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Wavelet minimum description length detrending for near-infrared spectroscopy
Jang, Kwang Eun,Tak, Sungho,Jung, Jinwook,Jang, Jaeduck,Jeong, Yong,Ye, Jong Chul SPIE - International Society for Optical Engineeri 2009 Journal of biomedical optics Vol.14 No.3
<P>Near-infrared spectroscopy (NIRS) can be employed to investigate brain activities associated with regional changes of the oxy- and deoxyhemoglobin concentration by measuring the absorption of near-infrared light through the intact skull. NIRS is regarded as a promising neuroimaging modality thanks to its excellent temporal resolution and flexibility for routine monitoring. Recently, the general linear model (GLM), which is a standard method for functional MRI (fMRI) analysis, has been employed for quantitative analysis of NIRS data. However, the GLM often fails in NIRS when there exists an unknown global trend due to breathing, cardiac, vasomotion, or other experimental errors. We propose a wavelet minimum description length (Wavelet-MDL) detrending algorithm to overcome this problem. Specifically, the wavelet transform is applied to decompose NIRS measurements into global trends, hemodynamic signals, and uncorrelated noise components at distinct scales. The minimum description length (MDL) principle plays an important role in preventing over- or underfitting and facilitates optimal model order selection for the global trend estimate. Experimental results demonstrate that the new detrending algorithm outperforms the conventional approaches.</P>
RNA-based dynamic genetic controllers: development strategies and applications
Jang, Sungho,Jang, Sungyeon,Yang, Jina,Seo, Sang Woo,Jung, Gyoo Yeol Elsevier 2018 Current opinion in biotechnology Vol.53 No.-
<P>Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for <I>de novo</I> design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Unique properties of RNA lead to the development of RNA-based dynamic genetic controllers. </LI> <LI> Natural riboswitches are re-engineered to detect new molecules. </LI> <LI> RNA-based regulatory mechanisms are exploited to construct novel dynamic RNA controllers. </LI> <LI> Computational methods and <I>in vitro</I>–<I>in vivo</I> selection enable <I>de novo</I> design of dynamic RNA controllers. </LI> <LI> Dynamic RNA controllers are utilized for metabolic engineering and synthetic biology. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>