Selection bias in gene extraction on the basis of microarray gene-expression data

In the context of cancer diagnosis and treatment, we consider the problem of constructing an accurate prediction rule on the basis of a relatively small number of tumor tissue samples of known type containing the expression data on very many (possibly thousands) genes. Recently, results have been presented in the literature suggesting that it is possible to construct a prediction rule from only a few genes such that it has a negligible prediction error rate. However, in these results the test error or the leave-one-out cross-validated error is calculated without allowance for the selection bias. There is no allowance because the rule is either tested on tissue samples that were used in the first instance to select the genes being used in the rule or because the cross-validation of the rule is not external to the selection process; that is, gene selection is not performed in training the rule at each stage of the cross-validation process. We describe how in practice the selection bias can be assessed and corrected for by either performing a cross-validation or applying the bootstrap external to the selection process. We recommend using 10-fold rather than leave-one-out cross-validation, and concerning the bootstrap, we suggest using the so-called. 632+ bootstrap error estimate designed to handle overfitted prediction rules. Using two published data sets, we demonstrate that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.

An everyday nostalgia: Memory and the fictions of belonging

In 1984, George Orwell presented the future as a dystopian vision, where everyday existence was governed and redefined by an oppressive regime. Winston Smith's daily duties at the Ministry of Truth involved the invention, rewriting and erasing of fragments of history as a means of perpetuating contentment, uniformity and control. History, as Orwell described it in the novel 'was a palimpsest, scraped clean and reinscribed exactly as often as was necessary.' More that a quarter of a century after the publication of 1984, Michel Foucault discussed the cinematic representation and misrepresentation of French history and identity in terms of what he called the manipulation of 'popular memory'. In what was tantamount to a diluted version of Orwell's palimpsestic histories, Foucault stated that 'people are not shown what they were, but what they must remember having been.' This paper will investigate notions of memory, identity and the everyday through a discussion of the community of Celebration in Florida. Conceived in the 1990s, Celebration was designed around a fictionalised representation of pre 1940s small town America, using nostalgia for a mythologised past to create a sense of comfort, community and conformity among its residents. Adapting issues raised by Orwell, Foucault and Baudrillard, this paper will discuss the way in which architecture, like film and literature, can participate in what Foucault discussed as the manipulation of popular memory, inducing and exploiting a nostalgia for an everyday past that that never really existed.

The Indotriradites dolianitii Morphon, a distinctive group of miospore species from the Lower Carboniferous of Gondwana

An emended diagnosis and generic reallocation are proposed for the trilete miospore Indotriradites dolianitii (Daemon, 1974) Loboziak et al., comb. nov. A new species, I. daemonii Loboziak et al., sp. nov., from Viséan strata of Western Gondwana, is erected. These two species, together with I. zosteriformis (Playford et Satterthwait) Playford, 1991 from the Viséan of Australia, belong to a cohesive morphological miospore category, here termed the Indotriradites dolianitii Morphon, which is evidently restricted to the Lower Carboniferous of Gondwana.

Radiizonates arcuatus, a distinctive new miospore species from the Lower Carboniferous of Western Gondwana

A new species of trilete zonate miospores, Radiizonates arcuatus, is established for Lower Carboniferous Western Gondwanan forms hitherto ascribed misguidedly to Radiizonates genuinus (Jushko) Loboziak and Alpern (1978), a Russian Lower Carboniferous species. The latter binomen is, moreover, not a valid combination and is more correctly designated as Vallatisporites genuinus (Jushko) Byvsheva, 1980. R. arcuatus is, from records to date, confined to westerly parts of Gondwana (Brazil, North Africa and Middle East), in which it is characteristic of Early Carboniferous strata, albeit with some slightly older and slightly younger occurrences.

Type specific and genotype cross reactive B epitopes of the L1 protein of HPV16 defined by a panel of monoclonal antibodies

Mouse monoclonal antibodies (mAbs) were raised against the major capsid protein, L1, of human papillomavirus type 16 (HPV16), produced in Escherichia coil with the expression plasmid pTrcL1. Epitope specificity could be assigned to 11 of these 12 antibodies using a series of linear peptides and fusion proteins from HPV16. One mAb (MC53) recognized a novel linear epitope that appears to be unique to the HPV16 genotype. A further 11 mAbs were characterized as recognizing novel and previously defined linear and conformational epitopes shared among more than one HPV genotype. The apparently genotype specific mAb could be useful for the development of diagnostic tests for vegetative virus infection in clinical specimens. (C) 1998 Academic Press.

The Australian public's perception of genetically-engineered foods

This paper describes a recent Australian survey on attitudes to genetically-engineered foods. Initial results of the survey are discussed and presented in tabular form. While there is some acceptance of particular genetically-engineered products, the results show that responfdents did have concerns over the long-term health effects of eating genetically-engineered foods and the potential risk to the environment. Respondents clearly endorsed labelling of the products and government control of the technology.

Experimental study of phase equilibria in the system PbO-ZnO-SiO2

An experimental study on the ternary system PbO-ZnO-SiO2, in air by high-temperature equilibration and quenching techniques followed by electron probe X-ray microanalysis was carried out as part of the wider research program on the six-component system PbO-ZnO-SiO2-CaO-FeO-Fe2O3, which combines experimental and thermodynamic computer modeling techniques to characterize zinc and lead industrial slags. Liquidus and solidus data were reported for all primary phase fields in the system PbO-ZnO-SiO2 in the temperature range 640 degrees C to 1400 degrees C (913 to 1673 K).

The murine cytomegalovirus chemokine homolog, m131/129, is a determinant of viral pathogenicity

Chemokines are important mediators of the early inflammatory response to infection and modify a wide range of host immune responses. Functional homologs of cellular chemokines have been identified in a number of herpesviruses, suggesting that the subversion of the host chemokine response contributes to the pathogenesis of these viruses. Transcriptional and reverse transcription-PCR analyses demonstrated that the murine cytomegalovirus (MCMV) chemokine homolog, m131, was spliced at the 3' end to the adjacent downstream open reading frame, m129, resulting in a predicted product of 31 kDa, which is significantly larger than most known chemokines. The in vivo impact of m131/129 was investigated by comparing the replication of MCMV mutants having m131/129 deleted (Delta m131/129) with that of wild-type (wt) MCMV. Our studies demonstrate that both wt and Delta m131/129 viruses replicated to equivalent levels during the first 2 to 3 days following in vivo infection. However, histological studies demonstrated that the early inflammatory response elicited by Delta m131/129 was reduced compared with that of wt MCMV. Furthermore, the Delta m131/129 mutants failed to establish a high-titer infection in the salivary glands, These results suggest that m131/129 possesses proinflammatory properties in vivo and is important for the dissemination of MCMV to or infection of the salivary gland. Notably, the Delta m131/129 mutants were cleared more rapidly from the spleen and liver during acute infection compared with wt MCMV. The accelerated clearance of the mutants was dependent on NK cells and cells of the CD4(+) CD8(+) phenotype. These data suggest that m131/129 may also contribute to virus mechanisms of immune system evasion during early infection, possibly through the interference of NK cells and T cells.