Identifying latent dynamic components in biological systems

In computational systems biology, the general aim is to derive regulatory models from multivariate readouts, thereby generating predictions for novel experiments. In the past, many such models have been formulated for different biological applications. The authors consider the scenario where a given model fails to predict a set of observations with acceptable accuracy and ask the question whether this is because of the model lacking important external regulations. Real‐world examples for such entities range from microRNAs to metabolic fluxes. To improve the prediction, they propose an algorithm to systematically extend the network by an additional latent dynamic variable which has an exogenous effect on the considered network. This variable''s time course and influence on the other species is estimated in a two‐step procedure involving spline approximation, maximum‐likelihood estimation and model selection. Simulation studies show that such a hidden influence can successfully be inferred. The method is also applied to a signalling pathway model where they analyse real data and obtain promising results. Furthermore, the technique can be employed to detect incomplete network structures.Inspec keywords: biology computing, RNA, splines (mathematics), maximum likelihood estimation, approximation theory, biochemistryOther keywords: latent dynamic components, biological systems, computational system biology, regulatory models, multivariate readouts, biological applications, external regulations, real‐world examples, microRNA, metabolic fluxes, latent dynamic variables, variable time course, two‐step procedure, spline approximation, maximum‐likelihood estimation, model selection, signalling pathway model, real data, incomplete network structures     

A TRNSYS-based simulation framework for the analysis of solar thermal and heat pump systems

The modeling and simulation of combined solar and heat pump (SHP) systems is a challenging task as it requires expert knowledge in modeling as well as in the behavior of the real systems. As an example of a SHP system, this work considers parallel solar thermal and heat pump systems with ground or air source heat pumps for the efficient energy supply of buildings. An introduction to SHP systems and the considered system concepts is given and the challenges in designing new models within the simulation environment TRNSYS are described. Finally, a TRNSYS-based stand-alone tool (SHP-SimFrame) ispresented which enables users to analyze predefined SHP concepts with hardly any knowledge in modeling and simulation itself.     

Load reduction on a clipper liberty wind turbine with linear parameter‐varying individual blade pitch control

The increasing size of modern wind turbines also increases the structural loads caused by effects such as turbulence or asymmetries in the inflowing wind field. Consequently, the use of advanced control algorithms for active load reduction has become a relevant part of current wind turbine control systems. In this paper, an individual blade pitch control law is designed using multivariable linear parameter‐varying control techniques. It reduces the structural loads both on the rotating and non‐rotating parts of the turbine. Classical individual blade pitch control strategies rely on single‐control loops with low bandwidth. The proposed approach makes it possible to use a higher bandwidth since it accounts for coupling at higher frequencies. A controller is designed for the utility‐scale 2.5 MW Liberty research turbine operated by the University of Minnesota. Stability and performance are verified using the high‐fidelity nonlinear simulation and baseline controllers that were directly obtained from the manufacturer. Copyright © 2017 John Wiley & Sons, Ltd.     

Reconstruction of graphs based on random walks

The analysis of complex networks is of major interest in various fields of science. In many applications we face the challenge that the exact topology of a network is unknown but we are instead given information about distances within this network. The theoretical approaches to this problem have so far been focusing on the reconstruction of graphs from shortest path distance matrices. Often, however, movements in networks do not follow shortest paths but occur in a random fashion. In these cases an appropriate distance measure can be defined as the mean length of a random walk between two nodes — a quantity known as the mean first hitting time.In this contribution we investigate whether a graph can be reconstructed from its mean first hitting time matrix and put forward an algorithm for solving this problem. A heuristic method to reduce the computational effort is described and analyzed. In the case of trees we can even give an algorithm for reconstructing graphs from incomplete random walk distance matrices.     

Pornography and Sexist Attitudes Among Heterosexuals

Using a probability‐based sample of young Danish adults and a randomized experimental design, this study investigated effects of past pornography consumption, experimental exposure to nonviolent pornography, perceived realism of pornography, and personality (i.e., agreeableness) on sexist attitudes (i.e., attitudes toward women, hostile and benevolent sexism). Further, sexual arousal mediation was assessed. Results showed that, among men, an increased past pornography consumption was significantly associated with less egalitarian attitudes toward women and more hostile sexism. Further, lower agreeableness was found to significantly predict higher sexist attitudes. Significant effects of experimental exposure to pornography were found for hostile sexism among low in agreeableness participants and for benevolent sexism among women. These experimental exposure effects were found to be mediated by sexual arousal.     

RHEED Intensity Oscillations for the Stoichiometric Growth of SrTiO3 Thin Films by Reactive Molecular Beam Epitaxy

The growth of high quality multicomponent oxide thin films by reactive molecular beam epitaxy (MBE) requires precise composition control. We report the use of in situ reflection high-energy electron diffraction (RHEED) for the stoichiometric deposition of SrTiO₃ (1 0 0) from independent strontium and titanium sources. By monitoring changes in the RHEED intensity oscillations as monolayer doses of strontium and titanium are sequentially deposited, the Sr:Ti ratio can be adjusted to within 1% of stoichiometry. Furthermore, the presence of a beat frequency in the intensity oscillation envelope allows the adjustment of the strontium and titanium fluxes so that a full monolayer of coverage is obtained with each shuttered dose of strontium or titanium. RHEED oscillations have also been employed to determine the doping concentration in barium- and lanthanum-doped SrTiO₃ films.     

Bistability of theDX center in GaAs and AlxGa1-xAs,and experimental tests for negativeU of theDX level

We summarize a large body of experimental and theoretical work, especially in Si-doped GaAs and Al _x Ga_1-x As, regarding the bistability of theDX center. There is good evidence that theDX center is just the simple donor, and that each donor can exist in either of two distinct lattice configurations, each with its own spectrum of bound electronic states. Generally, the substitutional configuration binds electrons in shallow hydrogenic states, but many observations also indicate a deep (highly localized) state ofA ₁ symmetry. These states are to be distinguished from bound states of a lattice-distorted configuration, the lowest-lying of which is the deepDX level. The occupation of theDX level in thermal equilibrium with the states of the conduction band can be reasonably well modeled by assuming thatDX is either a one-electron or a two-electron state, and we discuss the reasons for this ambiguity. However, we then show that such thermal equilibrium results are consistent with thermal capture and emission kineticsonly if we assume thatDX is a two-electron state. Our results thus support the model of Chadi and Chang in which the distorted configuration is stabilized by capture of two electrons. In other words, the defect exhibits negative effective correlation energy (negativeU).     

Anaphylactoid reactions in children receiving high-dose intravenous cyclosporine for reversal of tumor resistance: the causative role of improper dissolution of Cremophor EL

PURPOSE: An unusually high incidence of anaphylactoid reactions was observed during a phase I/II trial of high-dose intravenous cyclosporine (CsA) therapy to attenuate tumor multidrug resistance (MDR). Five of 21 children experienced severe anaphylactoid reactions shortly after initiation of the first or second CsA infusion. We hypothesized that improper dissolution of the vehicle Cremophor EL may have been a cause for these anaphylactoid reactions. METHODS: All nurses who had administered intravenous CsA were interviewed regarding their technique of preparing the infusion and the occurrence of an anaphylactoid reaction. The responses were statistically analyzed. The effect of various mixing techniques on the distribution of Cremophor EL in the infusion was experimentally evaluated. Different mixing techniques were used to assess their effect on the distribution of Cremophor EL in the solution. RESULTS: Analysis of the preparation techniques of the CsA infusion showed significant correlation between suboptimal mixing of CsA by nurses and the occurrence of anaphylactoid reactions (P = .02). Experimental simulation showed that suboptimal mixing results in an uneven distribution of Cremophor EL, which subsequently sinks to the bottom of the vial. CONCLUSION: Improper mixing of high-dose CsA infusions causes nonsolubilized Cremophor EL to sink to the outflow area of the bottle. An initial bolus infusion of highly concentrated Cremophor EL may produce an anaphylactoid-like response. This mechanism of toxicity is important to recognize, because it is easily preventable by proper preparation of the infusion, thus reducing the incidence of potentially life-threatening anaphylactoid reactions.