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212 results on '"Lin, Shau-Ping"'

1. An Efficient Approach for Identifying Important Biomarkers for Biomedical Diagnosis

Author

Huang, Jing-Wen, Chen, Yan-Hong, Phoa, Frederick Kin Hing, Lin, Yan-Han, and Lin, Shau-Ping

Subjects
Statistics - Methodology
Abstract

In this paper, we explore the challenges associated with biomarker identification for diagnosis purpose in biomedical experiments, and propose a novel approach to handle the above challenging scenario via the generalization of the Dantzig selector. To improve the efficiency of the regularization method, we introduce a transformation from an inherent nonlinear programming due to its nonlinear link function into a linear programming framework. We illustrate the use of of our method on an experiment with binary response, showing superior performance on biomarker identification studies when compared to their conventional analysis. Our proposed method does not merely serve as a variable/biomarker selection tool, its ranking of variable importance provides valuable reference information for practitioners to reach informed decisions regarding the prioritization of factors for further investigations.

Published
2023

5. Decentralized Supply Chain Optimization via Swarm Intelligence

Author

Singh, Karan, Liu, Hsin-Ping, Phoa, Frederick Kin Hing, Lin, Shau-Ping, Chen-Burger, Yun-Heh Jessica, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Tan, Ying, editor, Shi, Yuhui, editor, and Niu, Ben, editor

Published
2022
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7. Metaheuristic Optimization on Tensor-Type Solution via Swarm Intelligence and Its Application in the Profit Optimization in Designing Selling Scheme

Author

Phoa, Frederick Kin Hing, Liu, Hsin-Ping, Chen-Burger, Yun-Heh (Jessica), Lin, Shau-Ping, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Tan, Ying, editor, and Shi, Yuhui, editor

Published
2021
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8. Comparative global immune-related gene profiling of somatic cells, human pluripotent stem cells and their derivatives: implication for human lymphocyte proliferation.

Author

Wu, Chia-Eng, Yu, Chen-Wei, Chang, Kai-Wei, Chou, Wen-Hsi, Lu, Chen-Yu, Ghelfi, Elisa, Wu, Fang-Chun, Jan, Pey-Shynan, Huang, Mei-Chi, Allard, Patrick, Lin, Shau-Ping, Ho, Hong-Nerng, and Chen, Hsin-Fu

Subjects
Lymphocytes, Pluripotent Stem Cells, Humans, Cluster Analysis, Gene Expression Profiling, Lymphocyte Activation, Cell Differentiation, Immunity, Organ Specificity, Cell Lineage, Databases, Genetic, Embryonic Stem Cells, TOR Serine-Threonine Kinases, Transcriptome, CD24 Antigen, Databases, Genetic, Medicinal and Biomolecular Chemistry, Biochemistry & Molecular Biology
Abstract

Human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced PSCs (iPSCs), represent potentially unlimited cell sources for clinical applications. Previous studies have suggested that hPSCs may benefit from immune privilege and limited immunogenicity, as reflected by the reduced expression of major histocompatibility complex class-related molecules. Here we investigated the global immune-related gene expression profiles of human ESCs, hiPSCs and somatic cells and identified candidate immune-related genes that may alter their immunogenicity. The expression levels of global immune-related genes were determined by comparing undifferentiated and differentiated stem cells and three types of human somatic cells: dermal papilla cells, ovarian granulosa cells and foreskin fibroblast cells. We identified the differentially expressed genes CD24, GATA3, PROM1, THBS2, LY96, IFIT3, CXCR4, IL1R1, FGFR3, IDO1 and KDR, which overlapped with selected immune-related gene lists. In further analyses, mammalian target of rapamycin complex (mTOR) signaling was investigated in the differentiated stem cells following treatment with rapamycin and lentiviral transduction with specific short-hairpin RNAs. We found that the inhibition of mTOR signal pathways significantly downregulated the immunogenicity of differentiated stem cells. We also tested the immune responses induced in differentiated stem cells by mixed lymphocyte reactions. We found that CD24- and GATA3-deficient differentiated stem cells including neural lineage cells had limited abilities to activate human lymphocytes. By analyzing the transcriptome signature of immune-related genes, we observed a tendency of the hPSCs to differentiate toward an immune cell phenotype. Taken together, these data identify candidate immune-related genes that might constitute valuable targets for clinical applications.

Published
2017

9. Cholesterol homeostasis and oxidative stress-related novel plasma biomarkers for MSA patients

Author

Lin, Shau-Ping, primary, Wang, Hsiang-Hsuan Lin, additional, Huang, Jing-Wen, additional, Kuo, Mingche, additional, Tsai, Yi-Tzang, additional, Lu, Chia-Chen, additional, Chen, Yan-Hong, additional, Phoa, Frederick Kin Hing, additional, Kung, Pin-Jui, additional, Lin, Yan-Han, additional, Chu, Yung-Tsai, additional, Ju, Yan-Ru, additional, Shen, Tang-Long, additional, Hong, Chien-Tai, additional, Ochiya, Takahiro, additional, Ueda, Koji, additional, and Wu, Ruey-Meei, additional

Published
2024
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17. Plasma miR-203a-3p as a Novel Predictor of Dementia in Patients with Parkinson's Disease.

Author

Hsu, Ya-Fang, Lin, Shau-Ping, Chu, Yung-Tsai, Tsai, Yi-Tzang, Huang, Jing-Wen, Phoa, Frederick Kin Hing, and Wu, Ruey-Meei

Subjects
*PARKINSON'S disease, *DEMENTIA patients, *MEDICATION therapy management, *MILD cognitive impairment, *COGNITION disorders, *DEEP brain stimulation
Abstract

The early detection of cognitive decline in Parkinson's disease is important for providing drug therapy and non-pharmacological management. The circulating microRNAs present in plasma are promising biomarkers of PD with dementia (PDD) due to their critical roles in synaptic plasticity and the regulation of neurodegeneration-associated proteins. In this study, we aimed to identify plasma microRNAs that may differentiate PD with or without cognitive impairment. Global microRNA expression was obtained from a discovery set of 123 participants who were divided into four groups, namely normal controls (HC), PD with no dementia (PDND), PD with mild cognitive impairment (PD-MCI), and PDD, using next-generation sequencing. The BOLD selector was used for microRNA candidate selection. Six miRNAs, namely miR-203a-3p, miR-626, miR-662, miR-3182, miR-4274, and miR-4295, were clustered as potential candidates for use in identifying PDND from PD-MCI. Another independent cohort of 120 participants was further recruited in a validation step in order to detect candidate microRNAs via droplet digital PCR (ddPCR), which was used for its high sensitivity in detecting low miRNA concentrations. Our results show that the ratio of miR-203a-3p/miR-16-5p, in which miR-16-5p was used as a reference control miRNA, was significantly increased in PDD compared to that seen in PD-MCI and PDND individually, and was negatively correlated with the MoCA scores (r = −0.237, p = 0.024) in patients with PD. However, there was no significant difference in the ratio of miR-203a-3p/miR-16-5p between HC and PDND, PD-MCI, or PDD individually. The ROC curve of the logistic regression model, factoring in the variables of age, the ratio of miR-203a-3p/miR-16-5p, and the UPDRS III score, demonstrated an AUC of 0.883. Our findings suggest that the ratio of miR-203a-3p/miR-16-5p, used with age and motor score, could be a predictor of dementia among PD patients. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Discovery of HDAC6, HDAC8, and 6/8 Inhibitors and Development of Cell-Based Drug Screening Models for the Treatment of TGF-β-Induced Idiopathic Pulmonary Fibrosis

Author

Yu, Wei-Chieh, primary, Yeh, Tsung-Yu, additional, Ye, Chih-Hung, additional, Chong, Patrick Chun Theng, additional, Ho, Yi-Hsun, additional, So, Dorothy Kazuno, additional, Yap, Kah Yi, additional, Peng, Guan-Ru, additional, Shao, Chi-Hsuan, additional, Jagtap, Ajit Dhananjay, additional, Chern, Ji-Wang, additional, Lin, Chen-Si, additional, Lin, Shau-Ping, additional, Lin, Shuei-Liong, additional, Yu, Shu-Han, additional, and Yu, Chao-Wu, additional

Published
2023
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27. Metaheuristic Optimization on Tensor-Type Solution via Swarm Intelligence and Its Application in the Profit Optimization in Designing Selling Scheme

Author

Frederick Kin Hing Phoa, Hsin-Ping Liu, Yun-Heh Chen-Burger, and Lin Shau-Ping

Subjects
Scheme (programming language), Mathematical optimization, Speedup, Profit (accounting), Computer science, Tensor (intrinsic definition), Extension (predicate logic), Space (commercial competition), Swarm intelligence, computer, Metaheuristic, computer.programming_language
Abstract

Nature-inspired metaheuristic optimization has been widely used in many problems in industry and scientific investigations, but their applications in designing selling scheme are rare because the solution space in this kind of problems is usually high-dimensional, and their constraints are sometimes cross-dimensional. Recently, the Swarm Intelligence Based (SIB) method is proposed for problems in discrete domains, and it is widely applied in many mathematical and statistical problems that common metaheuristic methods seldom approach. In this work, we introduce an extension of the SIB method that handles solutions with many dimensions, or tensor solution in mathematics. We further speed up our method by implementing our algorithm with the use of CPU parallelization. We then apply this extended framework to real applications in designing selling scheme, showing that our proposed method helps to increase the profit of a selling scheme compared to those suggested by traditional methods.

Published
2021

28. Swarm Intelligence Optimisation Algorithms and Their Applications in a Complex Layer-Egg Supply Chain

Author

Karan Singh, Yun-Heh Chen-Burger, Lin Shau-Ping, and Frederick Kin Hing Phoa

Subjects
Supply chain management, Customer base, Computer science, Supply chain, Bio-inspired computing, Space (commercial competition), Swarm intelligence, Industrial engineering, Profit (economics), Domain (software engineering)
Abstract

Optimising processes in a supply chain can benefit enormously all participating companies and the entire supply chain, e.g. for cost-cutting or profit raising. Traditionally, simulation-based technologies are used for such purposes. However, such methods can be expensive and under-performing when the solution space is too large to be adequately explored. Biologically inspired computing approaches such as swarm intelligence algorithms are uniquely suited to solve complex, exponential, vectorial problems, such as those posed by multi-product supply chains connected with a large and diverse customer base and transportation methods. Although swarm intelligence algorithms have been used to optimise supply chains before, there has been little work on formalising and optimising the layer-egg supply chain, or the supply chain of a perishable product—where same/similar products can be packaged to form different product offerings to seek optimised configurations for different buyers based on different pricing and cost structures. In this paper, we introduce two new Swarm Intelligence algorithms and use them to optimise the profits of participating suppliers in a real-world layer-egg supply chain using its operational data, trade network, and demand & supply models. Several swarm intelligence algorithms were discussed and their performance was compared. Through this, we aim to understand how the complex domain of real-life layer-egg supply chain may be suitably formalised and optimised in a bid to help improve and sustain layer-egg supply chain’s financial well-beings.

Published
2021

30. Variants in Maternal Effect Genes and Relaxed Imprinting Control in a Special Placental Mesenchymal Dysplasia Case with Mild Trophoblast Hyperplasia

Author

Huang, Tien-Chi, primary, Chang, Kung-Chao, additional, Chang, Jen-Yun, additional, Tsai, Yi-Shan, additional, Yang, Yao-Jong, additional, Chang, Wei-Chun, additional, Mo, Chu-Fan, additional, Yu, Pei-Hsiu, additional, Chiang, Chun-Ting, additional, Lin, Shau-Ping, additional, and Kuo, Pao-Lin, additional

Published
2021
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33. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA

Author

Ooi, Steen K. T., Qiu, Chen, Bernstein, Emily, Li, Keqin, Jia, Da, Yang, Zhe, Erdjument-Bromage, Hediye, Tempst, Paul, Lin, Shau-Ping, Allis, C. David, Cheng, Xiaodong, and Bestor, Timothy H.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Steen K. T. Ooi [1, 6]; Chen Qiu [2, 6]; Emily Bernstein [3, 6]; Keqin Li [2, 6]; Da Jia [2]; Zhe Yang [2]; Hediye Erdjument-Bromage [4]; Paul Tempst [...]

Published
2007
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34. Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation

Author

Yang, Chih-Yi, primary, Lu, Rita Jui-Hsien, additional, Lee, Ming-Kang, additional, Hsiao, Felix Shih-Hsian, additional, Yen, Ya-Ping, additional, Cheng, Chun-Chun, additional, Hsu, Pu-Sheng, additional, Tsai, Yi-Tzang, additional, Chen, Shih-Kuo, additional, Liu, I-Hsuan, additional, Chen, Pao-Yang, additional, and Lin, Shau-Ping, additional

Published
2021
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39. Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast

Author

Yu, Yoyo Chih-Yun, primary, Hui, Tony ZK, additional, Kao, Tzu-Hao, additional, Liao, Hung-Fu, additional, Yang, Chih-Yi, additional, Hou, Chia-Chun, additional, Hsieh, Hsin-Ting, additional, Chang, Jen-Yun, additional, Tsai, Yi-Tzang, additional, Pinskaya, Marina, additional, Yang, Kai-Chien, additional, Chen, Yet-Ran, additional, Morillon, Antonin, additional, Tsai, Mong-Hsun, additional, and Lin, Shau-Ping, additional

Published
2020
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40. Correction: Dlk1-Dio3 locus-derived LncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity

Author

Yen, Ya-Ping, primary, Hsieh, Wen-Fu, additional, Tsai, Ya-Yin, additional, Lu, Ya-Lin, additional, Liau, Ee Shan, additional, Hsu, Ho-Chiang, additional, Chen, Yen-Chung, additional, Liu, Ting-Chun, additional, Chang, Mien, additional, Li, Joye, additional, Lin, Shau-Ping, additional, Hung, Jui-Hung, additional, and Chen, Jun-An, additional

Published
2020
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43. Imprinted small RNA genes

Author

Seitz, Hervé, Royo, Hélène, Lin, Shau-Ping, Youngson, Neil, Ferguson-Smith, Anne C., and Cavaillé, Jérôme

Published
2004

49. Author response: Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity

Author

Yen, Ya-Ping, primary, Hsieh, Wen-Fu, additional, Tsai, Ya-Yin, additional, Lu, Ya-Lin, additional, Liau, Ee Shan, additional, Hsu, Ho-Chiang, additional, Chen, Yen-Chung, additional, Liu, Ting-Chun, additional, Chang, Mien, additional, Li, Joye, additional, Lin, Shau-Ping, additional, Hung, Jui-Hung, additional, and Chen, Jun-An, additional

Published
2018
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