Bambusa ,MADS Domain Proteins ,Plant Science ,Flowers ,Genes, Plant ,Transcriptome ,Evolution, Molecular ,Hybrid transcriptomics ,Transformation, Genetic ,Gene Expression Regulation, Plant ,Gene expression ,Reproductive biology ,Botany ,Databases, Genetic ,RNA, Messenger ,Gene ,Phylogeny ,Regulation of gene expression ,Cell Nucleus ,Protein translocation ,Oryza sativa ,biology ,Sequence Analysis, RNA ,Reproduction ,fungi ,food and beverages ,Gene Expression Regulation, Developmental ,Molecular Sequence Annotation ,Oryza ,biology.organism_classification ,Juvenility ,ABCDE model ,Plant Leaves ,Protein Transport ,Gene Ontology ,In vitro flowering ,In situ hybridization ,Metabolic Networks and Pathways ,Research Article ,Subcellular Fractions - Abstract
Background: The bamboo Bambusa edulis has a long juvenile phase in situ, but can be induced to flower during in vitro tissue culture, providing a readily available source of material for studies on reproductive biology and flowering. In this report, in vitro-derived reproductive and vegetative materials of B. edulis were harvested and used to generate transcriptome databases by use of two sequencing platforms: Illumina and 454. Combination of the two datasets resulted in high transcriptome quality and increased length of the sequence reads. In plants, many MADS genes control flower development, and the ABCDE model has been developed to explain how the genes function together to create the different whorls within a flower. Results: As a case study, published floral development-related OsMADS proteins from rice were used to search the B. edulis transcriptome datasets, identifying 16 B. edulis MADS (BeMADS). The BeMADS gene expression levels were determined qRT-PCR and in situ hybridization. Most BeMADS genes were highly expressed in flowers, with the exception of BeMADS34. The expression patterns of these genes were most similar to the rice homologs, except BeMADS18 and BeMADS34, and were highly similar to the floral development ABCDE model in rice. Transient expression of MADS-GFP proteins showed that only BeMADS1 entered leaf nucleus. BeMADS18, BeMADS4, and BeMADS1 were located in the lemma nucleus. When co-transformed with BeMADS1, BeMADS15, 16, 13, 21, 6, and 7 translocated to nucleus in lemmas, indicating that BeMADS1 is a key factor for subcellular localization of other BeMADS. Conclusion: Our study provides abundant B. edulis transcriptome data and offers comprehensive sequence resources. The results, molecular materials and overall strategy reported here can be used for future gene identification and for further reproductive studies in the economically important crop of bamboo.
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- 2014
20. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss.
- Author
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Ruhlman, Tracey A., Wan-Jung Chang, Chen, Jeremy J. W., Yao-Ting Huang, Ming-Tsair Chan, Jin Zhang, De-Chih Liao, Blazier, John C., Xiaohua Jin, Ming-Che Shih, Jansen, Robert K., and Choun-Sea Lin
- Subjects
NADH dehydrogenase ,PLANT evolution ,PHYLOGENY ,PLANTS ,PLASTIDS - Abstract
Background: Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. Results: Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. Conclusion: The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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21. BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development.
- Author
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Ming-Che Shih, Ming-Lun Chou, Jin-Jun Yue, Cheng-Tran Hsu, Wan-Jung Chang, Swee-Suak Ko, De-Chih Liao, Yao-Ting Huang, Jeremy JW Chen, Jin-Ling Yuan, Xiao-Ping Gu, and Choun-Sea Lin
- Abstract
Background: The bamboo Bambusa edulis has a long juvenile phase in situ, but can be induced to flower during in vitro tissue culture, providing a readily available source of material for studies on reproductive biology and flowering. In this report, in vitro-derived reproductive and vegetative materials of B. edulis were harvested and used to generate transcriptome databases by use of two sequencing platforms: Illumina and 454. Combination of the two datasets resulted in high transcriptome quality and increased length of the sequence reads. In plants, many MADS genes control flower development, and the ABCDE model has been developed to explain how the genes function together to create the different whorls within a flower. Results: As a case study, published floral development-related OsMADS proteins from rice were used to search the B. edulis transcriptome datasets, identifying 16 B. edulis MADS (BeMADS). The BeMADS gene expression levels were determined qRT-PCR and in situ hybridization. Most BeMADS genes were highly expressed in flowers, with the exception of BeMADS34. The expression patterns of these genes were most similar to the rice homologs, except BeMADS18 and BeMADS34, and were highly similar to the floral development ABCDE model in rice. Transient expression of MADS-GFP proteins showed that only BeMADS1 entered leaf nucleus. BeMADS18, BeMADS4, and BeMADS1 were located in the lemma nucleus. When co-transformed with BeMADS1, BeMADS15, 16, 13, 21, 6, and 7 translocated to nucleus in lemmas, indicating that BeMADS1 is a key factor for subcellular localization of other BeMADS. Conclusion: Our study provides abundant B. edulis transcriptome data and offers comprehensive sequence resources. The results, molecular materials and overall strategy reported here can be used for future gene identification and for further reproductive studies in the economically important crop of bamboo. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
22. Involvement of STIM1 and Orai1 in EGF-mediated cell growth in retinal pigment epithelial cells.
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I-Hui Yang, Yao-Ting Tsai, Siou-Jin Chiu, Li-Teh Liu, Hsuan-Hung Lee, Ming-Feng Hou, Wen-Li Hsu, Ben-Kuen Chen, and Wei-Chiao Chang
- Subjects
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EPITHELIAL cells , *CELL proliferation , *RETINAL (Visual pigment) , *PHOSPHORYLATION , *MITOGEN-activated protein kinase kinase , *CELL migration - Abstract
Background: In non-excitable cells, one major route for calcium entry is through store-operated calcium (SOC) channels in the plasma membrane. These channels are activated by the emptying of intracellular Ca2+ store. STIM1 and Orai1 are major regulators of SOC channels. In this study, we explored the functions of STIM1 and Orai1 in epidermal growth factor (EGF)-induced cell proliferation and migration in retinal pigment epithelial cells (ARPE-19 cell line). Results: EGF triggers cell proliferation and migration in ARPE-19 cells. Cell proliferation and migration involve STIM1 and Orai1, as well as phosphorylation of extracellular signal-regulated protein kinase (ERK) 1/2, and Akt. Pharmacological inhibitors of SOC channels and siRNA of Orai1 and STIM1 suppress cell proliferation and migration. Pre-treatment of mitogen-activated protein kinase kinase (MEK) inhibitors and a phosphatidylinositol 3 kinases (PI3K) inhibitor attenuated cell proliferation and migration. However, inhibition of the SOC channels failed to prevent EGF-mediated ERK 1/2 and Akt phosphorylation. Conclusions: Our results showed that STIM1, Orai1, ERK 1/2, and Akt are key determinants of EGF-mediated cell growth in ARPE-19 cells. EGF is a potent growth molecule that has been linked to the development of PVR, and therefore, STIM1, Orai1, as well as the MEK/ERK 1/2 and PI3K/Akt pathways, might be potential therapeutic targets for drugs aimed at treating such disorders. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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23. LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs.
- Author
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Ming-Chih Wang, Feng-Chi Chen, Yen-Zho Chen, Yao-Ting Huang, and Trees-Juen Chuang
- Subjects
SINGLE nucleotide polymorphisms ,PROTEINS ,POPULATION ,GENOMES ,CHROMOSOMES ,WORLD Wide Web - Abstract
Background: Complex human diseases may be associated with many gene interactions. Gene interactions take several different forms and it is difficult to identify all of the interactions that are potentially associated with human diseases. One approach that may fill this knowledge gap is to infer previously unknown gene interactions via identification of non-physical linkages between different mutations (or single nucleotide polymorphisms, SNPs) to avoid hitchhiking effect or lack of recombination. Strong non-physical SNP linkages are considered to be an indication of biological (gene) interactions. These interactions can be physical protein interactions, regulatory interactions, functional compensation/antagonization or many other forms of interactions. Previous studies have shown that mutations in different genes can be linked to the same disorders. Therefore, non-physical SNP linkages, coupled with knowledge of SNP-disease associations may shed more light on the role of gene interactions in human disorders. A user-friendly web resource that integrates information about non-physical SNP linkages, gene annotations, SNP information, and SNP-disease associations may thus be a good reference for biomedical research. Findings: Here we extracted the SNPs located within the promoter or exonic regions of protein-coding genes from the HapMap database to construct a database named the Linkage-Disequilibrium-based Gene Interaction database (LDGIdb). The database stores 646,203 potential human gene interactions, which are potential interactions inferred from SNP pairs that are subject to long-range strong linkage disequilibrium (LD), or non-physical linkages. To minimize the possibility of hitchhiking, SNP pairs inferred to be non-physically linked were required to be located in different chromosomes or in different LD blocks of the same chromosomes. According to the genomic locations of the involved SNPs (i.e., promoter, untranslated region (UTR) and coding region (CDS)), the SNP linkages inferred were categorized into promoter-promoter, promoter-UTR, promoter-CDS, CDS-CDS, CDS-UTR and UTR-UTR linkages. For the CDS-related linkages, the coding SNPs were further classified into nonsynonymous and synonymous variations, which represent potential gene interactions at the protein and RNA level, respectively. The LDGIdb also incorporates human disease-association databases such as Genome-Wide Association Studies (GWAS) and Online Mendelian Inheritance in Man (OMIM), so that the user can search for potential disease-associated SNP linkages. The inferred SNP linkages are also classified in the context of population stratification to provide a resource for investigating potential population-specific gene interactions. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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24. Inference of chromosome-specific copy numbers using population haplotypes.
- Author
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Yao-Ting Huang and Min-Han Wu
- Subjects
- *
GENOMES , *CHROMOSOMES , *HEURISTIC algorithms , *LINKAGE disequilibrium , *POPULATION genetics - Abstract
Background: Using microarray and sequencing platforms, a large number of copy number variations (CNVs) have been identified in humans. In practice, because our human genome is a diploid, these platforms are limited to or more accurate for detecting total copy numbers rather than chromosome-specific copy numbers at each of the two homologous chromosomes. Nevertheless, the analysis of linkage disequilibrium (LD) between CNVs and SNPs indicates that distinct copy numbers often sit on their own background haplotypes. Results: We propose new computational models for inferring chromosome-specific copy numbers by distinguishing background haplotypes of each copy number. The formulated problems are shown to be NP-hard and approximation/heuristic algorithms are developed. Simulation indicates that our method is accurate and outperforms the existing approach. By testing the program in 60 parent-offspring trios, the inferred chromosome-specific copy numbers are highly consistent with the law of Mendelian inheritance. The distributions of copy numbers at chromosomal level are provided for 270 individuals in three HapMap panels. Conclusions: The estimation of chromosome-specific copy numbers using microarray or sequencing platforms was often confounded by a number of factors. This study showed that the integration of background haplotypes is able to improve the accuracies of copy number estimation at chromosome level, especially for the CNVs having strong LD with SNPs in proximity. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
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25. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b.
- Author
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Min-Sheng Peng, Palanichamy, Malliya Gounder, Yong-Gang Yao, Mitra, Bikash, Yao-Ting Cheng, Mian Zhao, Jia Liu, Hua-Wei Wang, Hui Pan, Wen-Zhi Wang, A-Mei Zhang, Wen Zhang, Dong Wang, Yang Zou, Yang Yang, Chaudhuri, Tapas Kumar, Qing-Peng Kong, and Ya-Ping Zhang
- Subjects
MITOCHONDRIAL DNA ,NUCLEIC acids ,GENES ,BIOLOGICAL evolution - Abstract
Background: Archaeological studies have revealed a series of cultural changes around the Last Glacial Maximum in East Asia; whether these changes left any signatures in the gene pool of East Asians remains poorly indicated. To achieve deeper insights into the demographic history of modern humans in East Asia around the Last Glacial Maximum, we extensively analyzed mitochondrial DNA haplogroup M9a'b, a specific haplogroup that was suggested to have some potential for tracing the migration around the Last Glacial Maximum in East Eurasia. Results: A total of 837 M9a'b mitochondrial DNAs (583 from the literature, while the remaining 254 were newly collected in this study) pinpointed from over 28,000 subjects residing across East Eurasia were studied here. Fiftynine representative samples were further selected for total mitochondrial DNA sequencing so we could better understand the phylogeny within M9a'b. Based on the updated phylogeny, an extensive phylogeographic analysis was carried out to reveal the differentiation of haplogroup M9a'b and to reconstruct the dispersal histories. Conclusions: Our results indicated that southern China and/or Southeast Asia likely served as the source of some post-Last Glacial Maximum dispersal(s). The detailed dissection of haplogroup M9a'b revealed the existence of an inland dispersal in mainland East Asia during the post-glacial period. It was this dispersal that expanded not only to western China but also to northeast India and the south Himalaya region. A similar phylogeographic distribution pattern was also observed for haplogroup F1c, thus substantiating our proposition. This inland post-glacial dispersal was in agreement with the spread of the Mesolithic culture originating in South China and northern Vietnam. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
26. Cardiac Glycosides Induce Resistance to Tubulin-Dependent Anticancer Drugs in Androgen-Independent Human Prostate Cancer.
- Author
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Dong-Ming Huang, Li Q., Jih-Hwa Guh, Li Q., Yao-Ting Huang, Li Q., Shih-Chieh Chueh, Hui-Po Wang, Li Q., and Che-Ming Teng, Li Q.
- Subjects
GLYCOSIDES ,TUBULINS ,PACLITAXEL ,ANTINEOPLASTIC agents ,PROSTATE ,CANCER - Abstract
Due to high prevalence and mortality and the lack of effective therapies, prostate cancer is one of the most crucial health problems in men. Drug resistance aggravates the situation, not only in human prostate cancer but also in other cancers. In this study, we report for the first time that cardiac glycosides (e.g. ouabain and digitoxin) induced resistance of human prostate cancer cells (PC-3) in vitro to tubulin-binding anticancer drugs, such as paclitaxel, colchicine, vincristine and vinblastine. Cardiac glycosides exhibited amazing ability to reverse the G2/M arrest of the cell cycle and cell apoptosis induced by tubulin-binding agents. However, neither ionomycin (a Ca[sup 2+] ionophore) nor veratridine (a Na[sup +] ionophore) mimicked the preventive action of cardiac glycosides, indicating that elevation of the intracellular Ca[sup 2+] concentration and Na[sup +] accumulation were not involved in the cardiac glycoside action. Furthermore, cardiac glycosides showed little influence on the effects induced by actinomycin D, anisomycin and doxorubicin, suggesting selectivity for microtubule-targeted anticancer drugs. Using in situ immunofluorescent detection of mitotic spindles, our data showed that cardiac glycosides diminished paclitaxel-induced accumulation of microtubule spindles; however, in a non-cell assay system, cardiac glycosides had little influence on colchicine- and paclitaxel-induced microtubule dynamics. Using an isotope-labeled assay method, we found that ouabain modestly but significantly inhibited the transport of [[sup 14] C]paclitaxel from the cytosol into the nucleus. It is suggested that cardiac glycosides inhibit the G2/M arrest induced by tubulin-binding anticancer drugs via an indirect blockade on microtubule function. The decline in transport of these drugs into the nucleus may partly explain the action of cardiac glycosides.Copyright © 2002 National Science Council, ROC and S. Karger AG, Basel [ABSTRACT FROM AUTHOR]
- Published
- 2002
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27. An efficient error correction algorithm using FM-index.
- Author
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Huang YT and Huang YW
- Subjects
- Animals, Bacteria genetics, Base Sequence, Caenorhabditis elegans genetics, Genome, Sequence Alignment, Time Factors, Algorithms, High-Throughput Nucleotide Sequencing methods
- Abstract
Background: High-throughput sequencing offers higher throughput and lower cost for sequencing a genome. However, sequencing errors, including mismatches and indels, may be produced during sequencing. Because, errors may reduce the accuracy of subsequent de novo assembly, error correction is necessary prior to assembly. However, existing correction methods still face trade-offs among correction power, accuracy, and speed., Results: We develop a novel overlap-based error correction algorithm using FM-index (called FMOE). FMOE first identifies overlapping reads by aligning a query read simultaneously against multiple reads compressed by FM-index. Subsequently, sequencing errors are corrected by k-mer voting from overlapping reads only. The experimental results indicate that FMOE has highest correction power with comparable accuracy and speed. Our algorithm performs better in long-read than short-read datasets when compared with others. The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads., Conclusions: FMOE is freely available at https://github.com/ythuang0522/FMOC .
- Published
- 2017
- Full Text
- View/download PDF
28. Kudiezi injection mitigates myocardial injury induced by acute cerebral ischemia in rats.
- Author
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Liu X, Tao Y, Wang F, Yao T, Fu C, Zheng H, Yan Y, Liang X, Jiang X, and Zhang Y
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- Animals, Glutathione metabolism, Humans, L-Lactate Dehydrogenase metabolism, Male, Malondialdehyde metabolism, Myocardial Ischemia etiology, Myocardial Ischemia metabolism, Oxidative Stress, Rats, Rats, Sprague-Dawley, Superoxide Dismutase metabolism, Brain Ischemia complications, Drugs, Chinese Herbal administration & dosage, Myocardial Ischemia drug therapy
- Abstract
Background: Kudiezi (KDZ) injection is commonly used in traditional Chinese medicine as treatment for cerebral infarction and angina pectoris. The present study investigated the therapeutic effects of KDZ injection on myocardial injury induced by acute cerebral ischemia and the possibly protective mechanisms., Methods: Rats were divided into three groups: sham, 6h-ischemia, and KDZ treatment (KDZ). The neurological deficits were determined by the Garcia score. The cerebral infarct volume was measured by 2,3,5-triphenyltetrazolium chloride (TTC) staining, and brain water content was also evaluated. Serum creatinine kinase (CK), lactate dehydrogenase (LDH), and creatine kinase-myocardial band (CK-MB) activity, myocardial tissue malondialdehyde (MDA) levels, L-Glutathione (GSH) levels, and superoxide dismutase (SOD) activity as well as mitochondrial cytochrome c oxidase (COX) activity were determined. Mitochondrial COX I and COX III mRNA expressions of myocardial tissues were measured by RT-PCR., Results: Impaired neurological function and brain edema were observed in the 6h-ischemia group. TTC staining showed that the 6h-ischemia group had larger infarct zones than the sham group. Myocardial ischemic changes (widened myocardial cell gap, cracks, and obvious edema) were detected in the 6h-ischemia group compared with the sham group, with elevated serum CK-MB activity and CK and LDH levels. Electrocardiography showed lower medium frequency (MF) and high frequency (HF) in the 6h-ischemia group compared with the sham group. In myocardial tissue, COX activity was elevated in the 6h-ischemia compared with the sham group, while SOD, GSH, and MDA levels, and COX I and COX III mRNA expressions remained unchanged. KDZ injection decreased neurological impairment, brain edema, gaps between cells, and infarct size. Compared with the 6h-ischemia group, it reduced serum CK-MB activity and CK and LDH levels, and MDA levels in myocardial tissue. KDZ significantly increased GSH levels, SOD activity, and mitochondria COX activity and the expression of COX I and COX III mRNA in myocardial tissue compared with the sham group., Conclusion: KDZ injection had a protective effect against cerebral ischemia in rats. KDZ injection could also alleviate myocardial injury after acute cerebral ischemia in rats. The possible mechanisms involve the regulation of the oxidative stress/antioxidant capacity after cerebral ischemia.
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- 2017
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29. BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development.
- Author
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Shih MC, Chou ML, Yue JJ, Hsu CT, Chang WJ, Ko SS, Liao DC, Huang YT, Chen JJ, Yuan JL, Gu XP, and Lin CS
- Subjects
- Databases, Genetic, Evolution, Molecular, Flowers genetics, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Ontology, MADS Domain Proteins metabolism, Metabolic Networks and Pathways genetics, Molecular Sequence Annotation, Oryza genetics, Phylogeny, Plant Leaves metabolism, Protein Transport, RNA, Messenger genetics, RNA, Messenger metabolism, Recombinant Fusion Proteins metabolism, Reproduction genetics, Sequence Analysis, RNA, Subcellular Fractions metabolism, Transformation, Genetic, Bambusa genetics, Bambusa growth & development, Cell Nucleus metabolism, Flowers growth & development, Genes, Plant, MADS Domain Proteins genetics, Transcriptome genetics
- Abstract
Background: The bamboo Bambusa edulis has a long juvenile phase in situ, but can be induced to flower during in vitro tissue culture, providing a readily available source of material for studies on reproductive biology and flowering. In this report, in vitro-derived reproductive and vegetative materials of B. edulis were harvested and used to generate transcriptome databases by use of two sequencing platforms: Illumina and 454. Combination of the two datasets resulted in high transcriptome quality and increased length of the sequence reads. In plants, many MADS genes control flower development, and the ABCDE model has been developed to explain how the genes function together to create the different whorls within a flower., Results: As a case study, published floral development-related OsMADS proteins from rice were used to search the B. edulis transcriptome datasets, identifying 16 B. edulis MADS (BeMADS). The BeMADS gene expression levels were determined qRT-PCR and in situ hybridization. Most BeMADS genes were highly expressed in flowers, with the exception of BeMADS34. The expression patterns of these genes were most similar to the rice homologs, except BeMADS18 and BeMADS34, and were highly similar to the floral development ABCDE model in rice. Transient expression of MADS-GFP proteins showed that only BeMADS1 entered leaf nucleus. BeMADS18, BeMADS4, and BeMADS1 were located in the lemma nucleus. When co-transformed with BeMADS1, BeMADS15, 16, 13, 21, 6, and 7 translocated to nucleus in lemmas, indicating that BeMADS1 is a key factor for subcellular localization of other BeMADS., Conclusion: Our study provides abundant B. edulis transcriptome data and offers comprehensive sequence resources. The results, molecular materials and overall strategy reported here can be used for future gene identification and for further reproductive studies in the economically important crop of bamboo.
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- 2014
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30. Involvement of STIM1 and Orai1 in EGF-mediated cell growth in retinal pigment epithelial cells.
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Yang IH, Tsai YT, Chiu SJ, Liu LT, Lee HH, Hou MF, Hsu WL, Chen BK, and Chang WC
- Subjects
- Calcium metabolism, Calcium Channels genetics, Cell Line, Cell Membrane metabolism, Cell Movement, Cell Proliferation, Humans, Membrane Proteins genetics, Mitogen-Activated Protein Kinase Kinases metabolism, Neoplasm Proteins genetics, ORAI1 Protein, Proto-Oncogene Proteins c-akt metabolism, Signal Transduction, Stromal Interaction Molecule 1, Calcium Channels metabolism, Epidermal Growth Factor metabolism, Membrane Proteins metabolism, Neoplasm Proteins metabolism, Retinal Pigment Epithelium metabolism
- Abstract
Background: In non-excitable cells, one major route for calcium entry is through store-operated calcium (SOC) channels in the plasma membrane. These channels are activated by the emptying of intracellular Ca²⁺ store. STIM1 and Orai1 are major regulators of SOC channels. In this study, we explored the functions of STIM1 and Orai1 in epidermal growth factor (EGF)-induced cell proliferation and migration in retinal pigment epithelial cells (ARPE-19 cell line)., Results: EGF triggers cell proliferation and migration in ARPE-19 cells. Cell proliferation and migration involve STIM1 and Orai1, as well as phosphorylation of extracellular signal-regulated protein kinase (ERK) 1/2, and Akt. Pharmacological inhibitors of SOC channels and siRNA of Orai1 and STIM1 suppress cell proliferation and migration. Pre-treatment of mitogen-activated protein kinase kinase (MEK) inhibitors and a phosphatidylinositol 3 kinases (PI3K) inhibitor attenuated cell proliferation and migration. However, inhibition of the SOC channels failed to prevent EGF-mediated ERK 1/2 and Akt phosphorylation., Conclusions: Our results showed that STIM1, Orai1, ERK 1/2, and Akt are key determinants of EGF-mediated cell growth in ARPE-19 cells. EGF is a potent growth molecule that has been linked to the development of PVR, and therefore, STIM1, Orai1, as well as the MEK/ERK 1/2 and PI3K/Akt pathways, might be potential therapeutic targets for drugs aimed at treating such disorders.
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- 2013
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31. LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs.
- Author
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Wang MC, Chen FC, Chen YZ, Huang YT, and Chuang TJ
- Subjects
- Cluster Analysis, Computational Biology, Exons, Genetic Association Studies, Genetic Predisposition to Disease, Haplotypes, Humans, Promoter Regions, Genetic, Systems Biology, User-Computer Interface, Databases, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide
- Abstract
Background: Complex human diseases may be associated with many gene interactions. Gene interactions take several different forms and it is difficult to identify all of the interactions that are potentially associated with human diseases. One approach that may fill this knowledge gap is to infer previously unknown gene interactions via identification of non-physical linkages between different mutations (or single nucleotide polymorphisms, SNPs) to avoid hitchhiking effect or lack of recombination. Strong non-physical SNP linkages are considered to be an indication of biological (gene) interactions. These interactions can be physical protein interactions, regulatory interactions, functional compensation/antagonization or many other forms of interactions. Previous studies have shown that mutations in different genes can be linked to the same disorders. Therefore, non-physical SNP linkages, coupled with knowledge of SNP-disease associations may shed more light on the role of gene interactions in human disorders. A user-friendly web resource that integrates information about non-physical SNP linkages, gene annotations, SNP information, and SNP-disease associations may thus be a good reference for biomedical research., Findings: Here we extracted the SNPs located within the promoter or exonic regions of protein-coding genes from the HapMap database to construct a database named the Linkage-Disequilibrium-based Gene Interaction database (LDGIdb). The database stores 646,203 potential human gene interactions, which are potential interactions inferred from SNP pairs that are subject to long-range strong linkage disequilibrium (LD), or non-physical linkages. To minimize the possibility of hitchhiking, SNP pairs inferred to be non-physically linked were required to be located in different chromosomes or in different LD blocks of the same chromosomes. According to the genomic locations of the involved SNPs (i.e., promoter, untranslated region (UTR) and coding region (CDS)), the SNP linkages inferred were categorized into promoter-promoter, promoter-UTR, promoter-CDS, CDS-CDS, CDS-UTR and UTR-UTR linkages. For the CDS-related linkages, the coding SNPs were further classified into nonsynonymous and synonymous variations, which represent potential gene interactions at the protein and RNA level, respectively. The LDGIdb also incorporates human disease-association databases such as Genome-Wide Association Studies (GWAS) and Online Mendelian Inheritance in Man (OMIM), so that the user can search for potential disease-associated SNP linkages. The inferred SNP linkages are also classified in the context of population stratification to provide a resource for investigating potential population-specific gene interactions., Conclusion: The LDGIdb is a user-friendly resource that integrates non-physical SNP linkages and SNP-disease associations for studies of gene interactions in human diseases. With the help of the LDGIdb, it is plausible to infer population-specific SNP linkages for more focused studies, an avenue that is potentially important for pharmacogenetics. Moreover, by referring to disease-association information such as the GWAS data, the LDGIdb may help identify previously uncharacterized disease-associated gene interactions and potentially lead to new discoveries in studies of human diseases.
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- 2012
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32. Inference of chromosome-specific copy numbers using population haplotypes.
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Huang YT and Wu MH
- Subjects
- Haplotypes, Humans, Linkage Disequilibrium, Algorithms, Chromosomes genetics, DNA Copy Number Variations, Genetics, Population, Genome, Human, Polymorphism, Single Nucleotide
- Abstract
Background: Using microarray and sequencing platforms, a large number of copy number variations (CNVs) have been identified in humans. In practice, because our human genome is a diploid, these platforms are limited to or more accurate for detecting total copy numbers rather than chromosome-specific copy numbers at each of the two homologous chromosomes. Nevertheless, the analysis of linkage disequilibrium (LD) between CNVs and SNPs indicates that distinct copy numbers often sit on their own background haplotypes., Results: We propose new computational models for inferring chromosome-specific copy numbers by distinguishing background haplotypes of each copy number. The formulated problems are shown to be NP-hard and approximation/heuristic algorithms are developed. Simulation indicates that our method is accurate and outperforms the existing approach. By testing the program in 60 parent-offspring trios, the inferred chromosome-specific copy numbers are highly consistent with the law of Mendelian inheritance. The distributions of copy numbers at chromosomal level are provided for 270 individuals in three HapMap panels., Conclusions: The estimation of chromosome-specific copy numbers using microarray or sequencing platforms was often confounded by a number of factors. This study showed that the integration of background haplotypes is able to improve the accuracies of copy number estimation at chromosome level, especially for the CNVs having strong LD with SNPs in proximity.
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- 2011
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33. Inland post-glacial dispersal in East Asia revealed by mitochondrial haplogroup M9a'b.
- Author
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Peng MS, Palanichamy MG, Yao YG, Mitra B, Cheng YT, Zhao M, Liu J, Wang HW, Pan H, Wang WZ, Zhang AM, Zhang W, Wang D, Zou Y, Yang Y, Chaudhuri TK, Kong QP, and Zhang YP
- Subjects
- Asia, Southeastern, Evolution, Molecular, Asia, Eastern, Humans, Phylogeny, Phylogeography, Asian People genetics, DNA, Mitochondrial genetics, Emigration and Immigration, Genetic Variation, Haplotypes
- Abstract
Background: Archaeological studies have revealed a series of cultural changes around the Last Glacial Maximum in East Asia; whether these changes left any signatures in the gene pool of East Asians remains poorly indicated. To achieve deeper insights into the demographic history of modern humans in East Asia around the Last Glacial Maximum, we extensively analyzed mitochondrial DNA haplogroup M9a'b, a specific haplogroup that was suggested to have some potential for tracing the migration around the Last Glacial Maximum in East Eurasia., Results: A total of 837 M9a'b mitochondrial DNAs (583 from the literature, while the remaining 254 were newly collected in this study) pinpointed from over 28,000 subjects residing across East Eurasia were studied here. Fifty-nine representative samples were further selected for total mitochondrial DNA sequencing so we could better understand the phylogeny within M9a'b. Based on the updated phylogeny, an extensive phylogeographic analysis was carried out to reveal the differentiation of haplogroup M9a'b and to reconstruct the dispersal histories., Conclusions: Our results indicated that southern China and/or Southeast Asia likely served as the source of some post-Last Glacial Maximum dispersal(s). The detailed dissection of haplogroup M9a'b revealed the existence of an inland dispersal in mainland East Asia during the post-glacial period. It was this dispersal that expanded not only to western China but also to northeast India and the south Himalaya region. A similar phylogeographic distribution pattern was also observed for haplogroup F1c, thus substantiating our proposition. This inland post-glacial dispersal was in agreement with the spread of the Mesolithic culture originating in South China and northern Vietnam.
- Published
- 2011
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34. Selecting additional tag SNPs for tolerating missing data in genotyping.
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Huang YT, Zhang K, Chen T, and Chao KM
- Subjects
- Algorithms, Chromosome Mapping, Computer Simulation, DNA Mutational Analysis, Databases, Genetic, Gene Frequency, Genetic Markers, Genetic Predisposition to Disease, Genome, Human, Haplotypes, Humans, Models, Genetic, Research Design, Sequence Analysis, DNA, Software, Computational Biology methods, Data Interpretation, Statistical, Genotype, Polymorphism, Single Nucleotide
- Abstract
Background: Recent studies have shown that the patterns of linkage disequilibrium observed in human populations have a block-like structure, and a small subset of SNPs (called tag SNPs) is sufficient to distinguish each pair of haplotype patterns in the block. In reality, some tag SNPs may be missing, and we may fail to distinguish two distinct haplotypes due to the ambiguity caused by missing data., Results: We show there exists a subset of SNPs (referred to as robust tag SNPs) which can still distinguish all distinct haplotypes even when some SNPs are missing. The problem of finding minimum robust tag SNPs is shown to be NP-hard. To find robust tag SNPs efficiently, we propose two greedy algorithms and one linear programming relaxation algorithm. The experimental results indicate that (1) the solutions found by these algorithms are quite close to the optimal solution; (2) the genotyping cost saved by using tag SNPs can be as high as 80%; and (3) genotyping additional tag SNPs for tolerating missing data is still cost-effective., Conclusion: Genotyping robust tag SNPs is more practical than just genotyping the minimum tag SNPs if we can not avoid the occurrence of missing data. Our theoretical analysis and experimental results show that the performance of our algorithms is not only efficient but the solution found is also close to the optimal solution.
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- 2005
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35. Cardiac glycosides induce resistance to tubulin-dependent anticancer drugs in androgen-independent human prostate cancer.
- Author
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Huang DM, Guh JH, Huang YT, Chueh SC, Wang HP, and Teng CM
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- Androgens physiology, Antineoplastic Agents, Phytogenic pharmacology, Cell Cycle drug effects, Humans, Male, Paclitaxel pharmacology, Antineoplastic Agents, Phytogenic therapeutic use, Drug Resistance, Neoplasm, Ouabain pharmacology, Paclitaxel therapeutic use, Prostatic Neoplasms drug therapy, Tubulin drug effects
- Abstract
Due to high prevalence and mortality and the lack of effective therapies, prostate cancer is one of the most crucial health problems in men. Drug resistance aggravates the situation, not only in human prostate cancer but also in other cancers. In this study, we report for the first time that cardiac glycosides (e.g. ouabain and digitoxin) induced resistance of human prostate cancer cells (PC-3) in vitro to tubulin-binding anticancer drugs, such as paclitaxel, colchicine, vincristine and vinblastine. Cardiac glycosides exhibited amazing ability to reverse the G2/M arrest of the cell cycle and cell apoptosis induced by tubulin-binding agents. However, neither ionomycin (a Ca(2+) ionophore) nor veratridine (a Na(+) ionophore) mimicked the preventive action of cardiac glycosides, indicating that elevation of the intracellular Ca(2+) concentration and Na(+) accumulation were not involved in the cardiac glycoside action. Furthermore, cardiac glycosides showed little influence on the effects induced by actinomycin D, anisomycin and doxorubicin, suggesting selectivity for microtubule-targeted anticancer drugs. Using in situ immunofluorescent detection of mitotic spindles, our data showed that cardiac glycosides diminished paclitaxel-induced accumulation of microtubule spindles; however, in a non-cell assay system, cardiac glycosides had little influence on colchicine- and paclitaxel-induced microtubule dynamics. Using an isotope-labeled assay method, we found that ouabain modestly but significantly inhibited the transport of [(14)C]paclitaxel from the cytosol into the nucleus. It is suggested that cardiac glycosides inhibit the G2/M arrest induced by tubulin-binding anticancer drugs via an indirect blockade on microtubule function. The decline in transport of these drugs into the nucleus may partly explain the action of cardiac glycosides., (Copyright 2002 National Science Council, ROC and S. Karger AG, Basel)
- Published
- 2002
- Full Text
- View/download PDF
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