Response to Kuhse

In this short paper, we respond to critics of our original paper, The agony of agonal respiration: is the last gasp necessary?. A common thread in both Hawryluckâ s and Kuhseâ s responses is the difficulties encountered when using the agentâ s intentions to make moral distinctions between using neuromuscular blocking drugs to palliate versus using neuromuscular blocking drugs to kill. Although this difficulty does exist we maintain that the intentions of the physician must matter when providing end-of-life care. Originally published Journal of Medical Ethics, Vol. 28, No. 4, Aug. 200

The commodification of human reproductive materials.

This essay develops a framework for thinking about the moral basis for the commnodification of human reproductive nmaterials. It argues that selling and buyinlg gametes and genes is morally acceptable although there should not be a market for zygotes, embryos, or genomes. Also a market in gametes and genes shouild be regutlated in order to address concerns about the adverse social consequences of conmmodification. Originally published Journal of Medical Ethics, Vol. 24, No. 6, Dec 199

GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products

<p>Abstract</p> <p>Background</p> <p>With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO).</p> <p>Results</p> <p>We present the freely available software package <it>GOSim</it>, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. <it>GOSim </it>extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. <it>GOSim </it>hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes.</p> <p>Conclusion</p> <p><it>GOSim </it>is implemented as a package for the statistical computing environment <it>R </it>and is distributed under GPL within the CRAN project.</p

Property-based interest propagation in ontology-based user model

We present an approach for propagation of user interests in ontology-based user models taking into account the properties declared for the concepts in the ontology. Starting from initial user feedback on an object, we calculate user interest in this particular object and its properties and further propagate user interest to other objects in the ontology, similar or related to the initial object. The similarity and relatedness of objects depends on the number of properties they have in common and their corresponding values. The approach we propose can support finer recommendation modalities, considering the user interest in the objects, as well as in singular properties of objects in the recommendation process. We tested our approach for interest propagation with a real adaptive application and obtained an improvement with respect to IS-A-propagation of interest values

Conflict of Interest Policies at Canadian Universities: Clarity and Content

[À l'origine dans / Was originally part of : ESPUM - Dép. médecine sociale et préventive - Travaux et publications]Abstract Discussions of conflict of interest (COI) in the university have tended to focus on financial interests in the context of medical research; much less attention has been given to COI in general or to the policies that seek to manage COI. Are university COI policies accessible and understandable? To whom are these policies addressed (faculty, staff, students)? Is COI clearly defined in these policies and are procedures laid out for avoiding or remedying such situations? To begin tackling these important ethical and governance questions, our study examines the COI policies at the Group of Thirteen (G13) leading Canadian research universities. Using automated readability analysis tools and an ethical content analysis, we begin the task of comparing the strengths and weaknesses of these documents, paying particular attention to their clarity, readability, and utility in explaining and managing COI.This study was supported by a grant from the Institute of Genetics of the Canadian Institutes of Health Researc

“Excellence R Us”: university research and the fetishisation of excellence

The rhetoric of “excellence” is pervasive across the academy. It is used to refer to research outputs as well as researchers, theory and education, individuals and organisations, from art history to zoology. But does “excellence” actually mean anything? Does this pervasive narrative of “excellence” do any good? Drawing on a range of sources we interrogate “excellence” as a concept and find that it has no intrinsic meaning in academia. Rather it functions as a linguistic interchange mechanism. To investigate whether this linguistic function is useful we examine how the rhetoric of excellence combines with narratives of scarcity and competition to show that the hypercompetition that arises from the performance of “excellence” is completely at odds with the qualities of good research. We trace the roots of issues in reproducibility, fraud, and homophily to this rhetoric. But we also show that this rhetoric is an internal, and not primarily an external, imposition. We conclude by proposing an alternative rhetoric based on soundness and capacity-building. In the final analysis, it turns out that that “excellence” is not excellent. Used in its current unqualified form it is a pernicious and dangerous rhetoric that undermines the very foundations of good research and scholarship

Propagating user interests in ontology-based user model

In this paper we address the problem of propagating user interests in ontology-based user models. Our ontology-based user model (OBUM) is devised as an overlay over the domain ontology. Using ontologies as the basis of the user profile allows the initial user behavior to be matched with existing concepts in the domain ontology. Such ontological approach to user profiling has been proven successful in addressing the cold-start problem in recommender systems, since it allows for propagation from a small number of initial concepts to other related domain concepts by exploiting the ontological structure of the domain. The main contribution of the paper is the novel algorithm for propagation of user interests which takes into account i) the ontological structure of the domain and, in particular, the level at which each domain item is found in the ontology; ii) the type of feedback provided by the user, and iii) the amount of past feedback provided for a certain domain object

Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

The lady vanishes: what's missing from the stem cell debate

Most opponents of somatic cell nuclear transfer and embryonic stem cell technologies base their arguments on the twin assertions that the embryo is either a human being or a potential human being, and that it is wrong to destroy a human being or potential human being in order to produce stem cell lines. Proponents’ justifications of stem cell research are more varied, but not enough to escape the charge of obsession with the status of the embryo. What unites the two warring sides in ‘the stem cell wars’ is that women are equally invisible to both: ‘the lady vanishes’. Yet the only legitimate property in the body is that which women possess in their reproductive tissue and the products of their reproductive labour. By drawing on the accepted characterisation in law of property as a bundle of rights, and on a Hegelian model of contract as mutual recognition, we can lessen the impact of the tendency to regard women and their eggs as merely receptacles and women’s reproductive labour as unimportant

Australian Education Joins the OECD : Federalism, Regionalization, and the Role of Education in a Time of Transition

This chapter argues that Australian interactions with the Organisation for Economic Co-operation and Development (OECD) in the field of education in the mid- to late-1970s pointed in two separate but not yet incompatible directions—one equity-oriented and the other more in line with the standardization and accountability regime typically identified with the OECD’s current policies—both of which favored a shift of authority toward the national level in educational policy-making. In the process, the chapter highlights the importance of considering movements between different spatial levels of analysis when tracing the ability of international organizations to get their ideas and visions “out of house.” The chapter first outlines the international and domestic contexts for Australia’s early involvement in the OECD, followed by a discussion of the negotiations of state and federal interests on the Australian Commonwealth Department of Education’s advisory committee on OECD matters. This discussion, in turn, frames the last three analytical sections of the chapter, on interactions between the OECD and the Australian education authorities at different levels on initiatives negotiating both the location of authority between these levels and the role of education at a time when the relation between its social and economic potential was up for revision.Non peer reviewe