Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

Background  

With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements.     

Effect of Feed Restriction on Performance and Postprandial Nutrient Metabolism in Pigs Co-Infected with Mycoplasma hyopneumoniae and Swine Influenza Virus

As nutritional status and inflammation are strongly connected, feeding and nutritional strategies could be effective to improve the ability of pigs to cope with disease. The aims of this study were to investigate the impact of a feed restriction on the ability of pigs to resist and be tolerant to a coinfection with Mycoplasma hyopneumoniae (Mhp) and the European H1N1 swine influenza virus, and the consequences for nutrient metabolism, with a focus on amino acids. Two groups of specific pathogen-free pigs were inoculated with Mhp and H1N1 21 days apart. One group was fed ad libitum, the other group was subjected to a two-week 40% feed restriction starting one week before H1N1 infection. The two respective mock control groups were included. Three days post-H1N1 infection, 200 g of feed was given to pigs previously fasted overnight and serial blood samples were taken over 4 hours to measure plasma nutrient concentrations. Throughout the study, clinical signs were observed and pathogens were detected in nasal swabs and lung tissues. Feed-restricted pigs presented shorter hyperthermia and a positive mean weight gain over the 3 days post-H1N1 infection whereas animals fed ad libitum lost weight. Both infection and feed restriction reduced postprandial glucose concentrations, indicating changes in glucose metabolism. Post-prandial plasma concentrations of the essential amino acids histidine, arginine and threonine were lower in co-infected pigs suggesting a greater use of those amino acids for metabolic purposes associated with the immune response. Altogether, these results indicate that modifying feeding practices could help to prepare animals to overcome an influenza infection. Connections with metabolism changes are discussed.     

Exon skipping in the sterol 27-hydroxylase gene leads to cerebrotendinous xanthomatosis

We report a new mutation in the sterol 27-hydroxylase (CYP 27) gene in a Dutch family with cerebrotendinous xanthomatosis: a G→A transition in the splice donor site in intron 4. This mutation leads to skipping of exon 4, resulting in a loss of 66 amino acids in the CYP 27 enzyme molecule. Received: 15 March 1997 / Accepted: 26 March 1997     

Biomedical implications from a morphoelastic continuum model for the simulation of contracture formation in skin grafts that cover excised burns

A continuum hypothesis-based model is developed for the simulation of the (long term) contraction of skin grafts that cover excised burns in order to obtain suggestions regarding the ideal length of splinting therapy and when to start with this therapy such that the therapy is effective optimally. Tissue is modeled as an isotropic, heterogeneous, morphoelastic solid. With respect to the constituents of the tissue, we selected the following constituents as primary model components: fibroblasts, myofibroblasts, collagen molecules, and a generic signaling molecule. Good agreement is demonstrated with respect to the evolution over time of the surface area of unmeshed skin grafts that cover excised burns between outcomes of computer simulations obtained in this study and scar assessment data gathered previously in a clinical study. Based on the simulation results, we suggest that the optimal point in time to start with splinting therapy is directly after placement of the skin graft on its recipient bed. Furthermore, we suggest that it is desirable to continue with splinting therapy until the concentration of the signaling molecules in the grafted area has become negligible such that the formation of contractures can be prevented. We conclude this study with a presentation of some alternative ideas on how to diminish the degree of contracture formation that are not based on a mechanical intervention, and a discussion about how the presented model can be adjusted.     

Ornithologische Notizen aus dem Ebrodelta

Zusammenfassung Im Ebrodelta ist, abgesehen von einigen Seen und Sümpfen, nur noch ein schmaler Küstenstreifen landwirtschaftlich ungenutzt. Hier hat sich ein Teil ursprünglichen Vogelreichtums erhalten, und hier wurde seit einigen Jahren eine Reihe faunistischer Erhebungen durchgeführt.Diese erbrachten mehrere erste Brutnachweise für Spanien oder die spanische Mittelmeerküste:Larus ridibundus, Sterna dougallii, St. sandvicensis, Haematopus ostralegus, Limosa limosa, Asio flammeus, Acrocephalus palustris. Als Rast- und Überwinterungsgebiet ist das Delta von großer Bedeutung, z. B. fürEgretta garzetta undPhoenicopterus ruber. Enge Beziehungen zur Camargue sind vielfach erkennbar, vielleicht sogar hinsichtlich der Ausbreitung vonLarus ridibundus undHaematopus ostralegus. Regelmäßige Wintervorkommen vonMarmaronetta angustirostris sind erwähnenswert.Es wird mit einigen bisher unbekannten Brutplätzen von Laro-Limicolen bekanntgemacht, von denen eine Kolonie vonSterna albifrons mit 300–400 Paaren besonders vermerkt sei. Für weitere Arten können Bestandsangaben gemacht werden.Dieses einzige, bedeutende Brut- und Rastgebiet zwischen Camargue und Coto Doñana ist in höchster Gefahr, durch intensivere landwirtschaftliche Nutzung und touristische Erschließung vernichtet zu werden.

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Resumen Datos ornitologicos sobre el Delta del Ebro. — Sin contar con charcas y marismas, el Delta del Ebro es una franja costera aun no explotada por la agricultura. Gracias a esto una numerosa variedad de aves ha podido mantenerse aprovechando las todavia persistentes condiciones orginarias del medio ambiente. Sobre estas aves se han venido acumulando en los ultimos años un buen acopio de observaciones.Se pudo constatar como nidificantes por primera vez en España o costas mediterranes a las siguientes especies:Larus ridibundus, Sterna dougalli, St. sandvicensis, Haematopus ostralegus, Limosa limosa, Asio flammeus, Acrocephalus palustris. Como lugar de invernada o refugio durante el paso el Delta del Ebro tiene un especial interes, por ejemplo paraEgretta garzetta yPhoenicopterus ruber. Se establecen algunas relaciones con la Camarga principalmente en cuanto a la expansión deLarus ridibundus yHaematopus ostralegus. Se mencionan invernadas regulares deMarmaronetta angustirostris. Se señalan algunos nuevos lugares de cria para Laro-Limicolas, merece destacarse el hallazgo de una colonia deSterna albifrons compuesta por unos 300–400 pares. Para otras especies se dan datos numerieos estimativos.El Delta del Ebro es un lugar unico y de gran importancia, situado entre la Camarga y el Coto de Doñana, que está hoy en peligro de desaparición debido a la colonización intensiva de la agricultura y a la creciente afluencia turistica.

     

Body size increase in insular rodent populations: a role for predators?

Insular mammalian populations living in areas of small size are often characterized by a drastic change in body mass compared to related continental populations or species. Generally, small mammals (less than 100 g) evolve into giant forms while large mammals (up to 100 g) evolve into dwarf forms. These changes, coupled with changes in other life, behavioural, physiological or demographic traits are referred to generally as the insular syndrome. We tested in this study the relative contribution of three factors — area of island, numbers of competitor species and number of predator species — to changes in body size of the woodmouse (Apodemus sylvaticus) in the Western Mediterranean Sea. Our results, based on a comparative analysis using the phylogenetic independent contrasts method, indicate that the increase in body size is related both to the decrease of island size and to the lower number of predator species. A decrease of competitor species does not seem to have an important effect.