3,380 research outputs found

    Mining whole sample mass spectrometry proteomics data for biomarkers: an overview

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    In this paper we aim to provide a concise overview of designing and conducting an MS proteomics experiment in such a way as to allow statistical analysis that may lead to the discovery of novel biomarkers. We provide a summary of the various stages that make up such an experiment, highlighting the need for experimental goals to be decided upon in advance. We discuss issues in experimental design at the sample collection stage, and good practise for standardising protocols within the proteomics laboratory. We then describe approaches to the data mining stage of the experiment, including the processing steps that transform a raw mass spectrum into a useable form. We propose a permutation-based procedure for determining the significance of reported error rates. Finally, because of its general advantages in speed and cost, we suggest that MS proteomics may be a good candidate for an early primary screening approach to disease diagnosis, identifying areas of risk and making referrals for more specific tests without necessarily making a diagnosis in its own right. Our discussion is illustrated with examples drawn from experiments on bovine blood serum conducted in the Centre for Proteomic Research (CPR) at Southampton University

    Restoration of a wild grey partridge shoot: a major development in the Sussex study, UK

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    Restauración de la caza de la perdiz pardilla: un importante progreso en el estudio de Sussex, Reino Unido Desde hace una generación se conoce la base científica de la gestión de la perdiz pardilla. Ésta incluye el control de los depredadores de nidos, la provisión de material para la nidificación, tener suficientes insectos para alimentar a las crías, y un control adecuado de la caza. Más recientemente también se ha considerado importante proveer alimento para las aves adultas y y hábitats para protegerlas de las aves rapaces. El abastecimiento del hábitat puede ser caro, pero en el Reino Unido los costos pueden recuperarse parcialmente mediante proyectos agro-medioambientales. El propietario de la tierra aún tiene que pagar por los servicios de los guardabosques. Desde 2003/2004, una parte del área de estudio de Sussex de la GWCT ha puesto en práctica estos principios de gestión ambiental, con la intención de restaurar la caza de la perdiz pardilla en esta zona del sur de Inglaterra. Los resultados han sido impresionantes, con un aumento de la densidad de parejas en primavera de 0,3/100 ha en 2003 hasta casi 20 parejas/100 ha en el 2010, en un área total de más de 10 km2. Durante los últimos dos años se ha practicado la caza de la perdiz pardilla y los propietarios de las tierras y sus equipos se han ganado el reconocimiento nacional por su labor conservacionista.Restauración de la caza de la perdiz pardilla: un importante progreso en el estudio de Sussex, Reino Unido Desde hace una generación se conoce la base científica de la gestión de la perdiz pardilla. Ésta incluye el control de los depredadores de nidos, la provisión de material para la nidificación, tener suficientes insectos para alimentar a las crías, y un control adecuado de la caza. Más recientemente también se ha considerado importante proveer alimento para las aves adultas y y hábitats para protegerlas de las aves rapaces. El abastecimiento del hábitat puede ser caro, pero en el Reino Unido los costos pueden recuperarse parcialmente mediante proyectos agro-medioambientales. El propietario de la tierra aún tiene que pagar por los servicios de los guardabosques. Desde 2003/2004, una parte del área de estudio de Sussex de la GWCT ha puesto en práctica estos principios de gestión ambiental, con la intención de restaurar la caza de la perdiz pardilla en esta zona del sur de Inglaterra. Los resultados han sido impresionantes, con un aumento de la densidad de parejas en primavera de 0,3/100 ha en 2003 hasta casi 20 parejas/100 ha en el 2010, en un área total de más de 10 km2. Durante los últimos dos años se ha practicado la caza de la perdiz pardilla y los propietarios de las tierras y sus equipos se han ganado el reconocimiento nacional por su labor conservacionista.The scientific basis of wild grey partridge management has been known for a generation. This includes controlling nest predators, providing nesting cover, having sufficient insect food for chicks and appropriate rates of shooting. More recently, measures such as providing food for adult birds and habitats for protection from birds of prey have also been considered important. Habitat provision can be expensive, but in the UK costs can be partially recovered through governmental agri–environment schemes. The landowner still needs to pay for the essential gamekeeper. Since 2003/04, one part of the Game & Wildlife Conservation Trust’s (GWCT) Sussex Study area has put these principles of environmental management into practice with the aim of restoring a wild grey partridge shoot to this part of Southern England. Results have been impressive, with the spring pair density increasing from 0.3 pairs/100 ha in 2003 to nearly 20 pairs/100 ha in 2010 on an area of just over 10 km2. Over the past two years a wild grey partridge shoot has taken place, and the landowner and his team have gained national recognition for their conservation work

    The effect of melt composition and oxygen fugacity on manganese partitioning between apatite and silicate melt

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    Oxygen fugacity and melt composition are both known to have a strong influence on the partitioning of trace elements between coexisting minerals and melt. Previous work has suggested that Mn partitioning between apatite and silicate melt may be strongly affected by oxygen fugacity and could, therefore, act as an oxybarometer. Here, we present a new study on the partitioning of Mn between apatite and melt at high temperature (1400–1250 °C) and 1 GPa pressure, for various melt compositions and oxygen fugacities (NNO +4.7 to NNO -10). We find that there is no demonstrable variation in the partition coefficient for Mn between apatite and silicate melt (D MnAp-m ) across the range of fO 2 conditions studied here. Instead, we find that D MnAp-m varies significantly with melt composition and that in particular, the proportion of non-bridging oxygens strongly influences partitioning of Mn between apatite and melt. We propose that variations in the Mn content of natural apatite, previously thought to reflect variations in fO 2 , are instead related to the degree of melt polymerisation. These findings are consistent with the results of Mn K-edge XANES spectroscopy, which demonstrate that Mn in coexisting apatite and silicate glass is present predominantly as Mn 2+ regardless of fO 2. Furthermore, XANES spectra from a series of silicate glasses synthesised at various oxygen fugacities demonstrate that Mn 2+ is the predominant species, and that the average Mn oxidation state does not vary over a wide range of fO 2 -T conditions

    Mean Field Renormalization Group for the Boundary Magnetization of Strip Clusters

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    We analyze in some detail a recently proposed transfer matrix mean field approximation which yields the exact critical point for several two dimensional nearest neighbor Ising models. For the square lattice model we show explicitly that this approximation yields not only the exact critical point, but also the exact boundary magnetization of a semi--infinite Ising model, independent of the size of the strips used. Then we develop a new mean field renormalization group strategy based on this approximation and make connections with finite size scaling. Applying our strategy to the quadratic Ising and three--state Potts models we obtain results for the critical exponents which are in excellent agreement with the exact ones. In this way we also clarify some advantages and limitations of the mean field renormalization group approach.Comment: 16 pages (plain TeX) + 8 figures (PostScript, appended), POLFIS-TH.XX/9
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