Structure Determination of the Top‐Loop of the Conserved 3′‐Terminal Secondary Structure in the Genome of Flaviviruses

To what extent small differences in RNA sequences (mutations) can have a profound impact on biology remains an intriguing question. This effect can be studied by using untranslated RNA regions as a model. We have studied the influence of mutations on the structure of an RNA hairpin that occurs in the 3′‐untranslated region (UTR) of Flaviviridae, and is known to have a large impact on the vector dependency of flaviviruses. Three related RNA sequences were studied by NMR spectroscopy. The selected sequences represent each one of the three clusters in the flavivirus genes (mosquito‐borne, tick‐borne, and no‐known‐vector viruses). A new strategy was used to obtain chemical shift signatures of carbonyl atoms in unlabeled uridine nucleobases to characterize their involvement in hydrogen bonding. Clear differences occur in the structures and stacking pattern of the three RNA hairpins. The observed differences cannot be predicted based on sequence analysis. A different biology can be correlated with a different RNA tertiary structure. The underlying biological mechanism, however, remains to be studied.     

Co–ZSM-5 catalysts in the decomposition of N2O and the SCR of NO with CH4: Influence of preparation method and cobalt loading

Co–ZSM-5 prepared via different methods with Co/Al ratios ranging from 0.03 to 0.83 are investigated in both the direct N₂O decomposition and the selective catalytic reduction (SCR) of NO with CH₄. UV–vis and H₂-TPR are used to get an insight in the active species in these reactions. It is observed that in catalysts with low Co loadings (Co/Al < 0.3) Co is predominantly present as mono-atomic Co species, located at ion exchange positions in ZSM-5. Higher Co loadings result in the formation of different kinds of Co-oxides, which constitute the majority of species in the over-exchanged catalysts (Co/Al > 0.5). The mono-atomic species show the highest activity in the direct decomposition of N₂O, whereas the oxidic Co species do not seem to contribute much to the overall decomposition. In the SCR, the Co-oxide species catalyze the combustion of CH₄ whereas the selectivity towards NO reduction is much increased at low Co loadings. Therefore, over-exchange of Co–ZSM-5 does not seem to be favorable for both the direct N₂O decomposition and the SCR of NO with CH₄. Co/Al ratios <0.3 give the best results both in terms of conversion and activity per Co atom in both reactions.     

Data fitting with geometric-programming-compatible softmax functions

Motivated by practical applications in engineering, this article considers the problem of approximating a set of data with a function that is compatible with geometric programming (GP). Starting with well-established methods for fitting max-affine functions, it is shown that improved fits can be obtained using an extended function class based on the softmax of a set of affine functions. The softmax is generalized in two steps, with the most expressive function class using an implicit representation that allows fitting algorithms to locally tune softness. Each of the proposed function classes is directly compatible with the posynomial constraint forms in GP. Max-monomial fitting and posynomial fitting are shown to correspond to fitting special cases of the proposed implicit softmax function class. The fitting problem is formulated as a nonlinear least squares regression, solved locally using a Levenberg–Marquardt algorithm. Practical implementation considerations are discussed. The article concludes with numerical examples from aerospace engineering and electrical engineering.