Soil carbon sequestration in Switzerland - the DOK trial

Organic systems, by closing nutrient cycles and making more efficient use of local (on-farm) resources, can contribute to mitigating climate change1. This is due to the fact that certain farming practices result in storage of carbon (C) in the soil (sequestration), thereby effectively reducing the amount of CO2 in the atmosphere. The DOK trial, a research project on the mitigation potential of Organic Agriculture has demonstrated this

Multicolor chromosome bar codes

Chromosome bar codes are multicolor banding patterns produced by fluorescence in situ hybridization (FISH) with differentially labeled and pooled sub-regional DNA probes. These molecular cytogenetic tools facilitate chromosome identification and the delineation of both inter- and intra-chromosomal rearrangements. We present an overview of the various conceptual approaches which can be largely divided into two classes: Simple bar codes designed for chromosome identification and complex bar codes for high resolution aberration screening of entire karyotypes. We address the issue of color redundancy and how to overcome this limitation by complementation of bar codes with whole chromosome painting probes. Copyright (c) 2006 S. Karger AG, Base

Don't Fall for Tuning Parameters: Tuning-Free Variable Selection in High Dimensions With the TREX

Lasso is a seminal contribution to high-dimensional statistics, but it hinges on a tuning parameter that is difficult to calibrate in practice. A partial remedy for this problem is Square-Root Lasso, because it inherently calibrates to the noise variance. However, Square-Root Lasso still requires the calibration of a tuning parameter to all other aspects of the model. In this study, we introduce TREX, an alternative to Lasso with an inherent calibration to all aspects of the model. This adaptation to the entire model renders TREX an estimator that does not require any calibration of tuning parameters. We show that TREX can outperform cross-validated Lasso in terms of variable selection and computational efficiency. We also introduce a bootstrapped version of TREX that can further improve variable selection. We illustrate the promising performance of TREX both on synthetic data and on a recent high-dimensional biological data set that considers riboflavin production in B. subtilis

Cellular Probabilistic Automata - A Novel Method for Uncertainty Propagation

We propose a novel density based numerical method for uncertainty propagation under certain partial differential equation dynamics. The main idea is to translate them into objects that we call cellular probabilistic automata and to evolve the latter. The translation is achieved by state discretization as in set oriented numerics and the use of the locality concept from cellular automata theory. We develop the method at the example of initial value uncertainties under deterministic dynamics and prove a consistency result. As an application we discuss arsenate transportation and adsorption in drinking water pipes and compare our results to Monte Carlo computations

Speeding up SOR Solvers for Constraint-based GUIs with a Warm-Start Strategy

Many computer programs have graphical user interfaces (GUIs), which need good layout to make efficient use of the available screen real estate. Most GUIs do not have a fixed layout, but are resizable and able to adapt themselves. Constraints are a powerful tool for specifying adaptable GUI layouts: they are used to specify a layout in a general form, and a constraint solver is used to find a satisfying concrete layout, e.g.\ for a specific GUI size. The constraint solver has to calculate a new layout every time a GUI is resized or changed, so it needs to be efficient to ensure a good user experience. One approach for constraint solvers is based on the Gauss-Seidel algorithm and successive over-relaxation (SOR). Our observation is that a solution after resizing or changing is similar in structure to a previous solution. Thus, our hypothesis is that we can increase the computational performance of an SOR-based constraint solver if we reuse the solution of a previous layout to warm-start the solving of a new layout. In this paper we report on experiments to test this hypothesis experimentally for three common use cases: big-step resizing, small-step resizing and constraint change. In our experiments, we measured the solving time for randomly generated GUI layout specifications of various sizes. For all three cases we found that the performance is improved if an existing solution is used as a starting solution for a new layout

Fisher-Wright model with deterministic seed bank and selection

Seed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. The applied techniques outline a path of approximating a stochastic delay differential equation by an appropriately rescaled stochastic differential equation, which is a common issue in statistical physics. We compute the equilibrium solution of the site-frequency spectrum and derive the times to fixation of an allele with and without selection. Finally, it is demonstrated that seed banks enhance the effect of selection onto the site-frequency spectrum while slowing down the time until the mutation-selection equilibrium is reached