Generalized Needleman–Wunsch algorithm for the recognition of T-cell epitopes

In this paper, we propose a new encoding technique that combines the different physicochemical properties of amino acids together with Needleman–Wunsch algorithm. The algorithm was tested in the recognition of T-cell epitopes. A series of SVM classifiers, where each SVM is trained using a different physicochemical property, combined with the “max rule” enables us to obtain an improvement over the state-of-the-art approaches.     

Differentiating stages of smoking intensity among adolescents: Stage-specific psychological and social influences.

Researchers' understanding of the impact of sociocultural and psychological factors on the various stages of adolescent smoking update is limited. Using national data, the authors examined transitions across smoking stages among adolescents (N=20,747) as a function of interpersonal, familial, and peer domains. Peer smoking was particularly influential on differentiating regular smoking, whereas alcohol use was most influential on earlier smoking. Although significant, depression and delinquency were attenuated in the context of other variables. Higher school grade was more likely to differentiate regular smoking from earlier smoking stages, whereas African American ethnicity and connectedness to school and family were protective of smoking initiation. Results lend support for an interactional approach to adolescent smoking, with implications for stage-matched prevention and intervention applications. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Isolation of a hydroxytyrosol-rich extract from olive leaves (<Emphasis Type="Italic">Olea Europaea</Emphasis> L.) and evaluation of its antioxidant properties and bioactivity

In this research, a phenol extract of high hydroxytyrosol (OLPE) content was obtained from olive leaves (Olea europaea L.), and subsequently tested under different contexts. The method used to obtain the OLPE basically involved two steps: the use of strongly-acid aqueous steam, generated from 10% HCl (v/v) at 100°C, to directly hydrolyse the native complex phenols from integral olive leaves, and OLPE recovery by liquid–liquid extraction with ethyl acetate. Hydrolysis time was 1 h. Finally, the dried extract was dissolved in distilled water. The OLPE total phenols were determined by Folin–Ciocalteu’s method and by HPLC analysis. Hydroxytyrosol was about 92% of the total phenols present in OLPE, and the yield was about 0.2% on fresh leaves. OLPE showed antioxidant effects on different food lipids and did not inhibit lactic acid bacteria growth; however, it showed cytotoxicity on NIH/3T3 fibroblasts and human umbilical vein endothelial cells at concentrations higher than 0.32 mM (as hydroxytyrosol).     

A Procedure for Evaluating the Compatibility of Surface Water Resources with Environmental and Human Requirements

This paper presents a novel and easy-to-use procedure for controlling and licensing water abstractions from a river based on establishing a balance between surface water resources and environmental and human requirements. Unlike other approaches relying on complex and detailed basin models, this is based simply on the use of the discharge duration curve to represent the available water resources. In particular, the scheme of analysis presented here is composed of four steps: 1) subdivision of a particular river reach into sub-reaches; 2) estimation of the availability of water along each sub-reach over a particular period of time by means of duration curves; 3) estimation of the environmental requirements (minimum instream flow—MIF) and quantities necessary for civil, agricultural and industrial uses over the same period, and 4) establishing a water balance model for each sub-reach, taking into consideration the effects produced by water resource use in the upstream sub-reaches. In particular, this procedure consents (a) quantification of the duration when abstractions are possible along each sub-reach, (b) quantification of the maximum abstraction needed to satisfy the volume requested (thereby enabling comparison with the amount the users can actually obtain through their structures and/or pumps) and (c) identification of situations in which users need to avail themselves of reservoirs for temporarily storing the water abstracted so that they do not exceed the availability on non-abstraction days. The procedure was successfully applied to a basin located in Emilia-Romagna, the Enza River, along which 9 sub-reaches were identified.     

Robust design via simulation experiments: a modified dual response surface approach

The existing procedures for robust design, devised for physical experiments, may be too limiting when the system can be simulated by a computer model. In this paper we introduce a modification of the dual response surface modelling, which incorporates the option of stochastically simulating some of the noise factors when their probabilistic behaviour is known. Our method generalizes both the crossed and the combined array approaches and finds a natural application to integrated parameter and tolerance design. The method appears suitable for designing complex measurement systems and in this paper is applied to the design of a high‐precision optical profilometer. Copyright © 2008 John Wiley & Sons, Ltd.     

A study of ionization electrons drifting large distances in liquid and solid argon

A two liter gridded ionization chamber was built and operated repeatedly to study electron transport in liquid and solid argon over distances up to 10 cm in drift fields of 0.01–2 kV/cm. A detailed analysis of the ionization pulse shape was performed, yielding information on both the degree of purity of the liquid and the electron drift velocity. Argon with an impurity concentration less than 0.2 ppb oxygen equivalent was obtained with a simple purification system. The measured attenuation length extrapolates to 7.5 m for liquid argon and to 1 m for solid argon at a drift field of 1 kV/cm.     

Proton-conducting membranes based on protic ionic liquids

New classes of proton-conducting membranes formed by incorporating Brönsted acid–base ionic liquids in a poly(vinyldenefluoride-co-hexafluoropropylene) PVdF polymer matrix, are here reported and discussed. We show that these membranes are characterized by high, thermally stable proton conductivity. However, this favourable property is in part contrasted by the release of the ionic liquid component, which may affect the long-term stability of the membranes. Various strategies are underway in our laboratory to solve this issue, and in this work we describe one of them, based on the dispersion of selected ceramic fillers in the polymer matrix. We show that this approach, while successful in enhancing the conductivity of the membranes, is not much effective in preventing the release of the ionic liquid component and thus, that other roads have to be explored to reach a satisfactory improvement of the integrity of the membrane.     

Sensor arrays to detect humic substances and Cu(II) in waters

The interaction between poly(o-ethoxyaniline) (POEA) adsorbed onto solid substrates and humic substances (HS) and Cu²⁺ ions has been investigated using UV–vis spectroscopy and atomic force microscopy (AFM). Both HS and Cu²⁺ are able to dope POEA and change film morphology. This interaction was exploited in a sensor array made with nanostructured films of POEA, sulfonated lignin and HS, which could detect small concentrations of HS and Cu²⁺ in water.     

Highly bright and photostable cyanine dye-doped silica nanoparticles for optical imaging: Photophysical characterization and cell tests

Spherical silica nanoparticles containing fluorescent trimethine indocyanine dyes (λ_abs = 547 nm, λ_em = 570 nm) were prepared using a water-in-oil microemulsion method. The nanoparticles were of 50 nm diameter and were almost monodispersed in aqueous solution at pH 5.5. Entrapment of dye molecules in the silica matrix stabilised photoemission over several hours of continuous irradiation. The photoemission intensity of the indocyanine was increased 13-fold over that recorded in solution. As each nanoparticle contained 110 dye molecules, the photoemission brightness of each particle was enhanced by three orders of magnitude. The fluorescent nanoparticles have been tested as imaging tools in in vitro tests. As an example of non-macrophagic cells, a highly differentiated neuronal cell line (GT1-7) was used and the results showed that the prepared nanoparticles can be incorporated into these cells with no apparent toxicity for up to three days.