Simultaneous extraction of order parameters and orientational distribution fuctions from 31[superscript]P NMR spectra of magnetically partially oriented phospholipid bilayers

Order parameter profiles extracted from the NMR spectra of model membranes are a valuable source of information about their structure and molecular motions. To al1alyze powder spectra the de-Pake-ing (numerical deconvolution) ~echnique can be used, but it assumes a random (spherical) dist.ribution of orientations in the sample. Multilamellar vesicles are known to deform and orient in the strong magnetic fields of NMR magnets, producing non-spherical orientation distributions. A recently developed technique for simultaneously extracting the anisotropies of the system as well as the orientation distributions is applied to the analysis of partially magnetically oriented 31p NMR spectra of phospholipids. A mixture of synthetic lipids, POPE and POPG, is analyzed to measure distortion of multilamellar vesicles in a magnetic field. In the analysis three models describing the shape of the distorted vesicles are examined. Ellipsoids of rotation with a semiaxis ratio of about 1.14 are found to provide a good approximation of the shape of the distorted vesicles. This is in reasonable agreement with published experimental work. All three models yield clearly non-spherical orientational distributions, as well as a precise measure of the anisotropy of the chemical shift. Noise in the experimental data prevented the analysis from concluding which of the three models is the best approximation. A discretization scheme for finding stability in the algorithm is outlined

Étude empirique des commentaires et application des techniques de résumé par extraction pour la redocumentation

La documentation des programmes aide les développeurs à mieux comprendre le code source pendant les tâches de maintenance. Toutefois, la documentation n’est pas toujours disponible ou elle peut être de mauvaise qualité. Le recours à la redocumentation s’avère ainsi nécessaire. Dans ce contexte, nous proposons de faire la redocumentation en générant des commentaires par application de techniques de résumé par extraction. Pour mener à bien cette tâche, nous avons commencé par faire une étude empirique pour étudier les aspects quantitatifs et qualitatifs des commentaires. En particulier, nous nous sommes intéressés à l’étude de la distribution des commentaires par rapport aux différents types d’instructions et à la fréquence de documentation de chaque type. Aussi, nous avons proposé une taxonomie de commentaires pour classer les commentaires selon leur contenu et leur qualité. Suite aux résultats de l’étude empirique, nous avons décidé de résumer les classes Java par extraction des commentaires des méthodes/constructeurs. Nous avons défini plusieurs heuristiques pour déterminer les commentaires les plus pertinents à l’extraction. Ensuite, nous avons appliqué ces heuristiques sur les classes Java de trois projets pour en générer les résumés. Enfin, nous avons comparé les résumés produits (les commentaires produits) à des résumés références (les commentaires originaux) en utilisant la métrique ROUGE.

Marine yeasts as source of single cell protein and immunostimulant for application in penaeid prawn culture systems

The study revealed the potential of marine yeasts as a source of single cell protein and immunostimulant for prawns. Prawns fed with the selected marine yeasts were showing more growth compared to the control feed and commercial feed. Yeasts being rich with proteins, vitamins and carbohydrates serve as a growth promoter for prawns as being evidenced in this study. The better performance of marine yeasts, D. hansenii S8 and S100 and C. tropicalis S186 compared to S. cerevisiae S36 as a feed supplement is worth investigating. Besides being a rich nutritional source, yeasts act as immunostimulants by virtue of its high carbohydrate (Beta, 1-3 glucan) and RNA content. Beta, 1-3 glucan, a cell wall component of yeasts /fungi is the most commonly used immunostimulant in aquaculture. The present study shows that even the whole cell yeast could serve as a good immunostimulant when supplied through diet. Extraction of Beta-1,3 glucan results in the removal of nutrients like proteins, vitamins etc. from the cell biomass.Utilization of the yeast biomass as such in the diet would help perform a dual role as nutritional component and immunostimulant for aquaculture applications.

Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction

Liquid chromatography-mass spectrometry (LC-MS) datasets can be compared or combined following chromatographic alignment. Here we describe a simple solution to the specific problem of aligning one LC-MS dataset and one LC-MS/MS dataset, acquired on separate instruments from an enzymatic digest of a protein mixture, using feature extraction and a genetic algorithm. First, the LC-MS dataset is searched within a few ppm of the calculated theoretical masses of peptides confidently identified by LC-MS/MS. A piecewise linear function is then fitted to these matched peptides using a genetic algorithm with a fitness function that is insensitive to incorrect matches but sufficiently flexible to adapt to the discrete shifts common when comparing LC datasets. We demonstrate the utility of this method by aligning ion trap LC-MS/MS data with accurate LC-MS data from an FTICR mass spectrometer and show how hybrid datasets can improve peptide and protein identification by combining the speed of the ion trap with the mass accuracy of the FTICR, similar to using a hybrid ion trap-FTICR instrument. We also show that the high resolving power of FTICR can improve precision and linear dynamic range in quantitative proteomics. The alignment software, msalign, is freely available as open source.

Experimental measurement and numerical simulation of horizontal-coupled slinky ground source heat exchangers

Results from both experimental measurements and 3D numerical simulations of Ground Source Heat Pump systems (GSHP) at a UK climate are presented. Experimental measurements of a horizontal-coupled slinky GSHP were undertaken in Talbot Cottage at Drayton St Leonard site, Oxfordshire, UK. The measured thermophysical properties of in situ soil were used in the CFD model. The thermal performance of slinky heat exchangers for the horizontal-coupled GSHP system for different coil diameters and slinky interval distances was investigated using a validated 3D model. Results from a two month period of monitoring the performance of the GSHP system showed that the COP decreased with the running time. The average COP of the horizontal-coupled GSHP was 2.5. The numerical prediction showed that there was no significant difference in the specific heat extraction of the slinky heat exchanger at different coil diameters. However, the larger the diameter of coil, the higher the heat extraction per meter length of soil. The specific heat extraction also increased, but the heat extraction per meter length of soil decreased with the increase of coil central interval distance.

Keyphrase extraction by synonym analysis of n-grams for e-journals categorisation

Automatic keyword or keyphrase extraction is concerned with assigning keyphrases to documents based on words from within the document. Previous studies have shown that in a significant number of cases author-supplied keywords are not appropriate for the document to which they are attached. This can either be because they represent what the author believes the paper is about not what it actually is, or because they include keyphrases which are more classificatory than explanatory e.g., “University of Poppleton” instead of “Knowledge Discovery in Databases”. Thus, there is a need for a system that can generate appropriate and diverse range of keyphrases that reflect the document. This paper proposes a solution that examines the synonyms of words and phrases in the document to find the underlying themes, and presents these as appropriate keyphrases. The primary method explores taking n-grams of the source document phrases, and examining the synonyms of these, while the secondary considers grouping outputs by their synonyms. The experiments undertaken show the primary method produces good results and that the secondary method produces both good results and potential for future work.

Prediction of the thermal performance of horizontal-coupled ground source heat exchangers

The thermal performance of a horizontal-coupled ground-source heat pump system has been assessed both experimentally and numerically in a UK climate. A numerical simulation of thermal behaviour of the horizontal-coupled heat exchanger for combinations of different ambient air temperatures, wind speeds, refrigerant temperature and soil thermal properties was studied using a validated 2D transient model. The specific heat extraction by the heat exchanger increased with ambient temperature and soil thermal conductivity, however it decreased with increasing refrigerant temperature. The effect of wind speed was negligible.

Contractual restrictions on lawful use of information: sole-source databases protected by the back door?

This article is concerned with the risks associated with the monopolisation of information that is available from a single source only. Although there is a longstanding consensus that sole-source databases should not receive protection under the EU Database Directive, and there are legislative provisions to ensure that lawful users have access to a database’s contents, Ryanair v PR Aviation challenges this assumption by affirming that the use of non-protected databases can be restricted by contract. Owners of non-protected databases can contractually exclude lawful users from taking the benefit of statutorily permitted uses, because such databases are not covered from the legislation that declares this kind of contract null and void. We argue that this judgment is not consistent with the legislative history and can have a profound impact on the functioning of the digital single market, where new information services, such as meta-search engines or price-comparison websites, base their operation on the systematic extraction and re-utilisation of materials available from online sources. This is an issue that the Commission should address in a forthcoming evaluation of the Database Directive.

Mutagenic and carcinogenic potential of a textile azo dye processing plant effluent that impacts a drinking water source

Recently a textile azo dye processing plant effluent was identified as one of the sources of mutagenic activity detected in the Cristais River, a drinking water source in Brazil [G.A. Umbuzeiro, D.A. Roubicek, C.M. Rech, M.I.Z. Sato, L.D. Claxton, Investigating the sources of the mutagenic activity found in a river using the Salmonella assay and different water extraction procedures, Chemosphere 54 (2004) 1589-1597]. Besides presenting high mutagenic activity in the Salmonella/microsome assay, the mutagenic nitro-aminoazobenzenes dyes CI Disperse Blue 373, Cl Disperse Violet 93, and CI Disperse Orange 37 [G.A. Umbuzeiro, H.S. Freeman, S.H. Warren, D.P Oliveira, Y. Terao, T. Watanabe, L.D. Claxton, the contribution of azo dyes in the mutagenic activity of the Cristais river, Chemosphere 60 (2005) 55-64] as well as benzidine, a known carcinogenic compound [T.M. Mazzo, A.A. Saczk, G.A. Umbuzeiro, M.V.B. Zanoni, Analysis of aromatic amines in surface waters receiving wastewater from textile industry by liquid chromatographic with eletrochemical detection, Anal. Lett., in press] were found in this effluent. After similar to 6 km from the discharge of this effluent, a drinking water treatment plant treats and distributes the water to a population of approximate 60,000. As shown previously, the mutagens in the DWTP intake water are not completely removed by the treatment. The water used for human consumption presented mutagenic activity related to nitro-aromatics and aromatic amines compounds probably derived from the cited textile processing plant effluent discharge [G.A. Umbuzeiro, D.A. Roubicek, C.M. Rech, M.I.Z.. Sato, L.D. Claxton, Investigating the sources of the mutagenic activity found in a river using the Salmonella assay and different water extraction procedures, Chemosphere 54 (2004) 1589-1597; G.A. Umbuzeiro, H.S. Freeman, S.H. Warren, D.P. Oliveira, Y. Terao, T. Watanabe, L.D. Claxton, the contribution of azo dyes in the multagenic activity of the Cristais river, Chemosphere 60 (2005) 55-64]. Therefore, it is important to evaluate the possible risks involved in the human consumption of this contaminated water. With that objective, one sample of the cited industrial effluent was tested for carcinogenicity in the aberrant crypt foci medium-term assay in colon of Wistar rats. The rats received the effluent in natura through drinking water at concentrations of 0.1%, 1%, and 10%. The effluent mutagenicity was also confirmed in the Salmonella/microsome assay with the strains TA98 and YG1041. There was an increased number of preneoplastic lesions in the colon of rats exposed to concentrations of 1% and 10% of the effluent, and a positive response for both Salmonella strains tested. These results indicate that the discharge of the effluent should be avoided in waters used for human consumption and show the sensitivity of the ACF crypt foci assay as an important tool to evaluate the carcinogenic potential of environmental complex mixtures. (c) 2006 Elsevier B.V. All rights reserved.

Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales

DNA-based studies have been one of the major interests in conservation biology of endangered species and in population genetics. As species and population genetic assessment requires a source of biological material, the sampling strategy can be overcome by non-destructive procedures for DNA isolation. An improved method for obtaining DNA from fish fins and scales with the use of an extraction buffer containing urea and further DNA purification with phenol-chloroform is described. The methodology combines the benefits of a non-destructive DNA sampling and its high efficiency. In addition, comparisons with other methodologies for isolating DNA from fish demonstrated that the present procedure also becomes a very attractive alternative to obtain large amounts of high-quality DNA for use in different molecular analyses. The DNA samples, isolated from different fish species, have been successfully used on random amplified polymorphic DNA (RAPD) experiments, as well as on amplification of specific ribosomal and mitochondrial DNA sequences. The present DNA extraction procedure represents an alternative for population approaches and genetic studies on rare or endangered taxa.

Determination of Zinc in Lubricating Oil by Flame MS Employing Ultrasonic Extraction

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Study of the enthalpy-entropy mechanism from water sorption of orange seeds (C. sinensis cv. Brazilian) for the use of agro-industrial residues as a possible source of vegetable oil production

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Supercritical extraction of pupunha (Guilielma speciosa) oil in a fixed bed using carbon dioxide

The pupunha (Guilielma speciosa) is the fruit of a palm tree typical of the Brazilian Northern region, whose stem is used as a source of heart of palm. The fruit, which is about 65% pulp, is a source of oil and carotenes. In the present work, an analysis of the kinetics of supercritical extraction of oil from the pupunha pulp is presented. Carbon dioxide was used as solvent. The extractions were carried out at 25 MPa and 323 K and 30 MPa and 318 K. The chemical composition of the extracts in terms of fatty acids was determined by gas chromatography. The amount of oleic acid, a saturated fatty acid, in the CO2 extracts was larger than that in the extract obtained with hexane. The overall extraction curves were modeled using the single-parameter model proposed in the literature to describe the desorption of toluene from activated coal.

Extraction of oil from pressed palm oil (Elaes guineensis) fibers using supercritical CO2

Residual fibers from palm oil production are a good source of carotene, since they contain more than 5% of the original oil, with about 5000 ppm of carotenoids. As carotenoids are thermosensitive molecules, supercritical CO₂ can be used for oil recovery, because this technique employs low temperatures. In this work results of oil extraction experiments from pressed palm oil fibers are shown. Fibers were from AGROPALMA, an industry which is located in Tailândia (Pará, Brazil). Extractions were carried out at 200, 250 and 300 bar and at temperatures of 45 and 55oC. Oil was analyzed by UV/vis spectrophotometry for total carotene determination. Results showed a large increase in extraction rate from 200 to 250 bar and a small variation from 250 to 300 bar. The total amount of carotenes did not increase in the course of extraction at 300 bar, but it showed a large increase at 200 and at 250 bar. Free fatty acids are present in amounts larger than those found in commercial oils.