Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design

One relatively new computational approach to the drug discoveryprocess involves calculating functional group maps of a targetstructure. Experimental functional group mapping techniqueshave also recently emerged. In this paper, the structure ofRNase A with two bound formates (i.e. carboxylate functionalities)is used as a model system to test the computational methodology.Functional group maps of the RNase A structure were calculatedusing the Multiple Copy Simultaneous Search (MCSS) method andcompared with experimentally determined formate and water positions.The calculations indicate that the protonation state of active-sitehistidines determines the ability of the enzyme to bind formate.The results also suggest an ordered binding mechanism for thetwo formates. An improved strategy for using the MCSS methodto design new candidate ligands is discussed.     

Distribution and dynamics of birds in a rural sub-Mediterranean landscape

The richness and abundance of birds in a sub-Mediterranean rural landscape (north Italy, Massa Carrara Province) were investigated across two spatial scales (10 km × 10 km and 5 km × 5 km), two functional scales (land use mosaic and ecotope) and two temporal scales (annual and seasonal).Information on birds collected using the line transect method was compared with some landscape attributes (altitude, orientation, patch size, distance from cultivations).Distribution, abundance and seasonal turnover of birds were described efficiently by land use cover and ecotopes, but altitude, orientation, patch size and neighboring patch types were also important.Pure crop areas and crops mixed within woodlands and farming villages were the areas preferred by birds especially out of the breeding period, although woodlands supported more stable birds assemblages over the year. The multiscalar approach proposed was an efficient strategy to investigate these bird assemblages living in a patchy rural mosaic in which resources were made seasonally available by agricultural practices.The recent landscape change due to abandonment of agriculture in most of the sub-Mediterranean mountainous rural areas and the consequent woodland encroachment were expected to produce impoverishment of both diversity and abundance of resident and migratory birds.     

Block-wise discretization accounting for structural constraints

This paper presents an approximate discretization method, named Mixed Euler-ZOH  (mE-ZOH), which can be applied to any continuous-time linear system. This method has been explicitly developed to preserve the system sparsity, a property that is particularly important when dealing with the analysis and design of distributed controllers for large-scale systems. In terms of stability preservation as a function of the sampling interval, we show that mE-ZOH  outperforms the classical forward Euler (fE) approach, which is the only known discretization method guaranteeing the preservation of sparsity for all possible sampling times. It is then shown that this new discretization method is capable of preserving stability for all sampling times for a wide classes of dynamical systems, including the important class of positive systems. Besides stability, also positivity of the resulting discrete-time system is preserved, contrarily to what happens for the fE approach. A couple of examples are reported to illustrate the main theoretical results of the paper.     

Embeddable reference electrodes for corrosion monitoring of reinforced concrete structures

Mixed‐metal oxide (MMO), graphite and laboratory‐made Ag/AgCl electrodes were electrochemically characterized to be used as reference electrodes embedded in concrete structures. Electrodes were studied in both, aqueous solutions of pH ranging from 7 to 13.5 and embedded into cement mortars; and the electrochemical studies were carried out in the absence and presence of chloride ions. Potential evolution, polarisation behaviour, galvanostatic pulse response and impedance characteristics of the electrodes were carried out in aqueous solutions. Besides, the electrochemical stability of the electrodes embedded in mortar was studied for an exposure period of two years. It was found that the MMO pseudo‐reference electrode is pH‐sensitive, the graphite pseudo‐reference electrode is oxygen sensitive and the Ag/AgCl pseudo‐reference electrode is chloride sensitive. Then, regarding the corrosion monitoring of steel rebars, care should be taken to avoid misleading interpretations of the corrosion potential measurements. However, any of them can be used to measure the corrosion rate of the rebars by means of traditional electrochemical techniques.     

Effect of cations on stress corrosion cracking: Ag-40Cd alloy in silver ion aqueous solutions containing a variety of foreign cations

Uhlig showed that cupric ions accelerated the stress corrosion cracking (SCC) of α-brass in ammoniacal solutions. When adding foreign metal cations (cadmium, zinc, cobalt and nickel) to the solutions, it was found that only the copper ion had an effect on the fracture time. The aim of the present work was to study if this is a more general phenomenon in SCC. To that purpose, a Ag-40Cd (at/o) alloy was strained in silver nitrate aqueous solutions containing a variety of foreign metal cations, at the equilibrium potential of the reaction: Ag⁺ + e⁻ = Ag. SCC was found in all cases. Silver ions specifically accelerated the crack propagation rate and the addition of foreign cations showed no significant effect on the phenomenon. Most of the cracks found were intergranular, and the specific effect of the cations could be explained through the surface mobility SCC mechanism.     

H.L. Van Trees (ed.) and K.L. Bell (ed.), Bayesian Bounds for parameter estimation and nonlinear filtering/tracking, Wiley & Sons Ltd, 2007 [Book review]

Parameter and random-process estimation play a central role in signal processing. A common requirement in the estimation problems is to predict and/or evaluate the error performance. This task is often complicated because the system and measurement models are typically non-linear with some inherent uncertainty. The error performance prediction is supposed to be theoretical - its goal is to establish the best achievable limit and is to be carried out even before one develops a suitable estimator. The error performance evaluation is usually done by Monte Carlo simulations once a candidate estimator has been built. Evaluation serves to assess the estimator quality by comparing its actual error with the theoretical prediction. The fundamental question in algorithm design is "Can we do better?" In this context, it is of paramount importance to find a theoretical bound on the error performance and compare it against the performance of various sub-optimal candidate estimators.     

Measure of electron cyclotron emission at multiple angles in high T(e) plasmas of JET

The oblique electron cyclotron emission (ECE) diagnostic installed at JET allows simultaneous analysis of the ECE spectra along three lines of sight (with toroidal angles of 0°, ～ 10°, and ～ 20°) and two linear polarizations for each oblique line of sight. The diagnostic is capable of measuring EC emission over the band of 75–800 GHz with 5 ms time resolution and 7.5 GHz spectral resolution, and it is designed to investigate the features of ECE spectra related to electron distribution in the thermal velocity range. Instrumental accuracy was assessed using sources at different temperatures (77–900 K) and with plasma emission. ECE from high temperature plasmas and in the presence of fast ions has been compared to simulations performed with the modeling code SPECE, setting an upper limit to possible discrepancies from thermal emission.     

Time-resolved diffuse optical spectroscopy up to 1700 nm by means of a time-gated InGaAs/InP single-photon avalanche diode

We present a new compact system for time-domain diffuse optical spectroscopy of highly scattering media operating in the wavelength range from 1100 nm to 1700 nm. So far, this technique has been exploited mostly up to 1100 nm: we extended the spectral range by means of a pulsed supercontinuum light source at a high repetition rate, a prism to spectrally disperse the radiation, and a time-gated InGaAs/InP single-photon avalanche diode working up to 1700 nm. A time-correlated single-photon counting board was used as processing electronics. The system is characterized by linear behavior up to absorption values of about 3.4 cm(-1) where the relative error is 17%. A first measurement performed on lipids is presented: the absorption spectrum shows three major peaks at 1200 nm, 1400 nm, and 1700 nm.     

Study of green Sicilian table olive fermentations through microbiological,chemical and sensory analyses

The production of five different green table olive cultivars was studied by a combined strategy consisting of chemical, microbiological and sensory analyses. Cultivable microflora of samples collected during processing was monitored by plate counts on seven synthetic culture media. In all samples Enterobacteriaceae, Pseudomonaceae, staphylococci, lactic acid bacteria and spore-forming bacteria were undetectable. Yeasts and moulds were countable from the day 42 (2 log CFU/ml) till the end of fermentation (6 log CFU/ml). The use of three different approaches for microorganism detection, including a culture-independent methodology, revealed the presence of barely three yeast species during the entire fermentation period: Candida parapsilosis, Pichia guilliermondii and Pichia kluyveri. Biochemical features of technological interest were evaluated for 94 strains in order to investigate their potential role in fermentation of green Sicilian table olives.