Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions

In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors.     

ARO: A new model free optimization algorithm for real time applications inspired by the asexual reproduction

This paper presents a new individual based optimization algorithm, which is inspired from asexual reproduction known as a remarkable biological phenomenon, called as asexual reproduction optimization (ARO). ARO can be essentially considered as an evolutionary based algorithm that mathematically models the budding mechanism of asexual reproduction. In ARO, a parent produces a bud through a reproduction operator; thereafter the parent and its bud compete to survive according to a performance index obtained from the underlying objective function of the optimization problem; this leads to the fitter individual. ARO adaptive search ability along with its strength and weakness points are fully described in the paper. Furthermore, the ARO convergence to the global optimum is mathematically analyzed. To approve the effectiveness of the ARO performance, it is tested with several benchmark functions frequently used in the area of optimization. Finally, the ARO performance is statistically compared with that of an improved genetic algorithm (GA). Results of simulation illustrate that ARO remarkably outperforms GA.     

Development of core to solve the multidimensional multiple-choice knapsack problem

The multidimensional multiple-choice knapsack problem (MMKP) is an extension of the 0–1 knapsack problem. The core concept has been used to design efficient algorithms for the knapsack problem but the core has not been developed for the MMKP so far. In this paper, we develop an approximate core for the MMKP and utilize it to solve the problem exactly.     

Utilising semantic technologies for intelligent indexing and retrieval of digital images

The proliferation of digital media has led to a huge interest in classifying and indexing media objects for generic search and usage. In particular, we are witnessing a colossal growth in digital image repositories that are difficult to navigate using free-text search mechanisms, which often return inaccurate matches as they in principle rely on statistical analysis of query keyword recurrence in the image annotation or surrounding text. In this paper we present a semantically-enabled image annotation and retrieval engine that is designed to satisfy the requirements of the commercial image collections market in terms of both accuracy and efficiency of the retrieval process. Our search engine relies on methodically structured ontologies for image annotation, thus allowing for more intelligent reasoning about the image content and subsequently obtaining a more accurate set of results and a richer set of alternatives matchmaking the original query. We also show how our well-analysed and designed domain ontology contributes to the implicit expansion of user queries as well as the exploitation of lexical databases for explicit semantic-based query expansion.     

Analysis of the Earthʼs magnetic field variations on the basis of a wavelet-based approach

In the present paper we will discuss a new wavelet-based approach aimed at processing and analyzing different features of complex geomagnetic signals. This approach makes it possible to automatically extract different kinds of disturbances in the Earth?s magnetic field variations, which characterize solar activity and help to predict magnetic storms. In order to analyze geomagnetic signals wavelet packets are used in order to isolate local variations for quiet and perturbed periods and determine their intensity. Furthermore, a new automatic method of calculating the index of geomagnetic activity K is suggested on the basis of forming a quiet-day diurnal variation (Sq-curve). This method allows us to do calculations in the way that is closest to that developed by J. Bartels, who introduced the K-index in 1938. The results are compared with those obtained by INTERMAGNET and the original method of J. Bartels and the advantages of the suggested method are clearly demonstrated. For geomagnetic data collected in high-latitude regions of our planet it has become possible to reduce the error of estimating the K-index by 20% and unlike the technique used by INTERMAGNET here all the calculations can be done automatically. We will use geomagnetic signals that were kindly provided to us by the Institute of Cosmophysical Research and Radio Wave Propagation (Paratunka, Kamchatka region, Far East of Russia) for the period from January, 2002 till December, 2010.     

Catalytic oxidation and flow detection of carbohydrates at ruthenium dioxide modified electrodes

Ruthenium dioxide (RuO2) containing carbon paste electrodes exhibiting electrocatalytic response toward carbohydrates are described. The electrocatalytic behavior is exploited for developing a highly stable and sensitive flow detection scheme for carbohydrates at a low and fixed potential (+0.4 V vs Ag/AgCl). The effects of pH, flow rate, operating potential, surface "loading", concentration, and other variables are explored. The electrode response was stable for more than 48 h, with a signal loss of less than 10% over this period. The detection limits at the picomole level and a relative standard deviation of 1.2% (n = 72) are reported. Electrocatalytic oxidation is described also for related polyhydroxyl compounds (aldonic and aldaric acids and alditols).     

Spectrophotometric and atomic absorption spectrometric determination of ramipril and perindopril through ternary complex formation with eosin and Cu(II)

Two sensitive, spectrophotometric and atomic absorption spectrometric procedures are developed for the determination of ramipril and perindopril. Both methods are based on the formation of a ternary complex, extractable with chloroform, between copper(II), eosin and the two cited drugs. Spectrophotometrically under the optimum condition, the ternary complexes showed an absorption maximum at 535 nm, with apparent molar absorptivities of 6.55 and 4.00 x 10(3) mol(-1) x cm(-1) and Sandell's sensitivities of 5.80 x 10(-2) and 1.04 x 10(-1) microg x cm(-2) for perindopril and ramipril, respectively. The solution of ternary complex obeyed Beer's law in concentration ranges 10-60 and 20-100 microg x ml(-1) for perindopril and ramipril, respectively. The proposed method was applied to the determination of the two cited drugs in pharmaceutical tablets. The atomic absorption spectrometric method, directly through the quantitative determination of copper content of the organic extract of the complex, was also investigated for the purpose of enhancing the sensitivity of the determination. The spectrophotometric and atomic absorption spectrometric procedures hold their accuracy and precision well when applied to the determination of ramipril and perindopril dosage forms.     

Hydration of granulated slag-alite in the presence of quartz

The aim of the present work was to study the effect of quartz on the hydration characteristics of hydrothermally hardened granulated slag-alite pastes. The pastes, of water: solid ratio 0.20, were moulded at a pressure of 50 kg cm^–2 and autoclaved at 10 atm for 0.5, 2, 6, 12 and 24 h. Compressive strengths of the hardened product were determined, and the kinetics of reaction were studied by the quantitative determination of free lime and combined water contents. The phases formed after autoclaving were determined using XRD techniques. The reaction mechanism of the system under investigation was discussed and correlated to the strength of the hardened product. It can be concluded that the addition of quartz to slag-alite mixture increases the strength of the final product. The strength obtained for samples with high alite content are higher than that of low-alite content. Finally, the addition of quartz assists the formation of tobermorite in the hardened specimens.     

Synthesis and dielectric relaxation behavior of 55B2O3–15SiO2– 30Na2O: WO3 glass system

55 B₂O₃ – 15 SiO₂ – 30 Na₂O: x WO₃, (x ranging from 0 to 5 wt%) glass composites were prepared according to the melt-quenching procedure. The prepared samples were characterized via X-ray diffraction and broad band dielectric spectroscopy (viz., dielectric constant (ε₁), tanδ and AC conductivity (σ_AC) over a wide range of frequency and temperature). No sharp peaks were shown in the XRD pattern and is evidence of the amorphous nature of the samples. It turns out that the values of ε₁ and ε₂ are increasing at higher temperatures particularly at lower frequencies. The energy barrier height, W_M values decreased as 0.27, 0.25 and 0.22 while showed value of 0.29 eV for 5.0 wt% WO₃. In the dielectric modulus plots, two relaxation processes are found especially on the higher temperature side. It also shifted a higher frequency with increasing temperature. The values of exponent s have been found to lie between 0.48 and 0.74, which confirms that the conduction mechanism in the glass samples follows the correlated barrier hopping model. By calculating the activation energy associated with the relaxation processes and DC conductivity, it was found that the values are close, which indicates that the same charges contribute to the two processes.     

Participatory Irrigation Management and Transfer: Setting the Guiding Principles for a Sustaining Monitoring & Evaluation System – a Focus on the Mediterranean

A major shortcoming of Participatory Irrigation Management and Irrigation Management Transfer (PIM/IMT) is the absence of Monitoring & Evaluation (M&E) systems that accompany these processes and become a major instrument to correct, improve and learn. Although at the global level some countries have exerted efforts to implement M&E systems, these still present limitations, as the review of the international experiences shows. The Mediterranean situation is even more dramatic since only Tunisia implements an M&E system, whereas Egypt has shyly moved in this direction with a limited practical application. This state of affairs led the authors to develop a set of guiding principles to develop an M&E system to be applied in countries where PIM/IMT is adopted. This paper revises the main international efforts devoted to assess the performance of PIM/IMT and the state of the art of these processes in Southern and Eastern Mediterranean Countries. Moreover, it sets the framework and analyses the main sustaining factors for the development of a new M&E system for these countries.