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.     

Porcine high molecular weight kininogen: its purification and properties as a thiol proteinase inhibitor as compared to human high molecular weight kininogen

1. High mol. wt kininogen (HMW kininogen) was purified to a homogeneous state from porcine plasma. 2. The protein exhibited a strong inhibitory activity for thiol proteinases such as ficin, papain and calpain I, whereas it did not inhibit serine proteinases, trypsin and chymotrypsin. 3. The mol. wt, isoelectric point, amino acid and carbohydrate compositions, stabilities to temperature and pH, kinetic constants, and immunological properties of the porcine HMW kininogen were determined and compared with those of human HMW kininogen.     

Isolation and analysis of monoclonal antibodies against various gangliosides

Female BALB/c mice were immunized with human melanoma (Mewo) cells containing ganglioside GD3 as a surface antigen. Immune splenocytes were fused with syngeneic P3-X63.Ag 8 myeloma cells. Antibodies produced by hybrid clones were analyzed by solid phase immunoassay. B, C, D and Q clones producing antibodies against Raja clavata brain gangliosides were obtained. Monoclonal B and C antibodies bound monosialogangliosides. Monoclonal D antibody bound a number of gangliosides but reacted predominantly with GD1a. Monoclonal Q antibody reacted selectively with GQ1c. It is assumed that ganglioside GQ1c is expressed on the melanoma cell surface and may be found only in the early stage of ontogenesis of high vertebrates.     

Variation in serotiny of three Banksia species along a climatic gradient

The degree of serotiny (i.e. the proportion of follicles remaining closed in each year's crop of cones since the last fire) was measured in Bank-sia attenuata, B. menziesii and B. prionotes at five sites along a climatic gradient extending 500 km north of Perth, Western Australia. The decrease in annual rainfall and increase in average temperature along the gradient paralleled a decrease in plant height and an increase in the degree of serotiny of all species. Extreme serotiny was recorded in the scrub-heath at the xeric end of the gradient whereas two species were essentially non-serotinous in the low woodland at the most mesic site. It is concluded that degree of serotiny is related to the fire characteristics of the site which depend on plant height. In xeric scrub-heath, the entire canopies of the Banksia spp. are consumed by fire which promotes massive release of seed. This facilitates recruitment in an otherwise unpredictable and unreliable seedbed. In mesic woodland, where cones rarely come into contact With flames, seeds are released spontaneously and site conditions are more conducive to recruitment in the inter-fire period.     

Pattern analysis of stem cell differentiation during <Emphasis Type="Italic">in vitro Arabidopsis</Emphasis> organogenesis

Plant somatic cells have the capability to switch their cell fates from differentiated to undifferentiated status under proper culture conditions, which is designated as totipotency. As a result, plant cells can easily regenerate new tissues or organs from a wide variety of explants. However, the mechanism by which plant cells have such remarkable regeneration ability is still largely unknown. In this study, we used a set of meristem-specific marker genes to analyze the patterns of stem cell differentiation in the processes of somatic embryogenesis as well as shoot or root organogenesis in vitro. Our studies furnish preliminary and important information on the patterns of the de novo stem cell differentiation during various types of in vitro organogenesis.     

Reassessing Neotropical angiosperm distribution patterns based on monographic data: a geometric interpolation approach

Monographic data rely on specimens deposited in herbaria and museums, which have been thoroughly revised by experts. However, monographic data have been rarely used to map species richness at large scale, mainly because of the difficulties caused by spatially heterogeneous sampling effort. In this paper we estimate patterns of species richness and narrow endemism, based on monographic data of 4,055 Neotropical angiosperm species. We propose a geometric interpolation method to derive species ranges at a 1° grid resolution. To this we apply an inverse distance-weighted summation scheme to derive maps of species richness and endemism. In the latter we also adjust for heterogeneous sampling effort. Finally, we test the robustness of the interpolated species ranges and derived species richness by applying the same method but using a leave-one-out-cross-validation (LOOCV). The derived map shows four distinct regions of elevated species richness: (1) Central America, (2) the Northern Andes, (3) Amazonia and (4) the Brazilian Atlantic coast (‘Mata Atlantica’). The region with the highest estimated species richness is Amazonia, with Central America following closely behind. Centers of narrow endemism are located over the entire Neotropics, several of them coinciding with regions of elevated species richness. Sampling effort has a minor influence on the interpolation of overall species richness, but it substantially influences the estimation of regions of narrow endemism. Thus, in order to improve maps of narrow endemism and resulting conservation efforts, more collection and identification activity is required.     

S100 alpha, CAPL, and CACY: molecular cloning and expression analysis of three calcium-binding proteins from human heart.

Elevated levels of intracellular calcium are a major cause of myocardial dysfunction. To find possible mediators of the deregulated calcium we searched for EF-hand calcium-binding proteins of the S100 family. By PCR technology we identified three members of the S100 protein family (S100 alpha, CACY, and CAPL) in the human heart. We cloned the corresponding cDNAs and examined their expression levels in various human tissues by Northern blot analysis. All three proteins are expressed at high levels in the human heart. Whereas CACY and CAPL mRNAs are expressed ubiquitously, S100 alpha mRNA is restricted to heart, skeletal muscle, and brain. Interestingly, the expression pattern of S100 alpha, CACY, and CAPL in human tissues differs significantly from that in rodent tissues.