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Lee, N.,Kwon, D. Y. Springer Science + Business Media 2016 Indian journal of microbiology Vol.56 No.4
<P>2,3-Dihydroxybiphenyl 1,2-dioxygenase (2,3-DBDO) is an extradiol-type dioxygenase that involved in third step of biphenyl degradation pathway. The nucleotide sequence of the bphC gene from Comamonas sp. SMN4, which encodes 2,3-DBDO with His-tag, was cloned into a plasmid pQE30 in E. coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the purified active 2,3-DBDO showed a single band around 33 kDa, corresponding the molecular mass of 2,3-DBDO subunit. Two fractions around 170 and 100 kDa were separated in gel filtration chromatography, but only former one (the fraction of 170 kDa) has 2,3-DBDO activity. The 2,3-DBDO was reported as the polymeric protein consisted of eight subunits. However, the fraction corresponding octameric protein of 2,3-DBDO was not found in the gel filtration chromatography. The 2,3-DBDO was exhibited the maximum activity at pH 9.0 and was stable at pH 8.0, relatively. The circular dichroism (CD) data showed that 2,3-DBDO had an alpha-helical folding structures at neutral pHs ranged from pH 4.5 to pH 9.0. However, this high stable folding structure was converted to unfolded structure in acidic region (pH 2.5) or in high pH (pH 12.0). The enzyme was thermally stable and active up to 40 A degrees C. The conformational data by CD spectra were consistent with the stability of 2,3-DBDO by checking the activity. The binding affinity (K (m) ) for 2,3-dihydroxybiphenyl, 3-metylcatechol, 4-methylcatechol and catechol was 11.7, 24 mu M, 50 mM and 625 mu M, respectively.</P>
Lee, N.,Choi, H.,Kim, S.H. North-Holland Pub. Co ; Elsevier Science Ltd 2016 Computational statistics & data analysis Vol.101 No.-
<P>We propose Bayesian shrinkage methods for coefficient estimation for high-dimensional vector autoregressive (VAR) models using scale mixtures of multivariate normal distributions for independently sampled additive noises. We also suggest an efficient selection procedure for the shrinkage parameter as a computationally feasible alternative to the traditional MCMC sampling methods for high-dimensional data. A shrinkage parameter is selected at the minimum point of a newly proposed score function which is asymptotically equivalent to the mean squared error of the model coefficients. The selected shrinkage parameter is presented in a closed form as a function of sample size, level of noise, and non-normality in data, and it can be efficiently estimated by using a suggested variation of cross validation. Consistency of both of the cross validation estimator and proposed shrinkage estimator is proved. The competitiveness of the proposed methods is demonstrated based on comprehensive experimental results using simulated data and high-dimensional plant gene expression data in the context of coefficient estimation and structural inference for VAR models. The proposed methods are applicable to high dimensional stationary time series with or without near unit roots. (C) 2016 Elsevier B.V. All rights reserved.</P>
Lee, N.,Jun, J.h.,Lee, D.S. Pergamon Press 2016 Clinical biochemistry Vol.49 No.9
Objectives: The advantage of Sysmex XN system is its performance of an automatic reflex test in white cell precursor (WPC) channel, which gives an accurate differential count. We performed a real-time evaluation of the automatic differential count according to WBC number with Sysmex XN series and demonstrated a significant differential impact on blast distinction depending on the number of WBC. Design and methods: We categorized the 49,699 specimen according to WBC number and compared the results of blast flagging in the white cell differential (WDF) channel and WPC channel on the basis of the results of manual differential count. Additionally, clinical impact of missed blasts after running WPC reflex test was analyzed. Results: For patients with WBC under 1.5x10<SUP>9</SUP>/L, blast flagging for WPC channel showed markedly decreased sensitivity (56%) compared to that of WDF mode (100%). Most of the patients with missed blasts in WPC mode were under chemotherapy or hematopoietic stem cell transplantation. The specificity and efficiency for WPC channel were much higher than that of WDF mode in all range of WBC. Conclusions: Considering the additional reagent cost required for the WPC channel, WPC reflex test is not suitable for patients with leukopenia if it is operated alone. Instead, manual blood film review or double-check with other supplemental equipment should be accompanied.
Phytochrome-interacting factor from Arabidopsis to liverwort
Lee, N.,Choi, G. Current Biology, Ltd ; Elsevier Science Ltd 2017 Current opinion in plant biology Vol.35 No.-
<P>Phytochromes are red and far-red light photoreceptors that regulate the responses of plants to light throughout their life cycles. Phytochromes do this in part by inhibiting the function of a group of basic helix-loop-helix transcription factors called phytochrome-interacting factors (PIFs). Arabidopsis has eight PIFs that function sometimes redundantly and sometimes distinctively depending on their expression patterns and protein stability, as well as on variations in the promoters they target in vivo. PIF-like proteins exist in other seed plants and non-vascular plants where they also regulate light responses. The mechanism by which phytochrome regulates light responses by promoting the degradation of the PIFs is conserved in liverwort, suggesting it must have evolved some time before the last common ancestor shared by seed plants and non-vascular plants.</P>