Bubble-free rapid microfluidic PCR

Lee, Sang Hun,Song, Jihwan,Cho, Byungrae,Hong, SoonGweon,Hoxha, Ori,Kang, Taewook,Kim, Dongchoul,Lee, Luke P. Elsevier 2019 Biosensors & Bioelectronics Vol.126 No.-

<P><B>Abstract</B></P> <P>Microfluidic polymerase chain reaction (PCR) has been of great interest owing to its ability to perform rapid and specific nucleic acid amplification and analysis on small volumes of samples. One of the major drawbacks of microfluidic PCR is bubble generation and reagent evaporation, which can cause malfunctions. Here, through theoretical modeling and characterization of bubble behavior, we propose a bubble-free microfluidic PCR device via controlled fluid transfer. Our approach exploits a thin impermeable polyethylene (PE) top layer that minimizes the generation of bubbles by inhibiting mass transport along a vertical direction. Simulation results demonstrate that a calculated mass flow difference of approximately 370% can be obtained by utilizing an impermeable membrane as the vertical barrier layer. To demonstrate proof-of-concept, two nanoporous polymeric materials, poly(dimethylsiloxane) (PDMS) and PE, were used for stand-alone self-powered sample loading (approximately 70 s) and for use as a vertical barrier layer, respectively. Consequently, we demonstrate successful amplification of the cMET gene, a nucleic acid (NA) biomarker for lung cancer, and complete an ultrafast PCR test in less than 3 min using a high powered Peltier-based thermal cycler under bubble-free conditions. This approach will result in a new paradigm for ultrafast molecular diagnosis and can facilitate NA-based nearly instantaneous diagnostics for point-of-care testing and for personalized and preventive medicine.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The major drawbacks of microfluidic PCR is bubble generation and reagent evaporation. </LI> <LI> A bubble-free microfluidic PCR device via controlled fluid transfer through theoretical modeling and characterization of bubble behavior. </LI> <LI> An impermeable polyethylene layer minimizes the generation of bubbles by inhibiting mass transport along a vertical direction. </LI> <LI> The microfluidic PCR chamber design with surrounding circumferential chamber for a guided-fluid transport of generated bubble. </LI> <LI> Successful nucleic acid amplification of the cMET gene, and an ultrafast PCR test in less than 3 min. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Test for Parameter Change in Linear Processes Based on Whittle's Estimator

Lee, Taewook,Lee, Sangyeol Taylor & Francis Inc. 2007 Communications in Statistics Vol.36 No.11

<P> In this article, we develop a cusum test for testing for parameter changes in linear processes based on Whittle's estimator. It is shown that under regularity conditions, the test statistic converges to the sup of a Brownian bridge. The result is particularly useful in handling the change point test in stationary ARMA processes. A simulation result is provided for illustration.</P>

Skewness of Gaussian Mixture Absolute Value GARCH(1, 1) Model

Lee, Taewook The Korean Statistical Society 2013 Communications for statistical applications and me Vol.20 No.5

This paper studies the skewness of the absolute value GARCH(1, 1) models with Gaussian mixture innovations (Gaussian mixture AVGARCH(1, 1) models). The maximum estimated-likelihood estimator (MELE) employed (a two- step estimation method in order to estimate the skewness of Gaussian mixture AVGARCH(1, 1) models. Through the real data analysis, the adequacy of adopting Gaussian mixture innovations is exhibited in reflecting the skewness of two major Korean stock indices.

Profiling and semiquantitative analysis of the cell surface proteome in human mesenchymal stem cells.

Lee, Sang Kwang,Kim, Jae Ho,Kim, Sung-Soo,Kang, Taewook,Park, Nam Hyun,Kwon, Kyung-Hoon,Lee, Sang Sook,Lee, Zee Won,Suh-Kim, Hae young,Cho, Kun,Yun, Su Yeoung,Han, Ji Young,Yoo, Jong Shin,An, Hyun Joo Springer-Verlag 2013 Analytical and bioanalytical chemistry Vol.405 No.16

<P>Mulitpotent mesenchymal stem cells (MSCs) derived from human bone marrow are promising candidates for the development of cell therapeutic strategies. MSC surface protein profiles provide novel biological knowledge concerning the proliferation and differentiation of these cells, including the potential for identifying therapeutic targets. Basic fibroblast growth factor (bFGF) affects cell surface proteins, which are associated with increased growth rate, differentiation potential, as well as morphological changes of MSCs in vitro. Cell surface proteins were isolated using a biotinylation-mediated method and identified using a combination of one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry. The resulting gel lines were cut into 20 bands and digested with trypsin. Each tryptic fragment was analyzed by liquid chromatography-electrospray ionization tandem mass spectrometry. Proteins were identified using the Mascot search program and the International Protein Index human database. Noble MSC surface proteins (n = 1,001) were identified from cells cultured either with (n = 857) or without (n = 667) bFGF-containing medium in three independent experiments. The proteins were classified using FatiGO to elucidate their function. We also confirmed the proteomics results using Western blotting and immunofluorescence microscopic analysis. The nature of the proteins identified makes it clear that MSCs express a wide variety of signaling molecules, including those related to cell differentiation. Among the latter proteins, four Ras-related Rab proteins, laminin-R, and three 14-3-3 proteins that were fractionated from MSCs cultured on bFGF-containing medium are implicated in bFGF-induced signal transduction of MSCs. Consequently, these finding provide insight into the understanding of the surface proteome of human MSCs.</P>

Consistency of minimizing a penalized density power divergence estimator for mixing distribution

Lee, Taewook,Lee, Sangyeol Springer-Verlag 2009 Statistical papers Vol.50 No.1

Wild bootstrap Ljung–Box test for residuals of ARMA models robust to variance change

Lee Taewook 한국통계학회 2022 Journal of the Korean Statistical Society Vol.51 No.4

Ljung–Box (LB) test is one of the most popular test for determining whether auto-correlations in residuals of fitted time series models exist or not. However, it may not be appropriate to apply LB test to time series data with variance change due to size distortions. In this paper, we proposed a wild bootstrap-based LB test for residuals of fitted ARMA models. Our simulation study shows that our wild bootstrap-based LB test achieves the correct sizes and comparable powers in finite samples in the presence of variance change.

Optical and electrical properties of Zn₂SiO₄:Mn²⁺ powder electroluminescent device

Lee, Sunghoon,Jeon, Byungjoo,Kang, Taewook,Lee, Wunho,Malik, Afandi Mohammad,Park, Seongwoo,Lim, Jimin,Park, Boowon,Jeong, Yongseok,kim, Jongsu Elsevier 2018 Journal of luminescence Vol.196 No.-

<P><B>Abstract</B></P> <P>Green-emission Zn<SUB>2</SUB>SiO<SUB>4</SUB>:Mn<SUP>2+</SUP> powder phosphor was applied for powder electroluminescence device through a screen printing method. The EL device consisted of silver nanowires as top electrode, 6μm-thick Zn<SUB>2</SUB>SiO<SUB>4</SUB>:Mn<SUP>2+</SUP> phosphor layer, 45µm -thick BaTiO<SUB>3</SUB> dielectric layer, and metal bottom electrode. The EL device showed the strong 525nm green emission spectrum. Its luminance-voltage dependence showed the exponential increase, and its luminance-frequency dependence showed the linear increase and then saturation behavior. It is notable that its temperature dependence showed the constant behavior at lower temperature, and then the drastic rising pattern up to Curie temperature of the dielectric layer (~ 120°C), and then the thermal quenching trend. The maximum luminance was 0.96cd/m<SUP>2</SUP> where the power consumption was 250W/m<SUP>2</SUP> at 420Vp and 400Hz, and thus the luminous efficiency was 0.012lm/W.</P>

Predicting transport and leakage behavior after injection of CO₂ infused water at CCS site with forced-gradient tracer test

Taewook Kim,Won-Tak Joun,Seung-Wook Ha,Seong-Sun Lee,Hong-Hyun Kim,Kang-Kun Lee 대한지질학회 2016 대한지질학회 학술대회 Vol.2016 No.10

Effect of biochemical and biomechanical factors on vascularization of kidney organoid-on-a-chip

Lee Han Na,Choi Yoon Young,Kim Jin Won,Lee Young Seo,최지욱,Kang Taewook,Kim Yong Kyun,Chung Bong Guen 나노기술연구협의회 2021 Nano Convergence Vol.8 No.35

Kidney organoids derived from the human pluripotent stem cells (hPSCs) recapitulating human kidney are the attractive tool for kidney regeneration, disease modeling, and drug screening. However, the kidney organoids cultured by static conditions have the limited vascular networks and immature nephron-like structures unlike human kidney. Here, we developed a kidney organoid-on-a-chip system providing fluidic flow mimicking shear stress with optimized extracellular matrix (ECM) conditions. We demonstrated that the kidney organoids cultured in our microfluidic system showed more matured podocytes and vascular structures as compared to the static culture condition. Additionally, the kidney organoids cultured in microfluidic systems showed higher sensitivity to nephrotoxic drugs as compared with those cultured in static conditions. We also demonstrated that the physiological flow played an important role in maintaining a number of physiological functions of kidney organoids. Therefore, our kidney organoid-on-a-chip system could provide an organoid culture platform for in vitro vascularization in formation of functional three-dimensional (3D) tissues.

Facile Fabrication of Large-Scale Porous and Flexible Three-Dimensional Plasmonic Networks

Lee, Yunjeong,Lee, Seungki,Jin, Chang Min,Kwon, Jung A,Kang, Taewook,Choi, Inhee American Chemical Society 2018 ACS APPLIED MATERIALS & INTERFACES Vol.10 No.33

<P>Assembling metallic nanoparticles and trapping target molecules within the probe volume of the incident light are important in plasmonic detection. Porous solid structures with three-dimensionally integrated metal nanoparticles would be very beneficial in achieving these objectives. Currently, porous inorganic oxides are being prepared under stringent conditions and further subjected to either physical or chemical attachment of metal nanoparticles. In this study, we propose a facile method to fabricate large-scale porous and flexible three-dimensional (3D) plasmonic networks. Initially, uncured polydimethylsiloxane (PDMS), in which metal ions are dissolved, diffuses spontaneously into the simple sugar crystal template via capillary action. As PDMS is cured, metal ions are automatically reduced to form a dense array of metal nanoparticles. After curing, the sugar template is easily removed by water treatment to obtain porous 3D plasmonic networks. We controlled the far-field scattering and near-field enhancement of the network by changing either the metal ion precursor or its concentration. To demonstrate the key advantages of our 3D plasmonic networks, such as simple fabrication, optical signal enhancement, and molecular trapping, we conducted sensitive Raman detection of several important molecules, including adenine, humidifier disinfectants, and volatile organic compounds.</P> [FIG OMISSION]</BR>