The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Geometric Interpretation of the Mixed Invariants of the Riemann Spinor

Mixed invariants are used to classify the Riemann spinor in the case of Einstein-Maxwell fields and perfect fluids. In the Einstein-Maxwell case these mixed invariants provide information as to the relative orientation of the gravitational and electromagnetic principal null directions. Consideration of the perfect fluid case leads to some results about the behaviour of the Bel-Robinson tensor regarded as a quartic form on unit timelike vectors.Comment: 31 pages, AMS-LaTe

The ethics of uncertainty for data subjects

Modern health data practices come with many practical uncertainties. In this paper, I argue that data subjects’ trust in the institutions and organizations that control their data, and their ability to know their own moral obligations in relation to their data, are undermined by significant uncertainties regarding the what, how, and who of mass data collection and analysis. I conclude by considering how proposals for managing situations of high uncertainty might be applied to this problem. These emphasize increasing organizational flexibility, knowledge, and capacity, and reducing hazard

Diasporic Security and Jewish Identity

This paper explores the relationship between identity and security through an investigation into Jewish diasporic identity. The paper argues that the convention of treating identity as an objective referent of security is problematic, as the Jewish diaspora experience demonstrates. The paper presents a new way of conceptualizing identity and security by introducing the concept of diasporic security. Diasporic security reflects the geographical experience of being a member of a trans-state community, of having a fluid identity that is shaped by sometimes contradictory discourses emanating from a community that resides both at home and abroad. In introducing the concept of diasporic security, the paper makes use of literature in Diaspora Studies, Security Studies, recent works in contemporary political theory and sociology, and Woody Allen's film, Deconstructing Harry (1997)

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology

Determinants of subject visit participation in a prospective cohort study of HTLV infection

<p>Abstract</p> <p>Background</p> <p>Understanding participation in a prospective study is crucial to maintaining and improving retention rates. In 1990–92, following attempted blood donation at five blood centers, we enrolled 155 HTLV-I, 387 HTLV-II and 799 HTLV seronegative persons in a long-term prospective cohort.</p> <p>Methods</p> <p>Health questionnaires and physical exams were administered at enrollment and 2-year intervals through 2004. To examine factors influencing attendance at study visits of the cohort participants we calculated odds ratios (ORs) with generalized estimated equations (GEE) to analyze fixed and time-varying predictors of study visit participation.</p> <p>Results</p> <p>There were significant independent associations between better visit attendance and female gender (OR = 1.31), graduate education (OR = 1.86) and income > $75,000 (OR = 2.68). Participants at two centers (OR = 0.47, 0.67) and of Black race/ethnicity (OR = 0.61) were less likely to continue. Higher subject reimbursement for interview was associated with better visit attendance (OR = 1.84 for$25 vs. $10). None of the health related variables (HTLV status, perceived health status and referral to specialty diagnostic exam for potential adverse health outcomes) significantly affected participation after controlling for demographic variables.</p> <p>Conclusion</p> <p>Increasing and maintaining participation by minority and lower socioeconomic status participants is an ongoing challenge in the study of chronic disease outcomes. Future studies should include methods to evaluate attrition and retention, in addition to primary study outcomes, including qualitative analysis of reasons for participation or withdrawal.</p

Reminiscence groups for people with dementia and their family carers: pragmatic eight-centre randomised trial of joint reminiscence and maintenance versus usual treatment: a protocol

The growing number of people with dementia, and the increasing cost of care, provides a major incentive to develop and test methods of supporting them in the community for longer. Most attention has been given to pharmacological interventions, but there is increasing recognition that psychosocial interventions may be equally effective, even preferable where medication has negative side-effects. Reminiscence groups, run by professionals and volunteers, which use photographs, recordings and other objects to trigger personal memories are probably the most popular therapeutic approach to working with people with dementia, but there is little evidence for their effectiveness and cost-effectiveness. The recent inclusion of family carers in groups with people with dementia, notably in our own pilot studies, has generated informal evidence that this joint approach improves relationships between people with dementia and their carers, and benefits both

Metatypical basal cell carcinoma: a clinical review

Background. Metatypical cell carcinoma can be considered as a new entity of skin cancer, being an intermediate typology between basal cell carcinomas and squamous cell carcinomas. The behaviour of the metatypical cell carcinoma lies between these two varieties of skin cancer. It is difficult to perform a differential diagnosis based on morphological and clinical features - therefore it is only possible by accurate histology. Methods. The authors have retrospectively analysed clinical records of 240 patients who were affected by metatypical skin cancer and who were treated by surgery, radiotherapy and chemotherapy. Results. MTC affected more males than females (62.5% vs 37.5%) than males. The most affected site was the cervicofacial area, 71.7%; then the trunk, 10%; the limbs, 9.6%; the scalp 3.7%; and other regions 5%. A recurrence occurred in 24 cases (10%), mainly in head and neck area. Conclusion. In this manuscript, the authors have emphasised the importance of conducting a differential diagnosis, and the importance of the specific treatment for metatypical skin cancer, even though more clinical studies and long-term follow-ups are required before establishing specific guidelines. © 2008 Tarallo et al; licensee BioMed Central Ltd

Governing through choice: Food labels and the confluence of food industry and public health discourse to create ‘healthy consumers’

Food industry and public health representatives are often in conflict, particularly over food labelling policies and regulation. Food corporations are suspicious of regulated labels and perceive them as a threat to free market enterprise, opting instead for voluntary labels. Public health and consumer groups, in contrast, argue that regulated and easy-to-read labels are essential for consumers to exercise autonomy and make healthy choices in the face of food industry marketing. Although public health and food industry have distinct interests and objectives, I argue that both contribute to the creation of the food label as a governmental strategy that depends on free-market logics to secure individual and population health. While criticism of ‘Big Food’ has become a growth industry in academic publishing and research, wider critique is needed that also includes the activities of public health. Such a critique needs to address the normalizing effect of neoliberal governmentality within which both the food industry and public health operate to reinforce individuals as ‘healthy consumers’. Drawing on Michel Foucault’s lectures at the Collège de France, I examine the food label through the lens of governmentality. I argue that the rationale operating through the food label combines nutrition science and free-market logics to normalize subjects as responsible for their own health and reinforces the idea of consumption as a means to secure population health from diet-related chronic diseases