2,574 research outputs found
Regioselective One-Pot Synthesis of Hydroxy-(S)-Equols Using Isoflavonoid Reductases and Monooxygenases and Evaluation of the Hydroxyequol Derivatives as Selective Estrogen Receptor Modulators and Antioxidants
No full textCopyright © 2022 Song, Lee, Kim, Kim, Lee, Kim, Lee, Kim, Kim and Kim.Several regiospecific enantiomers of hydroxy-(S)-equol (HE) were enzymatically synthesized from daidzein and genistein using consecutive reduction (four daidzein-to-equol–converting reductases) and oxidation (4-hydroxyphenylacetate 3-monooxygenase, HpaBC). Despite the natural occurrence of several HEs, most of them had not been studied owing to the lack of their preparation methods. Herein, the one-pot synthesis pathway of 6-hydroxyequol (6HE) was developed using HpaBC (EcHpaB) from Escherichia coli and (S)-equol-producing E. coli, previously developed by our group. Based on docking analysis of the substrate or products, a potential active site and several key residues for substrate binding were predicted to interpret the (S)-equol hydroxylation regioselectivity of EcHpaB. Through investigating mutations on the key residues, the T292A variant was verified to display specific mono-ortho-hydroxylation activity at C6 without further 3′-hydroxylation. In the consecutive oxidoreductive bioconversion using T292A, 0.95 mM 6HE could be synthesized from 1 mM daidzein, while 5HE and 3′HE were also prepared from genistein and 3′-hydroxydaidzein (3′HD or 3′-ODI), respectively. In the following efficacy tests, 3′HE and 6HE showed about 30∼200-fold higher EC50 than (S)-equol in both ERα and ERβ, and they did not have significant SERM efficacy except 6HE showing 10% lower β/α ratio response than that of 17β-estradiol. In DPPH radical scavenging assay, 3′HE showed the highest antioxidative activity among the examined isoflavone derivatives: more than 40% higher than the well-known 3′HD. In conclusion, we demonstrated that HEs could be produced efficiently and regioselectively through the one-pot bioconversion platform and evaluated estrogenic and antioxidative activities of each HE regio-isomer for the first time.N
%QLS SAS Macro: A SAS Macro for Analysis of Correlated Data Using Quasi-Least Squares
No full textQuasi-least squares (QLS) is an alternative computational approach for estimation of the correlation parameter in the framework of generalized estimating equations (GEE). QLS overcomes some limitations of GEE that were discussed in Crowder (1995). In addition, it allows for easier implementation of some correlation structures that are not available for GEE. We describe a user written SAS macro called %QLS, and demonstrate application of our macro using a clinical trial example for the comparison of two treatments for a common toenail infection. %QLS also computes the lower and upper boundaries of the correlation parameter for analysis of longitudinal binary data that were described by Prentice (1988). Furthermore, it displays a warning message if the Prentice constraints are violated. This warning is not provided in existing GEE software packages and other packages that were recently developed for application of QLS (in Stata, MATLAB, and R). %QLS allows for analysis of continuous, binary, or count data with one of the following working correlation structures: the first-order autoregressive, equicorrelated, Markov, or tri-diagonal structures.
간섭법과 이를 위한 기록 매체를 스캐닝하는 백색광을 사용한 두께 프로파일과 굴절률을 측정하기 위한 방법
No full textA method and a recording medium for measuring three-dimensional thickness profile and refractive index of transparent dielectric thin-film with some patterns or not, which is fabricated in the semiconductor and related industrial field, using white-light scanning interferometry is provided.A method for measuring a thickness profile using white-light scanning interferometry in optical system includes the following steps. A first step is to extracting a phase graph by acquiring an interference signal and performing Fourier transform. A second step is to extracting a mathematical phase graph through modeling of a measurement object. And a third step is to measuring a profile value and a thickness value by applying an optimization technique to an error function determined by using phase values which is acquired from said first step and said second step
Annotations to quantum statistical mechanics
No full textThis book is a rewritten and annotated version of Leo P. Kadanoff and Gordon Bayms lectures that were presented in the book Quantum Statistical Mechanics: Greens Function Methods in Equilibrium and Nonequilibrium Problems. The lectures were devoted to a discussion on the use of thermodynamic Greens functions in describing the properties of many-particle systems. The functions provided a method for discussing finite-temperature problems with no more conceptual difficulty than ground-state problems, and the method was equally applicable to boson and fermion systems and equilibrium and nonequilibrium problems. The lectures also explained nonequilibrium statistical physics in a systematic way and contained essential concepts on statistical physics in terms of Greens functions with sufficient and rigorous details. In-Gee Kim thoroughly studied the lectures during one of his research projects but found that the unspecialized method used to present them in the form of a book reduced their readability. He started the tedious work of rewriting and annotating them to fully understand the formalism of nonequilibrium quantum statistical mechanics. While doing so, he realized they can be a useful resource for students of modern physics but will have to be upgraded to match pace with the evolved curricula. Being aware that besides completing the course work and passing the relevant examinations, it is necessary for graduate students of modern physics to make the knowledge of a topic concrete in their minds. This book is a systematically prepared summary of those lectures and will be extremely useful for graduate students as well as senior researchers to settle down the key knowledge of the subject
A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction
No full textBackground To reduce drug side effects and enhance their therapeutic effect compared with single drugs, drug combination research, combining two or more drugs, is highly important. Conducting in-vivo and in-vitro experiments on a vast number of drug combinations incurs astronomical time and cost. To reduce the number of combinations, researchers classify whether drug combinations are synergistic through in-silico methods. Since unstructured data, such as biomedical documents, include experimental types, methods, and results, it can be beneficial extracting features from documents to predict anti-cancer drug combination synergy. However, few studies predict anti-cancer drug combination synergy using document-extracted features. Results We present a novel approach for anti-cancer drug combination synergy prediction using document-based feature extraction. Our approach is divided into two steps. First, we extracted documents containing validated anti-cancer drug combinations and cell lines. Drug and cell line synonyms in the extracted documents were converted into representative words, and the documents were preprocessed by tokenization, lemmatization, and stopword removal. Second, the drug and cell line features were extracted from the preprocessed documents, and training data were constructed by feature concatenation. A prediction model based on deep and machine learning was created using the training data. The use of our features yielded higher results compared to the majority of published studies. Conclusions Using our prediction model, researchers can save time and cost on new anti-cancer drug combination discoveries. Additionally, since our feature extraction method does not require structuring of unstructured data, new data can be immediately applied without any data scalability issues.N
Plasmid stability in a recombinant mammalian cell bioprocess
No full textA simple experimental method is devised to determine the fraction of plasmid-harboring cells in a bioprocess employing recombinant mammalian cells. The fraction of plasmid-harboring cells decreased as serum content in the growth medium decreased. The relatively higher increase in the generation time of the plasmid-harboring cell was primarily responsible for this decrease. The mathematical expression obtained for this fraction in terms of the two parameters, i.e. the generation time ratio and the plasmid-loss probability, could represent the experimental data extremely well. The numerical values of these parameters could show the inherent insight of the system. It was found that the data plot against time can draw us to a misleading conclusion of the absence of the effect of serum concentration.N
CICO: Chemically Induced Carcinogenesis Ontology
No full textIn vivo experiments have had a great impact on the development of biomedicine, and as a result, a variety of biomedical data is produced and provided to researchers. Standardization and ontology design were carried out for the systematic management and effective sharing of these data. As results of their efforts, useful ontologies such as the Experimental Factor Ontology (EFO), Disease Ontology (DO), Gene Ontology (GO), Chemical Entities of Biological Interest (ChEBI) were developed. However, these ontologies are not enough to provide knowledge about the experiments to researchers conducting in vivo studies. Specifically, in the experimental design process, the generation of cancer causes considerable time and research costs. Researchers conducting animal experiments need animals with signs of carcinogenesis that fits their research interests. Therefore, our study is intended to provide experimental data about inducing cancer in animals. In order to provide this data, we collect experimental data about chemical substances that cause cancer. After that, we design an ontology based on these data and link it with the Disease Ontology. Our research focuses largely on two aspects. The first is to create a knowledge graph that inter-links with other biomedical linked data. The second is to provide practical knowledge to researchers conducting in vivo experiments. In conclusion, our research is provided in the form of a web service, which makes it easy to use the SPARQL endpoint and search service.N
Generation of a recombinant antibody for sensitive detection of Pseudomonas aeruginosa
No full textPseudomonas aeruginosa (P. aeruginosa) is a major pathogen that causes nosocomial infections and often exhibits antibiotic resistance. Therefore, the development of an accurate method for detecting P. aeruginosa is required to control P. aeruginosa-related outbreaks. In this study, we established an enzyme-linked immunosorbent assay method for the sensitive detection of three P. aeruginosa strains, UCBPP PA14, ATCC 27853, and multidrug-resistant ATCC BAA-2108. We produced a recombinant antibody (rAb) against P. aeruginosa V‐antigen (PcrV), which is a needle tip protein of the type III secretion system of P. aeruginosa using mammalian cells with high yield and purity, and confirmed its P. aeruginosa binding efficiency. The rAb was paired with commercial anti-P. aeruginosa Ab for a sandwich ELISA, resulting in an antigen-concentration-dependent response with a limit of detection value of 230 CFU/mL. These results suggest that the rAb produced herein can be used for the sensitive detection of P. aeruginosa with a wide range of applications in clinical diagnosis and point-of-care testing. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12896-022-00751-9
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Traditional Korean Music in Contemporary Context: A Performance Guide to Gideon Gee Bum Kim's Kangkangsullae
No full textGideon Gee Bum Kim is an internationally-acclaimed contemporary Korean-Canadian composer. Kim has utilized traditional Korean music with Western composition techniques in some of his works. Kim created his own style by incorporating traditional Korean musical elements such as the scale, rhythmic diversity, syncopation, variation, ornamentation, and the progression of melody into a body of music that is otherwise contemporary and Western. The purpose of this study is to develop a performance guide for Gideon Gee Bum Kim's Kangkangsullae for string trio. Kangkangsullae trio is based on Korean historical, cultural and musical influences. I give a detailed historical and cultural background for this work and demonstrate how Kim integrated Western compositional techniques with traditional Korean music. My emphasis is on defining specific characteristics of traditional Korean music which will provide several points toward understanding Kim's compositional style
Trap column-based intact mass spectrometry for rapid and accurate evaluation of protein molecular weight
No full textThe determination of the molecular weight (MW) of a protein using high-resolution mass spectrometry (MS) is a crucial tool used to confirm whether the protein was correctly expressed and adequately purified. However, a non-volatile buffer is normally used for protein purification and storage. Therefore, a pre-treatment step using ultrafiltration (UF) is required to exchange the buffer with a volatile buffer prior to the introduction of the protein sample into the MS equipment. This pre-treatment step is time-consuming. In this study, a trap column-based pre-treatment method applied in a nano-LC system was developed for rapid and convenient analysis of the MW of proteins. First, the trap column system was compared with the conventional UF treatment system and non-treatment system using bovine serum albumin. Subsequently, the trap column system was applied to analyze the MW of commercially available and lab-synthesized recombinant proteins. The intensity of the base peak and signal-to-noise ratio of the trap column-based pre-treated protein were higher than those of the UF-treated protein. Moreover, the entire automated procedure of the trap column-based system was conducted within 20 min, which confirms its use in versatile and accurate protein identification
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