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A Novel Method for Estimating Nest Density in Bumblebee Populations from Molecular Genetic Markers 利用分子遗传标记估计大黄蜂种群巢密度的新方法
Japanese journal of biometrics Pub Date : 2018-08-01 DOI: 10.5691/JJB.39.23
T. Nomura
{"title":"A Novel Method for Estimating Nest Density in Bumblebee Populations from Molecular Genetic Markers","authors":"T. Nomura","doi":"10.5691/JJB.39.23","DOIUrl":"https://doi.org/10.5691/JJB.39.23","url":null,"abstract":"Bumblebees ( Bombus spp.) are important pollinators of both wildflowers and crops. In recent year, declines of population size have been reported in many Bumblebee species in various countries. In order to design effective conservation plans, nest (colony) density in a habitat is an essentially important information. In the present study, a novel method for estimating nest density using molecular genetic markers was proposed, by extending the concept of neighborhood size in population genetics. The proposed method was compared with the conventional method used in previous studies by applying to microsatellite data of Bombus hypocrite sapporoensis . Based on the obtained estimates of nest density, advantage and disadvantage of the two methods were discussed. An interpretation of estimate obtained by the proposed method was also presented from a viewpoint of conservation genetics.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116222956","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
Evaluation of Intrasubject Parallelism in Balanced Ex Vivo Bioassay Using One-sided Efficient Score Tests of Slope Difference Quantile 利用斜率差分位数的单侧有效评分检验评价平衡离体生物测定中受试者内平行度
Japanese journal of biometrics Pub Date : 2018-08-01 DOI: 10.5691/JJB.39.9
H. Uehara
{"title":"Evaluation of Intrasubject Parallelism in Balanced Ex Vivo Bioassay Using One-sided Efficient Score Tests of Slope Difference Quantile","authors":"H. Uehara","doi":"10.5691/JJB.39.9","DOIUrl":"https://doi.org/10.5691/JJB.39.9","url":null,"abstract":"In a relative potency assessment, it is necessary to make assumptions about the similarities between substances and their dose-response profile. For example, in a parallel line bioassay which uses the dose-response data within the linear response range, we need to demonstrate that the dose-response slopes of the study substances are approximately parallel. When using multiple animals for testing, it is also crucial to confirm that this parallelism exists not only for the averages but also within each animal (Uehara et al. 2016a). Meanwhile, when applying a linear mixed effect model to the analysis of parallel line assays, the between-substance difference of the slopes can be treated as a random effect. Thus, under a balanced assay design, we can derive an efficient score test to assess the quantile of the slope difference (McCulloch et al. 2008), which enables us to determine whether the majority of animals have their slope difference within the acceptable range. We applied this approach to the assessment of intrasubject parallelism with the intention of ameliorating the conservatism of our previous method (Uehara et al. 2016b). We present an example that uses the proposed method, along with the results of simulation studies.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129926775","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
The ASA Statement and P -values in Epidemiologic Research 流行病学研究中的ASA声明和P值
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.109
Tosiya Sato
{"title":"The ASA Statement and P -values in Epidemiologic Research","authors":"Tosiya Sato","doi":"10.5691/JJB.38.109","DOIUrl":"https://doi.org/10.5691/JJB.38.109","url":null,"abstract":"On March 7th, 2016, the American Statistical Association released its “ASA Statement on Statistical Significance and P -values,” which provided 6 principles to improve the conduct or interpretation of quantitative research. Misunderstanding and misuse of statistical tests and P -values were discussed many times in the epidemiologic field. In this paper, I gave a summary of the ASA statement and its translation process into Japanese. Then, I discussed how to avoid misunderstanding or misuse of statistical tests or P -values in epidemiologic observational studies.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116859429","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
p -value is a Useful and Excellent Measure for Reporting Results of Statistical Analysis on Clinical Data p值是临床资料统计分析报告结果的一种有效而优良的度量
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.153
T. Yanagawa
{"title":"p -value is a Useful and Excellent Measure for Reporting Results of Statistical Analysis on Clinical Data","authors":"T. Yanagawa","doi":"10.5691/JJB.38.153","DOIUrl":"https://doi.org/10.5691/JJB.38.153","url":null,"abstract":"Many clinical studies are conducted in Japan with sample sizes that are not determined statistically. Application of Neyman-Pearson type statistical tests to data from such studies is not justifiable and should be stopped. Also 5% significance level that is commonly employed in a clinical study without taking into account disease, drug and other factors is not justifiable. Alternatively, the use of p-value is recommended in this paper as a measure of showing the magnitude of difference of two treatments; it is the role of principal investigator to summarize the study results by considering disease, drug and other factors, sample sizes and p-value.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117149325","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
Reproducibility Crisis?—Diversity of Science and the p -value Problem in Ststistics 再现性危机?-科学多样性与统计学中的p值问题
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.117
N. Minaka
{"title":"Reproducibility Crisis?—Diversity of Science and the p -value Problem in Ststistics","authors":"N. Minaka","doi":"10.5691/JJB.38.117","DOIUrl":"https://doi.org/10.5691/JJB.38.117","url":null,"abstract":"The recent controversy over the use and abuse of p -values in statistical data analysis sheds a light on the epistemological diversity of scientific researches and the nature of science. Since the nineteenth century theoretical statisticians including Karl Pearson, Ronald A. Fisher, Jerzy Neyman, and Egon S.Pearson constructed the mathematical basis of modern statistics, for example, experimental design, sampling distributions, or hypothesis testing, etc. However, statistical reasoning as empirical inference is not necessarily limited to the Neyman-Pearson’s decision-making paradigm. Any kind of non-deductive inference—for example, abduction—also uses statistics as an exploratory tool for relative ranking among alternative hypotheses and models. We must understand not only the proper use of statistical methods and procedures but also the nature of each science to which statistics is applied.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114154752","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
P -value in Medical and Agricultural Research—Beyond p < 0.05 Paradigm— 医学和农业研究中的P值-超越P < 0.05范式
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.107
Hideki Saganami
{"title":"P -value in Medical and Agricultural Research—Beyond p < 0.05 Paradigm—","authors":"Hideki Saganami","doi":"10.5691/JJB.38.107","DOIUrl":"https://doi.org/10.5691/JJB.38.107","url":null,"abstract":"","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121398017","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
Statistical Methods for Evaluation of Bioactivity of Chemicals Using Quantitative High Throughput Screening 定量高通量筛选评价化学物质生物活性的统计方法
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.93
Asuka Nemoto, M. Ushijima
{"title":"Statistical Methods for Evaluation of Bioactivity of Chemicals Using Quantitative High Throughput Screening","authors":"Asuka Nemoto, M. Ushijima","doi":"10.5691/JJB.38.93","DOIUrl":"https://doi.org/10.5691/JJB.38.93","url":null,"abstract":"Quantitative high throughput sreening (qHTS) is a technique which has originally developed as a powerful tool for drug discovery and lately is expanding its application to the neighboring field, e.g. toxicological screening test for environmental chemicals. A wide variety of in-vitro biological activity of a large amount of chemical materials can be assayed with a low cost and in a short time period. As a result of two large-scale pharmacogenomic studies being published in 2012, the reproducibility of the result of screening assay of cytotoxicity for 15 drugs in 471 cell lines was revealed to be unexpectedly low. The necessity of developments of statistical methods suitable for qHTS data were emphasized. In this review, the authors explain 3 statistical methods with applications to qHTS data, which has been proposed since 2013: 1. robust ridge regression estimators for nonlinear models in the purpose of testing bioactivity of chemicals; 2. Bayesian hierarchical dose-response modeling; 3. using weighted entropy to rank chemicals. Characteristics of each method were compared, and the prospects were presented.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133779607","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
Informal Comments on the ASA 2016 Statement 对ASA 2016声明的非正式评论
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.163
Tetsuhisa Miwa
{"title":"Informal Comments on the ASA 2016 Statement","authors":"Tetsuhisa Miwa","doi":"10.5691/JJB.38.163","DOIUrl":"https://doi.org/10.5691/JJB.38.163","url":null,"abstract":"In 2016 the American Statistical Association published “ASA Statement on Statistical Significance and P -Values.” In this statement it seems that the use of statistical tests or p -values is discouraged because they are misused and misinterpreted. I doubt whether a statistical procedure such as test of significance should be rejected because it is misused and misinterpreted. I pose some questions about the ASA statement.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128357551","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
A Re-examination of Japanese Sample Size Calculation for Multi-regional Clinical Trial Evaluating Survival Endpoint 日本多地区临床试验评估生存终点的样本量计算方法的再检验
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.79
N. Hayashi, Y. Itoh
{"title":"A Re-examination of Japanese Sample Size Calculation for Multi-regional Clinical Trial Evaluating Survival Endpoint","authors":"N. Hayashi, Y. Itoh","doi":"10.5691/JJB.38.79","DOIUrl":"https://doi.org/10.5691/JJB.38.79","url":null,"abstract":"In planning a multi-regional clinical trial including Japan, the sample size for Japanese patients is often considered based on the probability of obtaining a consistent result between Japanese subpopulation and the overall study population, as recommended in the Japanese guideline “Basic Principles on Global Clinical Trials.” We review the commonly used existing method for Japanese sample size calculation based on obtaining a consistent result for survival endpoint. Through simulations, we note that Japanese sample size based on the existing method tended to have less actual power than the nominal power for consistency, especially when there is a large treatment effect. We propose alternative methods based on the delta method and numerical integrations. Our proposed methods give similar Japanese sample sizes, and our simulation studies show that our proposed methods provide the actual power close to the nominal power for consistency.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130031873","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
Confirmatory and Exploratory Analyses in Omics Studies with Particular Focus on Multiple Testing and P -value 组学研究的验证性和探索性分析，特别关注多重测试和P值
Japanese journal of biometrics Pub Date : 2018-03-01 DOI: 10.5691/JJB.38.127
S. Matsui
{"title":"Confirmatory and Exploratory Analyses in Omics Studies with Particular Focus on Multiple Testing and P -value","authors":"S. Matsui","doi":"10.5691/JJB.38.127","DOIUrl":"https://doi.org/10.5691/JJB.38.127","url":null,"abstract":"In this article, we discuss the role of P values in multiple testing to associate a large number of genetic or molecular features with a phenotypic variable of interest in biomedical omics studies. For multiple tests in such association analyses, we distinguish those conducted for confirmatory purpose, as seen in genome-wide association studies to determine disease-associated variants, from those for exploratory screening of associated features. For the latter, exploratory analysis, we discuss application of the ROC curve analysis used in diagnostic medicine, as an alternative, but more relevant framework, rather than the standard framework based on multiple testing that controls false positives only. Finally, partly based on arguments made in the field of omics studies, we make some comments on future endeavors by statisticians to disseminate discussions given in the ASA’s Statement on P -Values (Wasserstein and Lazar, 2016, The American Statistician, 70, 129-133) to improve statistical practice in various scientific fields.","PeriodicalId":365545,"journal":{"name":"Japanese journal of biometrics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128476828","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
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