Biometrical Journal最新文献

{"title":"The Replication of Equivalence Studies","authors":"Charlotte Micheloud,&nbsp;Leonhard Held","doi":"10.1002/bimj.202300232","DOIUrl":"10.1002/bimj.202300232","url":null,"abstract":"<p>Replication studies are increasingly conducted to assess the credibility of scientific findings. Most of these replication attempts target studies with a superiority design, but there is a lack of methodology regarding the analysis of replication studies with alternative types of designs, such as equivalence. In order to fill this gap, we propose two approaches, the two-trials rule and the sceptical two one-sided tests (TOST) procedure, adapted from methods used in superiority settings. Both methods have the same overall Type-I error rate, but the sceptical TOST procedure allows replication success even for nonsignificant original or replication studies. This leads to a larger project power and other differences in relevant operating characteristics. Both methods can be used for sample size calculation of the replication study, based on the results from the original one. The two methods are applied to data from the Reproducibility Project: Cancer Biology.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300232","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Group Integrative Dynamic Factor Models With Application to Multiple Subject Brain Connectivity","authors":"Younghoon Kim,&nbsp;Zachary F. Fisher,&nbsp;Vladas Pipiras","doi":"10.1002/bimj.202300370","DOIUrl":"10.1002/bimj.202300370","url":null,"abstract":"<div>\u0000 \u0000 <p>This work introduces a novel framework for dynamic factor model-based group-level analysis of multiple subjects time-series data, called GRoup Integrative DYnamic factor (GRIDY) models. The framework identifies and characterizes intersubject similarities and differences between two predetermined groups by considering a combination of group spatial information and individual temporal dynamics. Furthermore, it enables the identification of intrasubject similarities and differences over time by employing different model configurations for each subject. Methodologically, the framework combines a novel principal angle-based rank selection algorithm and a noniterative integrative analysis framework. Inspired by simultaneous component analysis, this approach also reconstructs identifiable latent factor series with flexible covariance structures. The performance of the GRIDY models is evaluated through simulations conducted under various scenarios. An application is also presented to compare resting-state functional MRI data collected from multiple subjects in autism spectrum disorder and control groups.</p></div>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-Dimensional Bayesian Semiparametric Models for Small Samples: A Principled Approach to the Analysis of Cytokine Expression Data","authors":"Giovanni Poli,&nbsp;Raffaele Argiento,&nbsp;Amedeo Amedei,&nbsp;Francesco C. Stingo","doi":"10.1002/bimj.70000","DOIUrl":"10.1002/bimj.70000","url":null,"abstract":"<p>In laboratory medicine, due to the lack of sample availability and resources, measurements of many quantities of interest are commonly collected over a few samples, making statistical inference particularly challenging. In this context, several hypotheses can be tested, and studies are not often powered accordingly. We present a semiparametric Bayesian approach to effectively test multiple hypotheses applied to an experiment that aims to identify cytokines involved in Crohn's disease (CD) infection that may be ongoing in multiple tissues. We assume that the positive correlation commonly observed between cytokines is caused by latent groups of effects, which in turn result from a common cause. These clusters are effectively modeled through a Dirichlet Process (DP) that is one of the most popular choices as nonparametric prior in Bayesian statistics and has been proven to be a powerful tool for model-based clustering. We use a spike–slab distribution as the base measure of the DP. The nonparametric part has been included in an additive model whose parametric component is a Bayesian hierarchical model. We include simulations that empirically demonstrate the effectiveness of the proposed testing procedure in settings that mimic our application's sample size and data structure. Our CD data analysis shows strong evidence of a cytokine gradient in the external intestinal tissue.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-Cohort Mixture Analysis: A Data Integration Approach With Applications on Gestational Age and DNA-Methylation-Derived Gestational Age Acceleration Metrics","authors":"Elena Colicino,&nbsp;Roberto Ascari,&nbsp;Hachem Saddiki,&nbsp;Francheska Merced-Nieves,&nbsp;Nicolò Foppa Pedretti,&nbsp;Kathi Huddleston,&nbsp;Robert O Wright,&nbsp;Rosalind J Wright,&nbsp;Program Collaborators for Environmental Influences on Child Health Outcomes","doi":"10.1002/bimj.202300270","DOIUrl":"10.1002/bimj.202300270","url":null,"abstract":"<div>\u0000 \u0000 <p>Data integration of multiple studies can provide enhanced exposure contrast and statistical power to examine associations between environmental exposure mixtures and health outcomes. Extant research has combined populations and identified an overall mixture–outcome association, without accounting for differences across studies. We extended the Bayesian Weighted Quantile Sum (BWQS) regression to a hierarchical framework to analyze mixtures across cohorts. The hierarchical BWQS (HBWQS) approach aggregates sample size of multiple cohorts to calculate an overall mixture index, thereby identifying the most harmful exposure(s) across cohorts; and provides cohort-specific associations between the overall mixture index and the outcome. We showed results from 10 simulated scenarios including four mixture components in three, eight, and ten populations, and two real-case examples on the association between prenatal metal mixture exposure—comprising arsenic, cadmium, and lead—and both gestational age and epigenetic-derived gestational age acceleration metrics. Simulated scenarios showed good empirical coverage and little bias for all HBWQS-estimated parameters. The Watanabe–Akaike information criterion showed a better average performance for the HBWQS regression than the BWQS across scenarios. HBWQS results incorporating cohorts within the national Environmental influences on Child Health Outcomes (ECHO) program from three different sites showed that the environmental mixture was negatively associated with gestational age in a single site. The HBWQS approach facilitates the combination of multiple cohorts and accounts for individual cohort differences in mixture analyses. HBWQS findings can be used to develop regulations, policies, and interventions regarding multiple co-occurring environmental exposures and it will maximize the use of extant publicly available data.</p>\u0000 </div>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimating the Sampling Distribution of Posterior Decision Summaries in Bayesian Clinical Trials","authors":"Shirin Golchi,&nbsp;James J. Willard","doi":"10.1002/bimj.70002","DOIUrl":"10.1002/bimj.70002","url":null,"abstract":"<p>Bayesian inference and the use of posterior or posterior predictive probabilities for decision making have become increasingly popular in clinical trials. The current practice in Bayesian clinical trials relies on a hybrid Bayesian-frequentist approach where the design and decision criteria are assessed with respect to frequentist operating characteristics such as power and type I error rate conditioning on a given set of parameters. These operating characteristics are commonly obtained via simulation studies. The utility of Bayesian measures, such as “assurance,” that incorporate uncertainty about model parameters in estimating the probabilities of various decisions in trials has been demonstrated. However, the computational burden remains an obstacle toward wider use of such criteria. In this article, we propose methodology which utilizes large sample theory of the posterior distribution to define parametric models for the sampling distribution of the posterior summaries used for decision making. The parameters of these models are estimated using a small number of simulation scenarios, thereby refining these models to capture the sampling distribution for small to moderate sample size. The proposed approach toward the assessment of conditional and marginal operating characteristics and sample size determination can be considered as simulation-assisted rather than simulation-based. It enables formal incorporation of uncertainty about the trial assumptions via a design prior and significantly reduces the computational burden for the design of Bayesian trials in general.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Landmarking for Left-Truncated Competing Risk Data","authors":"Theresa Unseld,&nbsp;Tobias Bluhmki,&nbsp;Jan Beyersmann,&nbsp;Evelin Beck,&nbsp;Stephanie Padberg,&nbsp;Regina Stegherr","doi":"10.1002/bimj.202400083","DOIUrl":"10.1002/bimj.202400083","url":null,"abstract":"<p>Landmarking is an alternative to complex multistate models when the aim is to calculate dynamic predictions. We develop the concept of landmarking for the case of left truncation and competing risks from the application background of drug safety assessment in pregnancy. The method is illustrated with a cohort study of the German Embryotox Pharmacovigilance Institute in Berlin to assess if the risk or the cumulative incidence of adverse pregnancy outcomes, like spontaneous abortions (SABs), is increased in fluoroquinolone-exposed women. Furthermore, we conduct an extensive simulation study to compare the dynamic predictions and coefficient estimates obtained by landmarking to those from nonparametric multistate models and classical time-dependent covariate Cox regression. The results from the simulation study indicate that attenuation of the effects is present in the landmark estimates, also in the complex setting considered here, but the estimates are still close to those from the multistate models. Regarding the Berlin fluoroquinolone data, the fluoroquinolone exposure of a pregnant woman in the first trimester seems to increase her cumulative incidence of elective termination of pregnancy over women never exposed before, but there is no evidence of a significantly increased risk or cumulative incidence in exposed women for SABs. This supports previous results on the same data, which were driven from an analysis without landmarking methods.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202400083","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Issue Information: Biometrical Journal 8'24","authors":"","doi":"10.1002/bimj.202470008","DOIUrl":"https://doi.org/10.1002/bimj.202470008","url":null,"abstract":"","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202470008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142525370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Firth-Type Penalized Methods of the Modified Poisson and Least-Squares Regression Analyses for Binary Outcomes","authors":"Satoshi Uno,&nbsp;Hisashi Noma,&nbsp;Masahiko Gosho","doi":"10.1002/bimj.202400004","DOIUrl":"https://doi.org/10.1002/bimj.202400004","url":null,"abstract":"<p>The modified Poisson and least-squares regression analyses for binary outcomes have been widely used as effective multivariable analysis methods to provide risk ratio and risk difference estimates in clinical and epidemiological studies. However, there is no certain evidence that assessed their operating characteristics under small and sparse data settings and no effective methods have been proposed for these regression analyses to address this issue. In this article, we show that the modified Poisson regression provides seriously biased estimates under small and sparse data settings. In addition, the modified least-squares regression provides unbiased estimates under these settings. We further show that the ordinary robust variance estimators for both of the methods have certain biases under situations that involve small or moderate sample sizes. To address these issues, we propose the Firth-type penalized methods for the modified Poisson and least-squares regressions. The adjustment methods lead to a more accurate and stable risk ratio estimator under small and sparse data settings, although the risk difference estimator is not invariant. In addition, to improve the inferences of the effect measures, we provide an improved robust variance estimator for these regression analyses. We conducted extensive simulation studies to assess the performances of the proposed methods under real-world conditions and found that the accuracies of the point and interval estimations were markedly improved by the proposed methods. We illustrate the effectiveness of these methods by applying them to a clinical study of epilepsy.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202400004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142435518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Confirmatory Adaptive Designs for Clinical Trials With Multiple Time-to-Event Outcomes in Multi-state Markov Models","authors":"Moritz Fabian Danzer,&nbsp;Andreas Faldum,&nbsp;Thorsten Simon,&nbsp;Barbara Hero,&nbsp;Rene Schmidt","doi":"10.1002/bimj.202300181","DOIUrl":"https://doi.org/10.1002/bimj.202300181","url":null,"abstract":"<p>The analysis of multiple time-to-event outcomes in a randomized controlled clinical trial can be accomplished with existing methods. However, depending on the characteristics of the disease under investigation and the circumstances in which the study is planned, it may be of interest to conduct interim analyses and adapt the study design if necessary. Due to the expected dependency of the endpoints, the full available information on the involved endpoints may not be used for this purpose. We suggest a solution to this problem by embedding the endpoints in a multistate model. If this model is Markovian, it is possible to take the disease history of the patients into account and allow for data-dependent design adaptations. To this end, we introduce a flexible test procedure for a variety of applications, but are particularly concerned with the simultaneous consideration of progression-free survival (PFS) and overall survival (OS). This setting is of key interest in oncological trials. We conduct simulation studies to determine the properties for small sample sizes and demonstrate an application based on data from the NB2004-HR study.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202300181","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142435517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Method for Nonparametric Statistical Inference for Niche Overlap in Multiple Species","authors":"Patrick B. Langthaler,&nbsp;Kai-Philipp Gladow,&nbsp;Oliver Krüger,&nbsp;Jonas Beck","doi":"10.1002/bimj.202400013","DOIUrl":"10.1002/bimj.202400013","url":null,"abstract":"<p>The understanding of species interactions and ecosystem dynamics hinges upon the study of ecological niches. Quantifying the overlap of Hutchinsonian-niches has garnered significant attention, with many recent publications addressing the issue. Prior work on estimating niche overlap often did not provide confidence intervals or assumed multivariate normality, seriously limiting applications in ecology, and biodiversity research. This paper extends a nonparametric approach, previously applied to the two-species case, to multiple species. For estimation, a consistent plug-in estimator based on rank sums is proposed and its asymptotic distribution is derived under weak conditions. The novel methodology is then applied to a study comparing the ecological niches of the Eurasian eagle owl, common buzzard, and red kite. These species share a habitat in Central Europe but exhibit distinct population trends. The analysis explores their breeding habitat preferences, considering the intricate competition dynamics and utilizing the nonparametric approach to niche overlap estimation. Our proposed method provides a valuable inferential tool for the quantitative evaluation of differences and overlap between niches.</p>","PeriodicalId":55360,"journal":{"name":"Biometrical Journal","volume":null,"pages":null},"PeriodicalIF":1.3,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/bimj.202400013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}