Stochastic Oscillations in Genetic Regulatory Networks: Application to Microarray Experiments

<p/> <p>We analyze the stochastic dynamics of genetic regulatory networks using a system of nonlinear differential equations. The system of <inline-formula><graphic file="1687-4153-2006-59526-i1.gif"/></inline-formula>-functions is applied to capture the role of RNA polymerase in the transcription-translation mechanism. Using probabilistic properties of chemical rate equations, we derive a system of stochastic differential equations which are analytically tractable despite the high dimension of the regulatory network. Using stationary solutions of these equations, we explain the apparently paradoxical results of some recent time-course microarray experiments where mRNA transcription levels are found to only weakly correlate with the corresponding transcription rates. Combining analytical and simulation approaches, we determine the set of relationships between the size of the regulatory network, its structural complexity, chemical variability, and spectrum of oscillations. In particular, we show that temporal variability of chemical constituents may decrease while complexity of the network is increasing. This finding provides an insight into the nature of "functional determinism" of such an inherently stochastic system as genetic regulatory network.</p

A user-friendly database for Participatory Plant Breeding programs

In a decentralized and participatory plant breeding (PPB) program, in contrast to conventional plant breeding, farmers select from a large number of genotypes over a number of cycles in several locations. As selection is for location-specific adaptation a PPB program based on, for example, four stages of selection, generates large, unbalanced data sets. With common spreadsheet software it is not possible, or it is at least very cumbersome to extract all the information, particularly the one that is related to genotype x environment (GE) interactions. Therefore, there is a need for an information system that makes it as easy as possible to retrieve and compare data over all given factors in the PPB-program. Due to a lack of education and financial resources in developing countries, the use of existing databases was not an option because of their complexity and/or price. We have built a simple, free and user-friendly database that allows to store, retrieve and analyze the plant breeding data. The database is implemented using the Java based HyperSQL Database Engine (HSQLDB) in the package of Open Office with links to the input formats of Genstat and GGEbiPlot. The proposed database is capable of managing the following data in a PPBprogram for barley: (I) trial data for any trial or field design (II) field data for any given trait (III) results from statistical analyses (IV) farmers selection individually or in groups

Learning Linear Causal Representations from Interventions under General Nonlinear Mixing

We study the problem of learning causal representations from unknown, latent interventions in a general setting, where the latent distribution is Gaussian but the mixing function is completely general. We prove strong identifiability results given unknown single-node interventions, i.e., without having access to the intervention targets. This generalizes prior works which have focused on weaker classes, such as linear maps or paired counterfactual data. This is also the first instance of causal identifiability from non-paired interventions for deep neural network embeddings. Our proof relies on carefully uncovering the high-dimensional geometric structure present in the data distribution after a non-linear density transformation, which we capture by analyzing quadratic forms of precision matrices of the latent distributions. Finally, we propose a contrastive algorithm to identify the latent variables in practice and evaluate its performance on various tasks.Comment: 38 page

Coherent frequency-down-conversion interface for quantum repeaters

We report a coherence-preserving photon frequency down-conversion experiment based on difference-frequency generation in a periodically poled Lithium niobate waveguide, at the single-photon level. The coherence of the process has been demonstrated by measuring the phase coherence of pseudo single-photon time-bin qubits after frequency conversion with an interference visibility of > 96 %. This interface could be of interest for quantum repeater based hybrid networks.Comment: 6 pages, 3 figure

Complementarity and Scientific Rationality

Bohr's interpretation of quantum mechanics has been criticized as incoherent and opportunistic, and based on doubtful philosophical premises. If so Bohr's influence, in the pre-war period of 1927-1939, is the harder to explain, and the acceptance of his approach to quantum mechanics over de Broglie's had no reasonable foundation. But Bohr's interpretation changed little from the time of its first appearance, and stood independent of any philosophical presuppositions. The principle of complementarity is itself best read as a conjecture of unusually wide scope, on the nature and future course of explanations in the sciences (and not only the physical sciences). If it must be judged a failure today, it is not because of any internal inconsistency.Comment: 29 page

Pushing forward white lupin as a local source for protein and nitrogen in Central Europe

White lupin (Lupinus albus L.) is a promising leguminous crop. Europe is fully dependent on protein and nitrogen fertilizer imports. This has tremendous negative effects both in Europe and the producing countries, such as loss of terrestrial biodiversity, pollution of freshwater, increase of greenhouse gases and soil acidification. Diverse crop-rotations with a substantial amount of pulses are a proven solution. The protein composition and yield potential of white lupin suggest that it could become the ‘Soy of the North’. Currently, the seed-borne pathogen Colletotrichum lupini is substantially impeding the cultivation of white lupin in Central Europe. We developed a DNA-based diagnostic test to identify and quantify the fungal pathogen in plants and seeds. This technique will allow us to improve our understanding of the Colletotrichum lupini life cycle and, thereby, lay the basis for an advanced resistance breeding approach

Nontrivial eigenvalues of the Liouvillian of an open quantum system

We present methods of finding complex eigenvalues of the Liouvillian of an open quantum system. The goal is to find eigenvalues that cannot be predicted from the eigenvalues of the corresponding Hamiltonian. Our model is a T-type quantum dot with an infinitely long lead. We suggest the existence of the non-trivial eigenvalues of the Liouvillian in two ways: one way is to show that the original problem reduces to the problem of a two-particle Hamiltonian with a two-body interaction and the other way is to show that diagram expansion of the Green's function has correlation between the bra state and the ket state. We also introduce the integral equations equivalent to the original eigenvalue problem.Comment: 5 pages, 2 figures, proceeding