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- ItemSimultaneous statistical inference for epigenetic data(San Francisco, California, US : PLOS, 2015) Schildknecht, Konstantin; Olek, Sven; Dickhaus, ThorstenEpigenetic research leads to complex data structures. Since parametric model assumptions for the distribution of epigenetic data are hard to verify we introduce in the present work a nonparametric statistical framework for two-group comparisons. Furthermore, epigenetic analyses are often performed at various genetic loci simultaneously. Hence, in order to be able to draw valid conclusions for specific loci, an appropriate multiple testing correction is necessary. Finally, with technologies available for the simultaneous assessment of many interrelated biological parameters (such as gene arrays), statistical approaches also need to deal with a possibly unknown dependency structure in the data. Our statistical approach to the nonparametric comparison of two samples with independent multivariate observables is based on recently developed multivariate multiple permutation tests. We adapt their theory in order to cope with families of hypotheses regarding relative effects. Our results indicate that the multivariate multiple permutation test keeps the pre-assigned type I error level for the global null hypothesis. In combination with the closure principle, the family-wise error rate for the simultaneous test of the corresponding locus/parameter-specific null hypotheses can be controlled. In applications we demonstrate that group differences in epigenetic data can be detected reliably with our methodology.
- ItemImpact of energy dissipation on interface shapes and on rates for dewetting from liquid substrates([London] : Macmillan Publishers Limited, part of Springer Nature, 2018) Peschka, Dirk; Bommer, Stefan; Jachalski, Sebastian; Seemann, Ralf; Wagner, BarbaraWe revisit the fundamental problem of liquid-liquid dewetting and perform a detailed comparison of theoretical predictions based on thin-film models with experimental measurements obtained by atomic force microscopy. Specifically, we consider the dewetting of a liquid polystyrene layer from a liquid polymethyl methacrylate layer, where the thicknesses and the viscosities of both layers are similar. Using experimentally determined system parameters like viscosity and surface tension, an excellent agreement of experimentally and theoretically obtained rim profile shapes are obtained including the liquid-liquid interface and even dewetting rates. Our new energetic approach additionally allows to assess the physical importance of different contributions to the energy-dissipation mechanism, for which we analyze the local flow fields and the local dissipation rates. Using this approach, we explain why dewetting rates for liquid-liquid systems follow no universal power law, despite the fact that experimental velocities are almost constant. This is in contrast to dewetting scenarios on solid substrates and in contrast to previous results for liquid-liquid substrates using heuristic approaches.
- ItemMore Specific Signal Detection in Functional Magnetic Resonance Imaging by False Discovery Rate Control for Hierarchically Structured Systems of Hypotheses(San Francisco, California, US : PLOS, 2016) Schildknecht, Konstantin; Tabelow, Karsten; Dickhaus, ThorstenSignal detection in functional magnetic resonance imaging (fMRI) inherently involves the problem of testing a large number of hypotheses. A popular strategy to address this multiplicity is the control of the false discovery rate (FDR). In this work we consider the case where prior knowledge is available to partition the set of all hypotheses into disjoint subsets or families, e. g., by a-priori knowledge on the functionality of certain regions of interest. If the proportion of true null hypotheses differs between families, this structural information can be used to increase statistical power. We propose a two-stage multiple test procedure which first excludes those families from the analysis for which there is no strong evidence for containing true alternatives. We show control of the family-wise error rate at this first stage of testing. Then, at the second stage, we proceed to test the hypotheses within each non-excluded family and obtain asymptotic control of the FDR within each family at this second stage. Our main mathematical result is that this two-stage strategy implies asymptotic control of the FDR with respect to all hypotheses. In simulations we demonstrate the increased power of this new procedure in comparison with established procedures in situations with highly unbalanced families. Finally, we apply the proposed method to simulated and to real fMRI data.
- ItemNumerical simulation of TEM images for In(Ga)As/GaAs quantum dots with various shapes(Dordrecht [u.a.] : Springer Science + Business Media B.V, 2020) Maltsi, Anieza; Niermann, Tore; Streckenbach, Timo; Tabelow, Karsten; Koprucki, ThomasWe present a mathematical model and a tool chain for the numerical simulation of TEM images of semiconductor quantum dots (QDs). This includes elasticity theory to obtain the strain profile coupled with the Darwin–Howie–Whelan equations, describing the propagation of the electron wave through the sample. We perform a simulation study on indium gallium arsenide QDs with different shapes and compare the resulting TEM images to experimental ones. This tool chain can be applied to generate a database of simulated TEM images, which is a key element of a novel concept for model-based geometry reconstruction of semiconductor QDs, involving machine learning techniques.
- ItemDetecting striations via the lateral photovoltage scanning method without screening effect(Dordrecht [u.a.] : Springer Science + Business Media B.V, 2021) Kayser, S.; Farrell, P.; Rotundo, N.The lateral photovoltage scanning method (LPS) detects doping inhomogeneities in semiconductors such as Si, Ge and SixGe1−x in a cheap, fast and nondestructive manner. LPS relies on the bulk photovoltaic effect and thus can detect any physical quantity affecting the band profiles of the sample. LPS finite volume simulation using commercial software suffer from long simulation times and convergence instabilities. We present here an open-source finite volume simulation for a 2D Si sample using the ddfermi simulator. For low injection conditions we show that the LPS voltage is proportional to the doping gradient. For higher injection conditions, we directly show how the LPS voltage and the doping gradient differ and link the physical effect of lower local resolution to the screening effect. Previously, the loss of local resolution was assumed to be only connected to the enlargement of the excess charge carrier distribution.
- ItemCorrection to: Numerical simulation of TEM images for In(Ga)As/GaAs quantum dots with various shapes(Dordrecht [u.a.] : Springer Science + Business Media B.V, 2021) Maltsi, Anieza; Niermann, Tore; Streckenbach, Timo; Tabelow, Karsten; Koprucki, ThomasCorrection to: Optical and Quantum Electronics (2020) 52:257 https://doi.org/10.1007/s11082-020-02356-y
- ItemImproving Accuracy and Temporal Resolution of Learning Curve Estimation for within- and across-Session Analysis(San Francisco, California, US : PLOS, 2016) Deliano, Matthias; Tabelow, Karsten; König, Reinhard; Polzehl, JörgEstimation of learning curves is ubiquitously based on proportions of correct responses within moving trial windows. Thereby, it is tacitly assumed that learning performance is constant within the moving windows, which, however, is often not the case. In the present study we demonstrate that violations of this assumption lead to systematic errors in the analysis of learning curves, and we explored the dependency of these errors on window size, different statistical models, and learning phase. To reduce these errors in the analysis of single-subject data as well as on the population level, we propose adequate statistical methods for the estimation of learning curves and the construction of confidence intervals, trial by trial. Applied to data from an avoidance learning experiment with rodents, these methods revealed performance changes occurring at multiple time scales within and across training sessions which were otherwise obscured in the conventional analysis. Our work shows that the proper assessment of the behavioral dynamics of learning at high temporal resolution can shed new light on specific learning processes, and, thus, allows to refine existing learning concepts. It further disambiguates the interpretation of neurophysiological signal changes recorded during training in relation to learning.
- ItemCalculation of the steady states in dynamic semiconductor laser models(Dordrecht [u.a.] : Springer Science + Business Media B.V, 2022) Radziunas, MindaugasWe discuss numerical challenges in calculating stable and unstable steady states of widely used dynamic semiconductor laser models. Knowledge of these states is valuable when analyzing laser dynamics and different properties of the lasing states. The example simulations and analysis mainly rely on 1(time)+1(space)-dimensional traveling-wave models, where the steady state defining conditions are formulated as a system of nonlinear algebraic equations. The performed steady state calculations reveal limitations of the Lang-Kobayashi model, explain nontrivial bias threshold relations in lasers with several electrical contacts, or predict and explain transient dynamics when simulating such lasers.