Chem-Bio Informatics Journal最新文献_第5页

Professor Toshio Fujita (1929-2017) as a pioneer of medicinal chemistry 藤田俊夫教授(1929-2017)是药物化学的先驱

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Chem-Bio Informatics Journal Pub Date : 2017-12-31 DOI: 10.1273/CBIJ.17.110

T. Ishikawa, K. Yuta, Y. Tada, A. Konagaya

引用次数: 0

Classification of Alzheimer’s disease and Parkinson’s disease using a support vector machine and probabilistic outputs 基于支持向量机和概率输出的阿尔茨海默病和帕金森病分类

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Chem-Bio Informatics Journal Pub Date : 2017-12-12 DOI: 10.1273/CBIJ.17.112

Asuka Hatabu, M. Harada, Yoshitake Takahashi, Shunsuke Watanabe, Kenya Sakamoto, Kousuke Okamoto, N. Kawashita, Yu-Shi Tian, T. Takagi

{"title":"Classification of Alzheimer’s disease and Parkinson’s disease using a support vector machine and probabilistic outputs","authors":"Asuka Hatabu, M. Harada, Yoshitake Takahashi, Shunsuke Watanabe, Kenya Sakamoto, Kousuke Okamoto, N. Kawashita, Yu-Shi Tian, T. Takagi","doi":"10.1273/CBIJ.17.112","DOIUrl":"https://doi.org/10.1273/CBIJ.17.112","url":null,"abstract":"Alzheimer's disease (AD) and Parkinson's disease (PD) are both prominent central nervous system diseases that are frequently diagnosed and studied using brain single-photon emission computed tomography (SPECT). Owing to divergent clinical features, AD and PD are often considered distinct diseases; however, it is difficult to distinguish AD from PD on SPECT. Tools for objectively analyzing differences between AD and PD on SPECT images are not currently available. To construct a model for discriminating AD from PD in Japanese patients, we used a support vector machine (SVM) and SPECT images acquired at two different time points after radiotracer injection to extract the determinant regions for classification. We assessed SPECT images from 68 Japanese patients with AD or PD. After pre-processing noise voxels, a non-linear SVM classification with Gaussian kernels was adopted to construct the predictive model. The best SVM model was highly accurate for distinguishing AD from PD. The accuracy of this model was 98.1% for leave-one-out cross-validation and 78.6% for the test set. Our data showed that the temporal, sub-lobar, parietal, limbic, and frontal areas exhibited decreased regional cerebral blood flow in AD; whereas the frontal, anterior, parietal, and occipital areas exhibited decreased regional cerebral blood flow in PD. Here, we present a useful SVM model for classifying AD versus PD using SPECT images and show the utility of two-time-point SPECT imaging for AD/PD discrimination.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2017-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78498277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Human serum albumin binding of 3, 5, 6, 7, 8, 3’, 4’- heptamethoxyflavone, a citrus flavonoid possessing a neuroprotective effect 人血清白蛋白结合3,5,6,7,8,3 '，4 ' -七甲基黄酮，一种具有神经保护作用的柑橘类黄酮

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Chem-Bio Informatics Journal Pub Date : 2017-11-10 DOI: 10.1273/CBIJ.17.103

Ayano Kakiuchi, Shion Ito, S. Okuyama, Y. Furukawa, T. Mizuma

{"title":"Human serum albumin binding of 3, 5, 6, 7, 8, 3’, 4’- heptamethoxyflavone, a citrus flavonoid possessing a neuroprotective effect","authors":"Ayano Kakiuchi, Shion Ito, S. Okuyama, Y. Furukawa, T. Mizuma","doi":"10.1273/CBIJ.17.103","DOIUrl":"https://doi.org/10.1273/CBIJ.17.103","url":null,"abstract":"3, 5, 6, 7, 8, 3’, 4’-heptamethoxyflavone (HMF), which is present in citrus fruits, has been reported to induce brain-derived neurotropic factor (BDNF) production, and have an anti-inflammatory effect. However, its pharmacokinetics is obscure. Therefore, as the first study of HMF pharmacokinetics, the reversible binding of HMF to human serum albumin (HSA) has been examined. For the binding examination and further pharmacokinetic study of HMF, a simple HPLC assay method was established first. The HPLC system equipped with a UV detector (HPLC-UV) and an isocratic mobile phase were used. The accuracy of intra-assay validation at each concentration from 1 to 100 M was from 97.2 to 101.6%, and the precision of intra-assay validation was less than 1.60%. For inter-assay validation, the accuracy was from 97.1 to 104.5%, and the precision was less than 2.24% from 1 to 100 M of HMF. The reversible binding of HMF to HSA was performed by the equilibrium dialysis method. The bound fraction of HMF to 4.6% HSA decreased from around 70% to 55% as the total concentration of HMF increased. This concentration dependency of the reversible binding suggests that HMF may have a specific binding site on the HSA molecule. The HPLC method established in this study is now being used for further investigation of HMF pharmacokinetics, such as intestinal absorption.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2017-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75924076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Interaction-based Approach for Affinity Prediction between Antigen Peptide and Human Leukocyte Antigen Using COMBINE Analysis 结合分析抗原肽与人白细胞抗原亲和预测的相互作用方法

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Chem-Bio Informatics Journal Pub Date : 2017-09-06 DOI: 10.1273/CBIJ.17.93

Shinya Nakamura, Rie Ohmura, I. Nakanishi

引用次数: 2

Myths in Modern Science: The Hydrogen Bond and its Surroundings. Part 1. The Hydrogen-Bond-Myth 现代科学中的神话:氢键及其周围环境。第1部分。的Hydrogen-Bond-Myth

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Chem-Bio Informatics Journal Pub Date : 2017-08-24 DOI: 10.1273/CBIJ.17.85

M. Nishio

引用次数: 0

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation 单链DNA，结合蛋白及其复合物的显式溶剂化:片段分子轨道计算的合适方案

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Chem-Bio Informatics Journal Pub Date : 2017-07-30 DOI: 10.1273/CBIJ.17.72

Yuto Komeij, Yoshio Okiyama, Y. Mochizuki, Kaori Fukuzawa

引用次数: 6

Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge 遗传网络推理后的先验知识利用:多知识集成

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Chem-Bio Informatics Journal Pub Date : 2017-06-17 DOI: 10.1273/CBIJ.17.53

Shuhei Kimura, Koji Kitazawa, M. Tokuhisa, M. Okada‐Hatakeyama

{"title":"Using A Priori Knowledge after Genetic Network Inference: Integrating Multiple Kinds of Knowledge","authors":"Shuhei Kimura, Koji Kitazawa, M. Tokuhisa, M. Okada‐Hatakeyama","doi":"10.1273/CBIJ.17.53","DOIUrl":"https://doi.org/10.1273/CBIJ.17.53","url":null,"abstract":"Several researchers have focused on the inference of genetic networks as a process for extracting useful information from gene expression data. Their work has led to the proposal of a number of methods for genetic network inference. Yet the genetic networks inferred by these methods often contain large numbers of false-positive regulations along with the true-positives. One effective way to reduce the number of erroneous regulations is to apply inference methods that use a priori knowledge on the properties of the genetic networks. The existing inference methods adopting this approach generally use a priori knowledge and the observed gene expression data simultaneously to determine whether or not the target genetic network actually contains each of the candidate regulations. In this study, we establish a new framework for “using a priori knowledge after genetic network inference.” The framework uses a priori knowledge only to modify the genetic network that has already been inferred by the other inference method. Based on this framework, we propose a new inference method that uses multiple kinds of a priori knowledge about genetic networks. The proposed method effectively combines multiple kinds of knowledge and computes the confidence values of regulations. Here, we confirm the effectiveness of the proposed method by applying it to artificial and actual genetic network inference problems. While only a small improvement is gained from the use of multiple kinds of a priori knowledge, we can improve the performance of many other existing inference methods by combining them with the method we propose here.","PeriodicalId":40659,"journal":{"name":"Chem-Bio Informatics Journal","volume":null,"pages":null},"PeriodicalIF":0.3,"publicationDate":"2017-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85374991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex 基于CYP3A4-托特罗定复合物多个初始结构的分子动力学模拟预测CYP3A4对托特罗定的代谢位点

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Chem-Bio Informatics Journal Pub Date : 2017-05-31 DOI: 10.1273/CBIJ.17.38

A. Sato, Hitomi Yuki, C. Watanabe, J. Saito, A. Konagaya, T. Honma

引用次数: 2

Competitive fragment assay for the selective inhibitor of WNKs kinase WNKs激酶选择性抑制剂的竞争性片段分析

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Chem-Bio Informatics Journal Pub Date : 2017-04-08 DOI: 10.1273/CBIJ.17.34

Nae Saito, Y. Tada, T. Okabe, T. Nagano

引用次数: 0

Docking simulation of fragment library compounds to find new leads for specific WNK kinase inhibitors 对接模拟片段文库化合物，寻找特异性WNK激酶抑制剂的新线索

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Chem-Bio Informatics Journal Pub Date : 2017-03-30 DOI: 10.1273/CBIJ.17.30

Nae Saito, Y. Tada, T. Okabe, T. Nagano

引用次数: 1