Structural influence of gene networks on their inference: analysis of C3NET

Background: The availability of large-scale high-throughput data possesses considerable challenges toward their functional analysis. For this reason gene network inference methods gained considerable interest. However, our current knowledge, especially about the influence of the structure of a gene network on its inference, is limited.

Structural similarity of directed universal hierarchical graphs: A low computational complexity approach

In the present paper we mainly introduce an efficient approach to measure the structural similarity of so called directed universal hierarchical graphs. We want to underline that directed universal hierarchical graphs can be obtained from generalized trees which are already introduced. In order to classify these graphs, we state our novel graph similarity method. As a main result we notice that our novel algorithm has low computational complexity. (c) 2007 Elsevier Inc. All rights reserved.

The first structural characterization of a [2.2]PHANEPHOS - Transition-metal complex: Structure of rac-[Pd(4,12-bis(diphenylphosphino)[2.2]paracyclophane)Cl-2]

The solid-state structure of the [2.2]PHANEPHOS-transition-metal complex rac-[Pd(4,12-bis(diphenylphosphino)[2.2]paracyclophane)Cl-2] has been established by single-crystal X-ray diffraction. The P-Pd-P bite angle is ideally suited to catalytic processes such as carbon-carbon cross-coupling reactions, which involve reductive elimination as the rate-determining step.

The effect of construction pattern and unit interlock on the structural behaviour of block pavements

The maintenance or even replacement of cracked pavements requires considerable financial resources and puts a large burden on the budgets of local councils. In addition to these costs, local councils also face liability claims arising from uneven or cracked pedestrian pavements. These currently cost the Manchester City Council and Preston City Council around £6 million a year each. Design procedures are empirical. A better understanding of the interaction between paving blocks, bedding sand and subbase was necessary in order to determine the mode of failure of pavements under load. Increasing applied stress was found to mobilise ‘‘rotational interlock’’, providing increased pavement stiffness and thus increased load dissipation resulting in lower transmitted stress on the subgrade. The indications from the literature
review were that pavements are designed to fail by excessive deformation and that paving blocks remained uncracked at failure. This was confirmed with experimental data which was obtained from tests on segments of pavements that were laid/constructed in a purpose built test frame in the laboratory.

Phase Behaviour, Interactions, and Structural Studies of (Amines+Ionic Liquids) Binary Mixtures

We present a study on the phase equilibrium behaviour of binary mixtures containing two 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}imide-based ionic liquids, [Cnmim] [NTf2] (n=2 and 4), mixed with diethylamine or triethylamine as a function of temperature and composition using different experimental techniques. Based on this work, two systems showing an LCST and one system with a possible hourglass shape are measured. Their phase behaviours are then correlated and predicted by using Flory–Huggins equations and the UNIQUAC method implemented in Aspen. The potential of the COSMO-RS methodology to predict the phase equilibria was also tested for the binary systems studied. However, this methodology is unable to predict the trends obtained experimentally, limiting its use for systems involving amines in ionic liquids. The liquid-state structure of the binary mixture ([C2mim] [NTf2]+diethylamine) is also investigated by molecular dynamics simulation and neutron diffraction. Finally, the absorption of gaseous ethane by the ([C2mim][NTf2]+diethylamine) binary mixture is determined and compared with that observed in the pure solvents.

Bidirectional, iterative approach to the structural delineation of the functional "Chemoprint" in GPR40 for agonist recognition

GPR40, free fatty acid receptor 1 (FFAR1), is a member of the GPCR superfamily and a possible target for the treatment of type 2 diabetes. In this work, we conducted a bidirectional iterative investigation, including computational modeling and site-directed mutagenesis, aimed at delineating amino acid residues forming the functional "chemoprint" of GPR40 for agonist recognition. The computational and experimental studies revolved around the recognition of the potent synthetic agonist GW9508. Our experimentally supported model suggested that H137(4.56), R183(5.39), N244(6.55), and R258(7.35) are directly involved in interactions with the ligand. We have proposed a polarized NH-pi interaction between H137(4.56) and GW9508 as one of the contributing forces leading to the high potency of GW9508. The modeling approach presented in this work provides a general strategy for the exploration of receptor-ligand interactions in G-protein coupled receptors beginning prior to acquisition of experimental data.

In Situ Single-Crystal Diffraction Studies of the Structural Transition of Metal-Organic Framework Copper 5-Sulfoisophthalate, Cu-SIP-3

The flexibility of the metal-organic framework Cu-2(OH)(C8H3O7S)(H2O)center dot 2H(2)O (Cu-SIP-3) toward reversible single-crystal to single-crystal transformations is demonstrated using in situ diffraction methods at variable temperature. At temperatures below a dehydration-induced phase transition (T < 370 K) the structure is confirmed as being hydrated. In the temperature range where the transition takes place (370 K < T < 405 K) no discrete, sharp Bragg peaks can be seen in the single-crystal X-ray diffraction pattern, indicating significant loss of long-range order. At temperatures higher than 405 K, the Bragg peaks return and the structure can be refined as dehydrated Cu-SIP-3. The loss of guest water molecules can be followed at temperatures below the phase transition giving insight into the mechanism of the dehydration. Addition of nitric oxide gas to the material above the gating opening pressure of 275 mbar also leads to loss of Bragg scattering in the diffraction pattern.

Structural investigation of the promotional effect of hydrogen during the selective catalytic reduction of NOx with hydrocarbons over Ag/Al2O3 catalysts

In situ EXAFS has been used to examine the hydrogen effect on the selective catalytic reduction of NOx over silver/alumina catalysts. For all SCR conditions used, with or without co-reductant (H-2 or CO), the catalyst structure remained the same. Significant changes in the catalyst were only found under reducing conditions. The enhanced activity found in the presence of hydrogen is thought to be due to a chemical effect and not the result of a change in the structure of the active site.