Development and Applications of Coarse-Grained Models for RNA

In contrast to proteins, much less attention has been focused on the development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force fields are not accurate enough to capture the properties of even simple nucleic acid constructs. In this article, we review our efforts to develop coarse-grained (CG) models that capture the underlying physics for the particular length scale of interest. Two models are discussed. One of them is the three interaction site (TIS) model, in which each nucleotide is represented by three beads corresponding to sugar, phosphate, and base. The other is the self-organized polymer (SOP) model, in which each nucleotide is represented as a single interaction center. Applications of the TIS model to study the complexity of hairpin formation and the effects of crowding in a shifting equilibrium between two conformations in human telomerase pseudoknot are described. The work on crowding illustrates a direct link to the activity of telomerase. We use the SOP model to describe the response of the Tetrahymena ribozyme to force. The simulated unfolding pathways agree well with single molecule pulling experiments. We also review predictions for the unfolding pathways for the Azoarcus ribozyme. The success of the CG applications to describe dynamics in RNA gives hope that more complex processes involving RNA-protein interactions can be tackled using variants of the proposed models.     

Remote sensing of wetlands in South America: status and challenges

South America has a large proportion of wetlands compared with other continents. While most of these wetlands were conserved in a relatively good condition until a few decades ago, pressures brought about by land use and climate change have threaten their integrity in recent years. The aim of this article is to provide a bibliometric analysis of the available scientific literature relating to the remote sensing of wetlands in South America. From 1960 to 2015, 153 articles were published in 63 different journals, with the number of articles published per year increasing progressively since 1990. This rise is also paralleled by an increase in the contribution of local authors. The most intensively studied regions are the wetland macrosystems of South American mega-rivers: the Amazon and Paraná Rivers, along with the Pantanal at the headwaters of Paraguay River. Few studies spanned more than two countries. The most frequent objectives were mapping, covering all types of wetlands with optical data, and hydrology, focusing on floodplain wetlands with microwave data as the preferred data source. The last decade substantial growth reflects an increase in technological and scientific capacities. Nevertheless, the state of the art regarding the remote sensing of wetlands in South America remains enigmatic. Fundamental questions and guidelines which may contribute to the understanding of the functioning of these ecosystems are yet to be fully defined and there is considerable dispersion in the use of data and remote-sensing approaches.     

Modellbasierte Entscheidungsunterstützung in Produktions- und Dienstleistungsnetzwerken

In this paper, we sketch some of the challenges that should be addressed in future research efforts for model-based decision support in manufacturing and service networks. This includes integration issues, taking into account the autonomy of the decision-making entities in face of information asymmetry, the modeling of preferences of the decision-makers, efficiently determining robust solutions, i.e. solutions that are insensitive with respect to changes in the problem data, and a reduction of the time needed for model building and usage. The problem solution cycle includes problem analysis, the design of appropriate algorithms and their performance assessment. We are interested in a prototypical integration of the proposed methods within application systems, which can be followed up with field tests of the extended application systems. We argue that the described research agenda requires the interdisciplinary collaboration of business and information systems engineering researchers with colleagues from management science, computer science, and operations research. In addition, we present some exemplifying, illustrative examples of relevant research results.     

Sulfite Action in Glycolytic Inhibition: In Vivo Real‐Time Observation by Hyperpolarized 13C NMR Spectroscopy

Detecting the molecular targets of xenobiotic substances in vivo poses a considerable analytical challenge. Here, we describe the use of an NMR‐based tracer methodology for the instantaneous in vivo observation of sulfur(IV) action on cellular metabolism. Specifically, we find that glycolytic flux is directed towards sulfite adducts of dihydroxyacetone phosphate and pyruvate as off‐pathway intermediates that obstruct glycolytic flux. In particular, the pyruvate–sulfite association hinders the formation of downstream metabolites. The apparent in vivo association constant of pyruvate and sulfite agrees with the apparent inhibition constant of CO₂ formation, thus supporting the importance of pyruvate interception in disturbing central metabolism and inhibiting NAD regeneration.     

Influence of the reaction time and the Triton x-100/Cyclohexane/Methanol/H2O ratio on the morphology and size of silica nanoparticles synthesized via sol–gel assisted by reverse micelle microemulsion

The present paper describes the synthesis of silica nanoparticles via the sol–gel method assisted by reverse micelle microemulsion, using reagents as Triton x-100/Cyclohexane/Methanol/H₂O, and also the effect on particle size of some synthesis parameters such as the water-surfactant molar ratio (R), Co-surfactant-surfactant (ρ), and synthesis time (t). The structure, morphology, and size of the silica nanoparticles were characterized with transmission electron microscopy and scanning electron microscopy. A variation of ρ = [Methanol]/[Triton X-100] affects the size, morphology, and dispersion of the particles. An increase in the concentration of methanol produces a decrease in particle size. The condition that resulted in smaller particle size, better spherical morphology, and monodispersity was when ρ = 7.6, which generated an approximate size of 83 ± 7 nm. The parameter R = [H₂O]/[Triton X-100] affects not only the size of the particles, but also their morphology. Higher values of R result in a decrease in the amount of catalyst present in the interior of the micelle, but in turn generate a greater amount of water, which results in a decrease in particle size and polydispersity. Time is a parameter that directly affects the size of the silica particles. The optimal time for the synthesis of nanoparticles was 2 h, resulting in silica nanoparticles of 25 ± 3 nm, monodisperse, with spherical morphology and without the presence of agglomerations.     

Surface texture of the milled surface of aluminum-ceramic composite

Journal of Mechanical Science and Technology - The work concerns the assessment of the parameters of the geometric structure of the surface of an aluminum-ceramic composite after milling in various...     

Effect of AMC on fixed‐rate traffic with hard delay constraints in mobile broadband systems

The adaptive modulation and coding (AMC) technique, which has been adopted by advanced mobile telecommunication systems, supports a flexible response to the random radio behaviour. As a result, the attained transmission rate over a wireless link is time varying. Hence, resource demands are not deterministic but fluctuating even for calls with constant bit rate service requirements. Consequently, constant bit rate calls are susceptible to a forced call termination because of insufficient resources not only in a target cell during inter‐cell handoffs but also in a serving cell during radio link deterioration. Furthermore, call blocking and dropping probabilities depend on radio propagation conditions among other factors and therefore they are dissimilar throughout a service area. The latter leads to unfairness problems. We analytically measure the impact of AMC on fixed‐rate service with hard delay constraints such as voice for different signal, mobility and traffic conditions. We consider a reference case (call requests are admitted into the system provided there are enough free resources) and two classes of admission control approaches: traditional (only inter‐cell handoffs are prioritised) and modified (all ongoing calls are prioritised). The reported results reveal conditions for which AMC affects voice call performance and can serve as guidelines on admission control design. Copyright © 2013 John Wiley & Sons, Ltd.     

Characterization of CVD Bonded Tyranno® Fibers Oxidized at High Temperatures

The oxidation of highly porous ceramic matrix composites (PCMCs) based on different Tyranno^® fibers has been analyzed by means of thermogravimetry and electron microscopy. Both uncoated fibers and PCMC materials exhibit parabolic kinetics between 900°C and 1250°C, these being faster for Ti‐doped than for Zr‐doped Tyranno fibers. Oxide layers in Ti‐doped fibers are porous and partially crystalline, whereas in Zr‐doped materials a significant fraction of relatively coarse β‐SiC grains is still found embedded in the amorphous silica matrix. On the other hand, the CVD‐SiC coatings exhibit higher oxidation rates from the outer surface than from the inner one, a phenomenon that has been associated not only with the more difficult access of oxygen to the inner face but also with the highly <111>  textured structure of these coatings, for which very different oxidation rates have been published for the inward and outward directions. Cracking phenomena observed above 1100°C for long dwelling times do not lead to an acceleration of the oxidation process, which could be due to the simultaneous crystallization of the amorphous silica layers.     

Physical and Functional Properties of Blackberry Freeze- and Spray-Dried Powders

The aim of the present work was to develop two products from blackberry juice by freeze and spray drying with potential use as food colorants or healthy ingredients. A characterization of the physical and functional properties of the powdered juices was done. Maltodextrin or a mixture of trehalose and maltodextrin were assessed as carrier matrices. Freeze-dried, maltodextrin-containing powders presented the best retention of bioactive compounds and antiradical activity; however, they showed a narrow relative humidity range for storage in the glassy state. Spray-dried powders showed better physical properties, bearing higher glass transition temperature and lower molecular mobility than freeze-dried formulations.