Statistical treatment of looking-time data.
Ontology highlight
ABSTRACT:
SUBMITTER: Csibra G
PROVIDER: S-EPMC4817233 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Infant research is hard. It is difficult, expensive, and time consuming to identify, recruit and test infants. As a result, ours is a field of small sample sizes. Many studies using infant looking time as a measure have samples of 8 to 12 infants per cell, and studies with more than 24 infants per cell are uncommon. This paper examines the effect of such sample sizes on statistical power and the conclusions drawn from infant looking time research. An examination of the state of the current literature suggests that most published looking time studies have low power, which leads in the long run to an increase in both false positive and false negative results. Three data sets with large samples (>30 infants) were used to simulate experiments with smaller sample sizes; 1000 random subsamples of 8, 12, 16, 20, and 24 infants from the overall samples were selected, making it possible to examine the systematic effect of sample size on the results. This approach revealed that despite clear results with the original large samples, the results with smaller subsamples were highly variable, yielding both false positive and false negative outcomes. Finally, a number of emerging possible solutions are discussed.
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Project description:BackgroundEven though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.ResultsIn the first approach, a multiple regression analysis model was developed to derive DeltaDeltaCt from estimation of interaction of gene and treatment effects. In the second approach, an ANCOVA (analysis of covariance) model was proposed, and the DeltaDeltaCt can be derived from analysis of effects of variables. The other two models involve calculation DeltaCt followed by a two group t-test and non-parametric analogous Wilcoxon test. SAS programs were developed for all four models and data output for analysis of a sample set are presented. In addition, a data quality control model was developed and implemented using SAS.ConclusionPractical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.
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Project description:BackgroundComparing metabolic profiles under different biological perturbations has become a powerful approach to investigating the functioning of cells. The profiles can be taken as single snapshots of a system, but more information is gained if they are measured longitudinally over time. The results are short time series consisting of relatively sparse data that cannot be analyzed effectively with standard time series techniques, such as autocorrelation and frequency domain methods. In this work, we study longitudinal time series profiles of glucose consumption in the yeast Saccharomyces cerevisiae under different temperatures and preconditioning regimens, which we obtained with methods of in vivo nuclear magnetic resonance (NMR) spectroscopy. For the statistical analysis we first fit several nonlinear mixed effect regression models to the longitudinal profiles and then used an ANOVA likelihood ratio method in order to test for significant differences between the profiles.ResultsThe proposed methods are capable of distinguishing metabolic time trends resulting from different treatments and associate significance levels to these differences. Among several nonlinear mixed-effects regression models tested, a three-parameter logistic function represents the data with highest accuracy. ANOVA and likelihood ratio tests suggest that there are significant differences between the glucose consumption rate profiles for cells that had been--or had not been--preconditioned by heat during growth. Furthermore, pair-wise t-tests reveal significant differences in the longitudinal profiles for glucose consumption rates between optimal conditions and heat stress, optimal and recovery conditions, and heat stress and recovery conditions (p-values <0.0001).ConclusionWe have developed a nonlinear mixed effects model that is appropriate for the analysis of sparse metabolic and physiological time profiles. The model permits sound statistical inference procedures, based on ANOVA likelihood ratio tests, for testing the significance of differences between short time course data under different biological perturbations.
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Project description:The purpose of the data presented in this article is to use it in ex post estimations of interest rate decisions by the European Central Bank (ECB), as it is done by Bletzinger and Wieland (2017) [1]. The data is of quarterly frequency from 1999 Q1 until 2013 Q2 and consists of the ECB's policy rate, inflation rate, real output growth and potential output growth in the euro area. To account for forward-looking decision making in the interest rate rule, the data consists of expectations about future inflation and output dynamics. While potential output is constructed based on data from the European Commission's annual macro-economic database, inflation and real output growth are taken from two different sources both provided by the ECB: the Survey of Professional Forecasters and projections made by ECB staff. Careful attention was given to the publication date of the collected data to ensure a real-time dataset only consisting of information which was available to the decision makers at the time of the decision.
| S-EPMC5671468 | biostudies-literature
Project description:MotivationMetabolomics is the study of the complement of small molecule metabolites in cells, biofluids and tissues. Many metabolomic experiments are designed to compare changes observed over time under two experimental conditions or groups (e.g. a control and drug-treated group) with the goal of identifying discriminatory metabolites or biomarkers that characterize each condition. A common study design consists of repeated measurements taken on each experimental unit thus producing time courses of all metabolites. We describe a statistical framework for estimating time-varying metabolic profiles and their within-group variability and for detecting between-group differences. Specifically, we propose (i) a smoothing splines mixed effects (SME) model that treats each longitudinal measurement as a smooth function of time and (ii) an associated functional test statistic. Statistical significance is assessed by a non-parametric bootstrap procedure.ResultsThe methodology has been extensively evaluated using simulated data and has been applied to real nuclear magnetic resonance spectroscopy data collected in a preclinical toxicology study as part of a larger project lead by the COMET (Consortium for Metabonomic Toxicology). Our findings are compatible with the previously published studies.AvailabilityAn R script is freely available for download at http://www2.imperial.ac.uk/~gmontana/sme.htm.
| S-EPMC3129523 | biostudies-literature
Project description:The most common objective for response-adaptive clinical trials is to seek to ensure that patients within a trial have a high chance of receiving the best treatment available by altering the chance of allocation on the basis of accumulating data. Approaches that yield good patient benefit properties suffer from low power from a frequentist perspective when testing for a treatment difference at the end of the study due to the high imbalance in treatment allocations. In this work we develop an alternative pairwise test for treatment difference on the basis of allocation probabilities of the covariate-adjusted response-adaptive randomization with forward-looking Gittins Index (CARA-FLGI) Rule for binary responses. The performance of the novel test is evaluated in simulations for two-armed studies and then its applications to multiarmed studies are illustrated. The proposed test has markedly improved power over the traditional Fisher exact test when this class of nonmyopic response adaptation is used. We also find that the test's power is close to the power of a Fisher exact test under equal randomization.
| S-EPMC7614356 | biostudies-literature
Project description:Research on infants' reasoning abilities often rely on looking times, which are longer to surprising and unexpected visual scenes compared to unsurprising and expected ones. Few researchers have examined more precise visual scanning patterns in these scenes, and so, here, we recorded 8- to 11-month-olds' gaze with an eye tracker as we presented a sampling event whose outcome was either surprising, neutral, or unsurprising: A red (or yellow) ball was drawn from one of three visible containers populated 0%, 50%, or 100% with identically colored balls. When measuring looking time to the whole scene, infants were insensitive to the likelihood of the sampling event, replicating failures in similar paradigms. Nevertheless, a new analysis of visual scanning showed that infants did spend more time fixating specific areas-of-interest as a function of the event likelihood. The drawn ball and its associated container attracted more looking than the other containers in the 0% condition, but this pattern was weaker in the 50% condition, and even less strong in the 100% condition. Results suggest that measuring where infants look may be more sensitive than simply how much looking there is to the whole scene. The advantages of eye tracking measures over traditional looking measures are discussed.
| S-EPMC5142767 | biostudies-literature
Project description:BackgroundLocal similarity analysis (LSA) of time series data has been extensively used to investigate the dynamics of biological systems in a wide range of environments. Recently, a theoretical method was proposed to approximately calculate the statistical significance of local similarity (LS) scores. However, the method assumes that the time series data are independent identically distributed, which can be violated in many problems.ResultsIn this paper, we develop a novel approach to accurately approximate statistical significance of LSA for dependent time series data using nonparametric kernel estimated long-run variance. We also investigate an alternative method for LSA statistical significance approximation by computing the local similarity score of the residuals based on a predefined statistical model. We show by simulations that both methods have controllable type I errors for dependent time series, while other approaches for statistical significance can be grossly oversized. We apply both methods to human and marine microbial datasets, where most of possible significant associations are captured and false positives are efficiently controlled.ConclusionsOur methods provide fast and effective approaches for evaluating statistical significance of dependent time series data with controllable type I error. They can be applied to a variety of time series data to reveal inherent relationships among the different factors.
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Project description:IntroductionEstimating treatment effects as time savings in disease progression may be more easily interpretable than assessing the absolute difference or a percentage reduction. In this study, we investigate the statistical considerations of the existing method for estimating time savings and propose alternative complementary methods.MethodsWe propose five alternative methods to estimate the time savings from different perspectives. These methods are applied to simulated clinical trial data that mimic or modify the Clinical Dementia Rating Sum of Boxes progression trajectories observed in the Clarity AD lecanemab trial.ResultsOur study demonstrates that the proposed methods can generate more precise estimates by considering two crucial factors: (1) the absolute difference between treatment arms, and (2) the observed progression rate in the treatment arm.DiscussionQuantifying treatment effects as time savings in disease progression offers distinct advantages. To provide comprehensive estimations, it is important to use various methods.HighlightsWe explore the statistical considerations of the current method for estimating time savings. We proposed alternative methods that provide time savings estimations based on the observed absolute differences. By using various methods, a more comprehensive estimation of time savings can be achieved.
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Project description:Although great improvements have been achieved in the fields of diagnosing and treating patients with giant-cell arteritis (GCA) in the last decades, several questions remain unanswered. The progressive increase in the number of older people, together with growing awareness of the disease and use of advanced diagnostic tools by healthcare professionals, foretells a possible increase in both prevalence and number of newly diagnosed patients with GCA in the coming years. A thorough clarification of pathogenetic mechanisms and a better definition of clinical subsets are the first steps toward a better understanding of the disease and, subsequently, toward a better use of existing and future therapeutic options. Examination of the role of different imaging techniques for GCA diagnosing and monitoring, optimization, and personalization of glucocorticoids and other immunosuppressive agents, further development and introduction of novel drugs, identification of prognostic factors for long-term outcomes and management of treatment discontinuation will be the central topics of the research agenda in years to come.
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