Bioinformática: base de datos de matrices de expresión génica para su análisis vía web

El IBB ha desarrollado un servidor de aplicaciones: http://revolutionresearch.uab.es para el análisis de microarrays. Estas microarrays las obtienen y las suben a la base de datos local los usuarios de la aplicación. En la presente memoria se detalla el proceso realizado para automatizar la subida de microarrays públicas a la base de datos local. Estas microarrays se obtendrán del NCBI. El proceso de descarga de microarrays se realizará cada dos meses y estará sincronizado con un proceso de descarga de genes marcadores de microarrays del NCBI. En la memoria también se describen las fases realizadas para crear la interfaz web para gestionar estas microarrays públicas y las modificaciones realizadas sobre el aplicativo web para permitir realizar análisis con estas microarrays.

Generalized canonical correlation analysis of matrices with different row and column orders

A Method is offered that makes it possible to apply generalized canonicalcorrelations analysis (CANCOR) to two or more matrices of different row and column order. The new method optimizes the generalized canonical correlationanalysis objective by considering only the observed values. This is achieved byemploying selection matrices. We present and discuss fit measures to assessthe quality of the solutions. In a simulation study we assess the performance of our new method and compare it to an existing procedure called GENCOM,proposed by Green and Carroll. We find that our new method outperforms the GENCOM algorithm both with respect to model fit and recovery of the truestructure. Moreover, as our new method does not require any type of iteration itis easier to implement and requires less computation. We illustrate the methodby means of an example concerning the relative positions of the political parties inthe Netherlands based on provincial data.

Analysis of matched matrices

We consider the joint visualization of two matrices which have common rowsand columns, for example multivariate data observed at two time pointsor split accord-ing to a dichotomous variable. Methods of interest includeprincipal components analysis for interval-scaled data, or correspondenceanalysis for frequency data or ratio-scaled variables on commensuratescales. A simple result in matrix algebra shows that by setting up thematrices in a particular block format, matrix sum and difference componentscan be visualized. The case when we have more than two matrices is alsodiscussed and the methodology is applied to data from the InternationalSocial Survey Program.

Spatial weights : constructing weight-compatible exchange matrices from proximity matrices

Exchange matrices represent spatial weights as symmetric probability distributions on pairs of regions, whose margins yield regional weights, generally well-specified and known in most contexts. This contribution proposes a mechanism for constructing exchange matrices, derived from quite general symmetric proximity matrices, in such a way that the margin of the exchange matrix coincides with the regional weights. Exchange matrices generate in turn diffusive squared Euclidean dissimilarities, measuring spatial remoteness between pairs of regions. Unweighted and weighted spatial frameworks are reviewed and compared, regarding in particular their impact on permutation and normal tests of spatial autocorrelation. Applications include tests of spatial autocorrelation with diagonal weights, factorial visualization of the network of regions, multivariate generalizations of Moran's I, as well as "landscape clustering", aimed at creating regional aggregates both spatially contiguous and endowed with similar features.

Density matrices and momentum distributions in 3He-4He mixtures

We report variational calculations, in the hypernetted-chain (HNC)-Fermi-HNC scheme, of one-body density matrices and one-particle momentum distributions for 3He-4He mixtures described by a Jastrow correlated wave function. The 4He condensate fractions and the 3He strength poles are examined and compared with the Monte Carlo available results. The agreement has been found to be very satisfactory. Their density dependence is also studied.

Unconventional magnetic behavior of iron-oxide nanoparticles in polymeric matrices

We report the results of magnetization and 57Fe Mössbauer spectroscopy measurements performed in the temperature range 5-300 K on composites containing iron¿oxide nanoparticles encased in polystyrene type resins. After carrying out a suitable field treatment in order to decouple the particles from the matrix, a fraction of the particles freely rotate in response to an applied magnetic field

Minimal analytical characterisation of engineered nanomaterials need for hazard assessment in biological matrices

The safe and responsible development of engineered nanomaterials (ENM), nanotechnology-based materials and products, together with the definition of regulatory measures and implementation of "nano"-legislation in Europe require a widely supported scientific basis and sufficient high quality data upon which to base decisions. At the very core of such a scientific basis is a general agreement on key issues related to risk assessment of ENMs which encompass the key parameters to characterise ENMs, appropriate methods of analysis and best approach to express the effect of ENMs in widely accepted dose response toxicity tests. The following major conclusions were drawn: Due to high batch variability of ENMs characteristics of commercially available and to a lesser degree laboratory made ENMs it is not possible to make general statements regarding the toxicity resulting from exposure to ENMs. 1) Concomitant with using the OECD priority list of ENMs, other criteria for selection of ENMs like relevance for mechanistic (scientific) studies or risk assessment-based studies, widespread availability (and thus high expected volumes of use) or consumer concern (route of consumer exposure depending on application) could be helpful. The OECD priority list is focussing on validity of OECD tests. Therefore source material will be first in scope for testing. However for risk assessment it is much more relevant to have toxicity data from material as present in products/matrices to which men and environment are be exposed. 2) For most, if not all characteristics of ENMs, standardized methods analytical methods, though not necessarily validated, are available. Generally these methods are only able to determine one single characteristic and some of them can be rather expensive. Practically, it is currently not feasible to fully characterise ENMs. Many techniques that are available to measure the same nanomaterial characteristic produce contrasting results (e.g. reported sizes of ENMs). It was recommended that at least two complementary techniques should be employed to determine a metric of ENMs. The first great challenge is to prioritise metrics which are relevant in the assessment of biological dose response relations and to develop analytical methods for characterising ENMs in biological matrices. It was generally agreed that one metric is not sufficient to describe fully ENMs. 3) Characterisation of ENMs in biological matrices starts with sample preparation. It was concluded that there currently is no standard approach/protocol for sample preparation to control agglomeration/aggregation and (re)dispersion. It was recommended harmonization should be initiated and that exchange of protocols should take place. The precise methods used to disperse ENMs should be specifically, yet succinctly described within the experimental section of a publication. 4) ENMs need to be characterised in the matrix as it is presented to the test system (in vitro/ in vivo). 5) Alternative approaches (e.g. biological or in silico systems) for the characterisation of ENMS are simply not possible with the current knowledge. Contributors: Iseult Lynch, Hans Marvin, Kenneth Dawson, Markus Berges, Diane Braguer, Hugh J. Byrne, Alan Casey, Gordon Chambers, Martin Clift, Giuliano Elia1, Teresa F. Fernandes, Lise Fjellsbø, Peter Hatto, Lucienne Juillerat, Christoph Klein, Wolfgang Kreyling, Carmen Nickel1, and Vicki Stone.

Minimal analytical characterization of engineered nanomaterials needed for hazard assessment in biological matrices.

Abstract This paper presents the outcomes from a workshop of the European Network on the Health and Environmental Impact of Nanomaterials (NanoImpactNet). During the workshop, 45 experts in the field of safety assessment of engineered nanomaterials addressed the need to systematically study sets of engineered nanomaterials with specific metrics to generate a data set which would allow the establishment of dose-response relations. The group concluded that international cooperation and worldwide standardization of terminology, reference materials and protocols are needed to make progress in establishing lists of essential metrics. High quality data necessitates the development of harmonized study approaches and adequate reporting of data. Priority metrics can only be based on well-characterized dose-response relations derived from the systematic study of the bio-kinetics and bio-interactions of nanomaterials at both organism and (sub)-cellular levels. In addition, increased effort is needed to develop and validate analytical methods to determine these metrics in a complex matrix.

Aplicaciones de la Teoría de Matrices en Matemática Discreta

Se describen algunas aplicaciones de la teoría de matrices a diversos temas pertenecientes alámbito de la matem\'atica discreta.

Technical Note: Dissolved organic matter fluorescence a finite mixture approach to deconvolve excitation-emission matrices

The analysis of the shape of excitation-emission matrices (EEMs) is a relevant tool for exploring the origin, transport and fate of dissolved organic matter (DOM) in aquatic ecosystems. Within this context, the decomposition of EEMs is acquiring a notable relevance. A simple mathematical algorithm that automatically deconvolves individual EEMs is described, creating new possibilities for the comparison of DOM fluorescence properties and EEMs that are very different from each other. A mixture model approach is adopted to decompose complex surfaces into sub-peaks. The laplacian operator and the Nelder-Mead optimisation algorithm are implemented to individuate and automatically locate potential peaks in the EEM landscape. The EEMs of a simple artificial mixture of fluorophores and DOM samples collected in a Mediterranean river are used to describe the model application and to illustrate a strategy that optimises the search for the optimal output.

Solid phase extraction of iron and lead in environmental matrices on amberlite xad-1180/pv

A solid phase extraction procedure using Amberlite XAD-1180/Pyrocatechol violet (PV) chelating resin for the determination of iron and lead ions in various environmental samples was established. The procedure is based on the sorption of lead(II) and iron(III) ions onto the resin at pH 9, followed by elution with 1 mol/L HNO3 and determination by flame atomic absorption spectrometry. The influence of alkaline, earth alkaline and some transition metals, as interferents, are discussed. The recoveries for the spiked analytes were greater than 95%. The detection limits for lead and iron by FAAS were 0.37 µg/L and 0.20 µg/L, respectively. Validation of the method described here was performed by using three certified reference materials (SRM 1515 Apple Leaves, SRM 2711 Montana Soil and NRCC-SLRS-4 Riverine Water). The procedure was successfully applied to natural waters and human hair.

A low-cost ultrasonic spray dryer to produce spherical microparticles from polymeric matrices

The spray-drying technique has been widely used for drying heat-sensitive foods, pharmaceuticals, and other substances, because it leads to rapid solvent evaporation from droplets. This method involves the transformation of a feed from a fluid state into a dried particulate, by spraying the feed into a hot medium. Despite being most often considered a dehydration process, spray drying can also be used as an encapsulation method. Therefore, this work proposes the use of a simple and low-cost ultrasonic spray dryer system to produce spherical microparticles. This equipment was successfully applied to the preparation of dextrin microspheres on a laboratory scale and for academic purposes.

Un método de bajo costo para la determinación de cobre a nivel de vestigios en matrices de interés ambiental por espectrofotometría en fase sólida (EFS)

A method for determining copper by solid phase spectrophotometry (SPS) was optimized using the Doehlert design. Copper(II) was sorbed on a styrene-divinylbenzene anion-exchange resin as a Cu(II)-1-(2-pyridylazo)-2-naphthol (PAN) complex, at pH 7.0. Resin phase absorbances at 560 and 800 nm were measured directly. The detection limit was found to be 2.5 µg L-1. The relative standard deviation on ten replicate determinations of 10 µg Cu(II) in 1000 mL samples was 1.1%. The linear range of the determination was 5.0-100 µg L-1. The method was applied successfully to the determination of Cu(II) in natural water and vegetable samples.

Building bone tissue: matrices and scaffolds in physiology and biotechnology

Deposition of bone in physiology involves timed secretion, deposition and removal of a complex array of extracellular matrix proteins which appear in a defined temporal and spatial sequence. Mineralization itself plays a role in dictating and spatially orienting the deposition of matrix. Many aspects of the physiological process are recapitulated in systems of autologous or xenogeneic transplantation of osteogenic precursor cells developed for tissue engineering or modeling. For example, deposition of bone sialoprotein, a member of the small integrin-binding ligand, N-linked glycoprotein family, represents the first step of bone formation in ectopic transplantation systems in vivo. The use of mineralized scaffolds for guiding bone tissue engineering has revealed unexpected manners in which the scaffold and cells interact with each other, so that a complex interplay of integration and disintegration of the scaffold ultimately results in efficient and desirable, although unpredictable, effects. Likewise, the manner in which biomaterial scaffolds are "resorbed" by osteoclasts in vitro and in vivo highlights more complex scenarios than predicted from knowledge of physiological bone resorption per se. Investigation of novel biomaterials for bone engineering represents an essential area for the design of tissue engineering strategies.