The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Rousseau's divorce of the good from history -- Kant formalizes the divorce -- Democracy's deliberation -- The rehabilitation of prejudice -- Tradition's deliberation -- Deliberation and modernity.

This article argues that Thomas Aquinas's virtue ethics approach to just war theory provides a solid ethical foundation for thinking about the problem of war. After briefly indicating some shortcomings of contemporary views of international justice, including pacifism, legalism, progressivism, realism, pragmatism, and consequentialism, the article examines Aquinas's question ?On War? in the Summa Theologiae. It then attempts to show that Aquinas's thinking on war is rooted in his understanding of the virtues by providing a brief overview of how the (...) cardinal virtues (prudence, justice, fortitude, temperance) and theological virtues (faith, hope, and charity) are connected to just war considerations. (shrink)

The paper describes and discusses unethical behavior in organizations, as a result of (interacting) disputable leadership and ethical climate. This paper presents and analyzes the well-known bond trading scandal at Salomon Brother to demonstrate the development of an unethical organizational culture under the leadership of John Gutfreund. The paper argues that leaders shape and reinforce an ethical or unethical organizational climate by what they pay attention to, how they react to crises, how they behave, how they allocate rewards, and how (...) they hire and fire individuals. (shrink)

Neurological diseases, particularly in the context of aging, have serious impacts on quality of life and can negatively affect bone health. The brain-bone axis is critically important for skeletal metabolism, sensory innervation, and endocrine cross-talk between these organs. This review discusses current evidence for the cellular and molecular mechanisms by which various neurological disease categories, including autoimmune, developmental, dementia-related, movement, neuromuscular, stroke, trauma, and psychological, impart changes in bone homeostasis and mass, as well as fracture risk. Likewise, how bone may (...) affect neurological function is discussed. Gaining a better understanding of brain-bone interactions, particularly in patients with underlying neurological disorders, may lead to development of novel therapies and discovery of shared risk factors, as well as highlight the need for broad, whole-health clinical approaches toward treatment. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The Metaphysical Club, a gathering of intellectuals in the 1870s associated with Harvard, is widely recognized as the crucible where pragmatism, America's distinctively original philosophy, was refined and proclaimed. Louis Menand's bestseller about the group was a dramatic publishing success. However, only three actual members - Oliver Wendell Holmes Jr., Charles S. Peirce, and William James - appear in this book, alongside other thinkers such as John Dewey who were never in the Club. The Real Metaphysical Club tells the full (...) story of how this influential group shifted the course of philosophy in America. In addition to pioneering pragmatism, the group explored radical empiricism and idealism, and formulated personalism and process philosophy, equally important developments. This volume contains thirty-seven important writings dating from 1870 to 1885 by the real members of the Metaphysical Club. The first section centers on pragmatism and science; the second part collects writings of the lawyers; and the third part covers idealist and personalist philosophers. Many of these writings have never been reprinted before, and nothing like this impressive collection has ever been attempted. A general introduction provides a narrative history, and the editors' three introductions to the volume's sections vividly bring to life the intense meetings, sustained debates, and pioneering thought from the Metaphysical Club. (shrink)

Deep brain stimulation is an experimental procedure for treatment-resistant depression. Some results show promise, but blinded trials had limited success. Ethical questions center on vulnerability: especially on whether depressed patients can weigh the risks and benefits effectively, whether depression causes “desperation,” and whether media portrayals create unrealistic hopes. We interviewed 24 psychiatric inpatients with treatment-resistant depression, qualitatively analyzing their comments. Most had minimal interest in deep brain stimulators. Some might consider them if their depression worsened, if alternatives were exhausted, or (...) if the evidence were stronger. Fears focused on the surgery, adverse effects, and the novelty of the device. Patients felt the depression interfered with their ability to weigh the risks and benefits. Patients seemed highly attuned to the risks, and were skeptical that the treatment would be effective. We conclude that ethical concerns about vulnerability remain, yet patients with treatment-resistant depression were thoughtful and cautious about trying a novel therapy. (shrink)

While experience often affords important knowledge and insight that is difficult to garner through observation or testimony alone, it also has the potential to generate conflicts of interest and unrepresentative perspectives. We call this tension the paradox of experience. In this paper, we first outline appeals to experience made in debates about access to unproven medical products and disability bioethics, as examples of how experience claims arise in bioethics and some of the challenges raised by these claims. We then motivate (...) the idea that experience can be an asset by appealing to themes in feminist and moral epistemology, distinguishing between epistemic and justice-based appeals. Next, we explain the concern that experience may be a liability by appealing to empirical work on cognitive biases and theoretical work about the problem of partial representation. We conclude with preliminary recommendations for addressing the paradox and offer several questions for future discussion. (shrink)

This quantitative study of 3557 high school teachers from 44 states assesses the implications of the social studies teacher-coach. The study compares social studies teacher-coaches and non-coaches in terms of teacher demographics and school contexts, disciplines taught, and instructional preferences. Substantial differences between coaches and non-coaches were found across gender, community type, and teaching experiences. Teacher-coaches disproportionately taught general classes such as government, Economics, and Geography, while non-coaches are more likely to teach Advanced Placement courses. Finally, self-report data measuring teacher's (...) instructional preferences indicates that teacher-coaches were more likely to indicate implementation of lectures, textbooks, worksheets, and videos, while non-coaches were more likely to indicate preference for examining photographs, artifacts, or primary materials. (shrink)

ABSTRACTInitial evaluations generalise to new contexts, whereas counter-attitudinal evaluations are context-specific. Counter-attitudinal information may not change evaluations in new contexts beca...

Background: Genetic tests for schizophrenia may introduce risks and benefits. Among young adults at clinical high risk for psychosis, little is known about their concerns and how they assess potential risks. Methods: We conducted semistructured interviews with 15 young adults at clinical high risk for psychosis to ask about their concerns. Results: Participants expressed concerns about test reliability, data interpretation, stigma, psychological harm, family planning, and privacy. Participants’ responses showed some departure from the ethics literature insofar as participants were primarily (...) interested in reporting their results to people to whom they felt emotionally close, and expressed little consideration of biological closeness. Additionally, if tests showed an increased genetic risk for schizophrenia, four clinical high-risk persons felt obligated to tell an employer and another three would “maybe” tell an employer, even in the absence of clinical symptoms. Conclusions: These findings suggest opportunities for clinicians and genetic counselors to intervene with education and support. (shrink)

This paper examines heterogeneous impacts of gendered household headship and control of resources on food security in rural Tanzania. Analysis with minimal attention to heterogeneity in gender considerations indicates no differences in household food security between male and female-headed households. But with a more differentiated household headship variable and accounting for gendered differences in resource ownership, the results differ markedly. Using more gender-disaggregated variables, our results show significant differences between female-headed and male-headed households. In these results we find support for (...) the claim that gender norms in the study villages often restrict women’s access to resources, resulting in more vulnerable female-headed households. Female-headed households with no male adults present are particularly vulnerable. The study also points to specific opportunities for enhanced food security with attention to female and joint ownership of livestock. These results represent a hopeful sign that efforts to enhance female livestock ownership could be a useful strategy to address lower levels of food consumption in these Tanzanian villages. (shrink)

This article looks at Colossians 2-3:17 and John 17:13-26 as the base texts to see the commonalities between Johannine and Pauline conceptions of Theosis. First, the article looks at indwelling and participation as the methods of Theosis in the two traditions. Second, the role of mimesis is seen to be integral in these texts' concepts of Theosis. Third, the article looks at hope and glory that believers have and look forward to as indicative of their deification. The study begins by (...) defining the term Theosis and its cognate terms - deification and divinisation - properly, within an Orthodox Christian context. CONTRIBUTION: The goal is to see and detail the concept of Theosis in Pauline and Johannine literature, looking at Colossians 2-3:17 and John 17:13-26 specifically. As such, the present study will broaden the discussion the doctrine of Theosis as it appears in the Christian scriptures. (shrink)