The chief sources of groundwater contamination on farms come from point sources and diffuse sources. Possible point sources are feedlots, poorly-sited manure piles, septic sewage-treatment systems—all of which can release nitrate, phosphates and bacteria— and sites of chemical spills. Diffuse sources are typified by excess fertilizer leaching from a number of arable fields. The basis of quality standards for drinking-water is discussed in relation to common contaminants present on farms. Samples of drinking-water were collected in 1991–1992 from wells on about (...) 1,200 farms in order to study the quality of rural groundwater in Ontario. Analysis showed that approximately one third of wells were contaminated with bacteria, 14% were contaminated with nitrate, two wells were contaminated with pesticide, but 40% were considered unsafe because of the presence of at least one contaminant. These values were similar to those reported for similar regions in the U.S. There was no significant effect of agricultural practice on the proportion of contaminated samples. One response of Ontario's farmers to information on water quality has been to initiate their own program, the Environmental Farm Plan, which has 23 modules by which the risk of environmental contamination can be assessed. Government policies for agriculture can be expected to influence farming practices. However, the literature suggests that the consequences of policies aimed at reducing environmental contamination are poorly understood, not least because the instruments used for implementation can have widely differing impacts. The need for discussions on the ethics surrounding the relationship between food producers and consumers with regard to environmental contamination is identified. (shrink)

This collection of essays on themes in the work of John Locke , George Berkeley , and David Hume , provides a deepened understanding of major issues raised in the Empiricist tradition. In exploring their shared belief in the experiential nature of mental constructs, The Empiricists illuminates the different methodologies of these great Enlightenment philosophers and introduces students to important metaphysical and epistemological issues including the theory of ideas, personal identity, and skepticism. It will be especially useful in courses devoted (...) to the history of modern philosophy. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Embryogenesis requires the precise movement and reorganization of many cell and tissue types. Presumably, cell surface receptors allow cells to interact selectively with adjacent cells and with the extracellular environment, as well as initiate differentiative events by transducing appropriate signals across the plasma membrane. One cell surface component that serves as a receptor during a variety of cellular interactions is β1,4‐galactosyltransferase. Cell surface galactosyltransferase participates in diverse cellular interactions by binding its specific glycoconjugate substrate on adjacent cell surfaces or in (...) the extracellular matrix. Biochemical, immunological, and molecular probes are being used to better define cell surface galactosyl‐transferase functional in cellular interactions during fertilization, intercellular adhesion, cell migration, and growth control. (shrink)

Co-authored letter to the APA to take a lead role in the recognition of teaching in the classroom, based on the participation in an interdisciplinary Conference on the Role of Advocacy in the Classroom back in 1995. At the time of this writing, the late Myles Brand was the President of Indiana University and a member of the IU Department of Philosophy.

XLRI, in association with a few Tata Group companies, established the XLRI-JRD Tata Foundation in Business Ethics in 1991 to mark their long-standing commitment and contribution to business ethics in India. The foundation seeks to address this by publicly affirming the urgent need for ethics in business and the need to bring about a conducive culture in which it can thrive.

We investigated how people interpret conditionals and how stable their interpretation is over a long series of trials. Participants were shown the colored patterns on each side of a six-sided die, and were asked how sure they were that a conditional holds of the side landing upwards when the die is randomly thrown. Participants were presented with 71 trials consisting of all combinations of binary dimensions of shape (e.g., circles and squares) and color (e.g., blue and red) painted onto the (...) sides of each die. In two experiments (N1 = 66, N2 = 65), the conditional event was the dominant interpretation, followed by conjunction, and material conditional responses were negligible. In both experiments, the percentage of participants giving a conditional event response increased from around 40% at the beginning of the task to nearly 80% at the end, with most participants shifting from a conjunction interpretation. The shift was moderated by the order of shape and color in each conditional’s antecedent and consequent: participants were more likely to shift if the antecedent referred to a color. In Experiment 2 we collected response times: conditional event interpretations took longer to process than conjunction interpretations (mean difference 500 ms). We discuss implications of our results for mental models theory and probabilistic theories of reasoning. (shrink)

The issue of directed donation of organs from deceased donors for transplantation has recently risen to the fore, given greater significance by the relatively stagnant rate of deceased donor donation in the UK. Although its status and legitimacy is explicitly recognized across the USA, elsewhere a more cautious, if not entirely negative, stance has been taken. In England, Wales and Northern Ireland, the Human Tissue Act 2004, and in Scotland the Human Tissue (Scotland) Act 2006, are both silent in this (...) regard. Although so-called conditional donation, donation to (or perhaps withheld from) a specific class, has been outlawed as a product of guidance issued by the Secretary of State for Health issued in the wake of the controversial incident occurring in the North of England in 1998, its intended application to ‘directed’ donation is less certain. Directed and conditional donations challenge the traditional construct of altruistic donation and impartial (equitable) allocation in a very immediate and striking fashion. They implicitly raise important questions as to whether the body or parts of the body are capable of being owned, and by whom. This paper attempts to explore the notion of donor ownership of body parts and its implications for both directed and conditional donation. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Primordial emotions are the subjective element of the instincts which are the genetically programmed behaviour patterns which contrive homeostasis. They include thirst, hunger for air, hunger for food, pain and hunger for specific minerals etc.There are two constituents of a primordial emotion—the specific sensation which when severe may be imperious, and the compelling intention for gratification by a consummatory act. They may dominate the stream of consciousness, and can have plenipotentiary power over behaviour.It is hypothesized that early in animal evolution (...) complex reflex mechanisms in the basal brain subserving homeostatic responses, in concert with elements of the reticular activating system subserving arousal, melded functionally with regions embodied in the progressive rostral development of the telencephalon. This included the emergent limbic and paralimbic areas, and the insula. This phylogenetically ancient organization subserved the origin of consciousness as the primordial emotion, which signalled that the organisms existence was immediately threatened. Neuroimaging confirms major activations in regions of the basal brain during primordial emotions in humans. The behaviour of decorticate humans and animals is discussed in relation to the possible existence of primitive awareness.Neuroimaging of the primordial emotions reveals that rapid gratification of intention by a consummatory act such as ingestion causes precipitate decline of both the initiating sensation and the intention. There is contemporaneous rapid disappearance of particular regions of brain activation which suggests they may be part of the jointly sufficient and severally necessary activations and deactivations which correlate with consciousness [Crick, F. & Koch, C. . A framework for consciousness. NatureNeuroscience,6, 119–126]. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

An important contribution to the foundations of probability theory, statistics and statistical physics has been made by E. T. Jaynes. The recent publication of his collected works provides an appropriate opportunity to attempt an assessment of this contribution. * Review of E. T. JAYNES (1983): Papers on Probability, Statistics and Statistical Physics. Edited by R. D. Rosenkrantz. D. Reidel Publishing Company. US $49.50. Pp. xxiv + 434. We are grateful to Harvey Brown, Kenneth Denbigh, Udi Makov and Oliver Penrose for (...) their valuable criticisms of this paper. (shrink)

Health care workers with needlestick exposures to patients' blood often request a test of the patient for evidence of infection with human immunodeficiency virus. If the patient refuses the test, a conflict develops between the interests of the health care worker and those of the patient. Traditional approaches to this dilemma attempt to balance the rights or utilities of abstract patients and health care workers. While these approaches have the advantage of offering clear guidelines in advance of conflict, the interests (...) of the actual participants may differ from those used to create the guidelines. In nonmedical settings, conflicts are often resolved efficiently through negotiation and monetary exchanges. Although negotiated monetary settlements between health care workers and patients may be an impractical way to resolve medical conflicts, models developed from these perspectives provide insights into the individual interests of physicians and patients. Changing existing rules about medical record documentation, or increasing the penalties for the misuse of medical information, may satisfy the interests on both sides of the conflict and so represent integrative bargaining solutions. Even so, as the relationship between health care workers and their patients evolves, more explicit strategies for negotiation may become a reasonable solution to the problem of conflict. (shrink)

Advances in technology are bringing greater insight into the mind, raising a host of privacy concerns. However, the basic psychological mechanisms underlying the perception of privacy violations are poorly understood. Here, we explore the relation between the perception of privacy violations and access to information related to one’s “self.” In two studies using demographically diverse samples, we find that privacy violations resulting from various monitoring technologies are mediated by the extent to which the monitoring is thought to provide access to (...) self-relevant information, and generally neuromonitoring did not rate among the more invasive monitoring types. However, brain monitoring was judged to be more of a privacy violation when described as providing access to self-relevant information than when no such access was possible, and control participants did not judge the invasiveness of neuromonitoring any differently than those told it provided no access to self-relevant information. (shrink)

Objectives: To discover the current state of opinion and practice among doctors in Victoria, Australia, regarding end-of-life decisions and the legalisation of voluntary euthanasia. Longitudinal comparison with similar 1987 and 1993 studies.Design and participants: Cross-sectional postal survey of doctors in Victoria.Results: 53% of doctors in Victoria support the legalisation of voluntary euthanasia. Of doctors who have experienced requests from patients to hasten death, 35% have administered drugs with the intention of hastening death. There is substantial disagreement among doctors concerning the (...) definition of euthanasia.Conclusions: Disagreement among doctors concerning the meaning of the term euthanasia may contribute to misunderstanding in the debate over voluntary euthanasia. Among doctors in Victoria, support for the legalisation of voluntary euthanasia appears to have weakened slightly over the past 17 years. Opinion on this issue is sharply polarised. (shrink)

We praise Arbib et al.'s Neural organization for its support of the integration of different levels of analysis, while noting that it does not always achieve what it advocates. We extend this approach into an area of neuropsychological activity in need of the structure offered by Organization at the intersection of the conflated fields of executive function and frontal lobe function.