Design of Experiments for Screening

The aim of this paper is to review methods of designing screening experiments, ranging from designs originally developed for physical experiments to those especially tailored to experiments on numerical models. The strengths and weaknesses of the various designs for screening variables in numerical models are discussed. First, classes of factorial designs for experiments to estimate main effects and interactions through a linear statistical model are described, specifically regular and nonregular fractional factorial designs, supersaturated designs and systematic fractional replicate designs. Generic issues of aliasing, bias and cancellation of factorial effects are discussed. Second, group screening experiments are considered including factorial group screening and sequential bifurcation. Third, random sampling plans are discussed including Latin hypercube sampling and sampling plans to estimate elementary effects. Fourth, a variety of modelling methods commonly employed with screening designs are briefly described. Finally, a novel study demonstrates six screening methods on two frequently-used exemplars, and their performances are compared

Sensitivity analysis and related analysis: A survey of statistical techniques

This paper reviews the state of the art in five related types of analysis, namely (i) sensitivity or what-if analysis, (ii) uncertainty or risk analysis, (iii) screening, (iv) validation, and (v) optimization. The main question is: when should which type of analysis be applied; which statistical techniques may then be used? This paper distinguishes the following five stages in the analysis of a simulation model. 1) Validation: the availability of data on the real system determines which type of statistical technique to use for validation. 2) Screening: in the simulation's pilot phase the really important inputs can be identified through a novel technique, called sequential bifurcation, which uses aggregation and sequential experimentation. 3) Sensitivity analysis: the really important inputs should be This approach with its five stages implies that sensitivity analysis should precede uncertainty analysis. This paper briefly discusses several case studies for each phase.Experimental Design;Statistical Methods;Regression Analysis;Risk Analysis;Least Squares;Sensitivity Analysis;Optimization;Perturbation;statistics

Trajectory-based differential expression analysis for single-cell sequencing data

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital to discover genes that are (i) associated with the lineages in the trajectory, or (ii) differentially expressed between lineages, to illuminate the underlying biological processes. Current data analysis procedures, however, either fail to exploit the continuous resolution provided by trajectory inference, or fail to pinpoint the exact types of differential expression. We introduce tradeSeq, a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of both within-lineage and between-lineage differential expression. By incorporating observation-level weights, the model additionally allows to account for zero inflation. We evaluate the method on simulated datasets and on real datasets from droplet-based and full-length protocols, and show that it yields biological insights through a clear interpretation of the data. Downstream of trajectory inference for cell lineages based on scRNA-seq data, differential expression analysis yields insight into biological processes. Here, Van den Berge et al. develop tradeSeq, a framework for the inference of within and between-lineage differential expression, based on negative binomial generalized additive models

Deterministic versus Stochastic Sensitivity Analysis in Investment Problems: An Environmental Case Study

Sensitivity analysis in investment problems is an important tool to determine which factors can jeopardize the future of the investment.Information on the probability distribution of those factors that affect the investment is mostly lacking.In those situations the analysts have two options: (i) apply a method that does not require knowledge of that distribution, or (ii) make assumptions about the distribution.In both approaches sensitivity analysis should result in practical information about the actual importance of potential factors.For approach (i) we apply statistical design of experiments (DOE) in combination with regression analysis or meta-modeling.For approach (ii) we investigate five types of relationships between the model output and each individual factor; Pearson's p, Spearman's rank correlation, and location, dispersion, and statistical dependence.We introduce two distribution types popular with practitioners: uniform and triangular.In an environmental case study both approaches identify the same factors as important.sensitivity analysis;experimental design;investment analysis;simulation

Review of Sensitivity Analysis Methods and Experience for Geological Disposal of Radioactive waste and Spent Nuclear Fuel

This reports gives an overview of sensitivity methods (screening, global and response surface based) that are suitable for safety analysis of a repository for radioactive waste or spent nuclear fuel. The theorerical background of the methods, their limitations and suitability for different analyses are discussed and illustrated by examples.JRC.F.7-Energy systems evaluatio

Quantitative assessment of the regenerative and mineralogenic performances of the zebrafish caudal fin

The ability of zebrafish to fully regenerate its caudal fin has been explored to better understand the mechanisms underlying de novo bone formation and to develop screening methods towards the discovery of compounds with therapeutic potential. Quantifying caudal fin regeneration largely depends on successfully measuring new tissue formation through methods that require optimization and standardization. Here, we present an improved methodology to characterize and analyse overall caudal fin and bone regeneration in adult zebrafish. First, regenerated and mineralized areas are evaluated through broad, rapid and specific chronological and morphometric analysis in alizarin red stained fins. Then, following a more refined strategy, the intensity of the staining within a 2D longitudinal plane is determined through pixel intensity analysis, as an indicator of density or thickness/volume. The applicability of this methodology on live specimens, to reduce animal experimentation and provide a tool for in vivo tracking of the regenerative process, was successfully demonstrated. Finally, the methodology was validated on retinoic acid-and warfarin-treated specimens, and further confirmed by micro-computed tomography. Because it is easily implementable, accurate and does not require sophisticated equipment, the present methodology will certainly provide valuable technical standardization for research in tissue engineering, regenerative medicine and skeletal biology

Theory of Sorption Hysteresis in Nanoporous Solids: II. Molecular condensation

Motivated by the puzzle of sorption hysteresis in Portland cement concrete or cement paste, we develop in Part II of this study a general theory of vapor sorption and desorption from nanoporous solids, which attributes hysteresis to hindered molecular condensation with attractive lateral interactions. The classical mean-field theory of van der Waals is applied to predict the dependence of hysteresis on temperature and pore size, using the regular solution model and gradient energy of Cahn and Hilliard. A simple "hierarchical wetting" model for thin nanopores is developed to describe the case of strong wetting by the first monolayer, followed by condensation of nanodroplets and nanobubbles in the bulk. The model predicts a larger hysteresis critical temperature and enhanced hysteresis for molecular condensation across nanopores at high vapor pressure than within monolayers at low vapor pressure. For heterogeneous pores, the theory predicts sorption/desorption sequences similar to those seen in molecular dynamics simulations, where the interfacial energy (or gradient penalty) at nanopore junctions acts as a free energy barrier for snap-through instabilities. The model helps to quantitatively understand recent experimental data for concrete or cement paste wetting and drying cycles and suggests new experiments at different temperatures and humidity sweep rates.Comment: 26 pages, 10 fig

Solar flare-related eruptions followed by long-lasting occultation of the emission in the He II 304 A line and in microwaves

Plasma with a temperature close to the chromospheric one is ejected in solar eruptions. Such plasma can occult some part of emission of compact sources in active regions as well as quiet solar areas. Absorption phenomena can be observed in the microwave range as the so-called 'negative bursts' and also in the He II 304 A line. The paper considers three eruptive events associated with rather powerful flares. Parameters of absorbing material of an eruption are estimated from multi-frequency records of a 'negative burst' in one event. 'Destruction' of an eruptive filament and its dispersion like a cloud over a huge area observed as a giant depression of the 304 A line emission has been revealed in a few events. One such event out of three ones known to us is considered in this paper. Another event is a possibility.Comment: 23 pages, 8 figures, submitted for publication in Astronomy Report