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)

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)

This paper consists of commentaries about and the reprint of an autobiographical essay authored by Italian medium Eusapia Palladino and published in 1910. The details of the essay are discussed in terms of the writings of other individuals about the life and performances of the medium. The essay conveys a view of Palladino as a person who has suffered much in life and has a mission to help scientific research into mediumship. Typical of the positive emphasis in autobiographies in general, (...) the medium did not discuss negative aspects of her performances. Due to the fact that the essay appeared during Palladino's visit to New York City in which many authors branded her as a fraud, it may be speculated that the purpose of this autobiography was to elicit sympathy from the American public. While some of the statements that Palladino made about phenomena are consistent with the statements of other authors who have written about her, there are several statements that show alternate or incomplete versions of particular events in her life. The differences suggests that Palladino's essay and other discussions about the medium's life are not reliable when it comes to specific details and to biographical accuracy. (shrink)

Both unipolar and bipolar depression have been linked with impairments in executive functioning. In particular, mood symptom severity is associated with differences in common EF, a latent measure of general EF abilities. The relationship between mood disorders and EF is particularly salient in adolescence and young adulthood when the ongoing development of EF intersects with a higher risk of mood disorder onset. However, it remains unclear if common EF impairments have associations with specific symptom dimensions of mood pathology such as (...) blunted positive affect, mood instability, or physiological arousal, or if differences in common EF more broadly relate to what is shared across various symptom domains, such as general negative affect or distress. To address this question, bifactor models can be applied to simultaneously examine the shared and unique contributions of particular mood symptom dimensions. However, no studies to our knowledge have examined bifactor models of mood symptoms in relation to measures of common EF. This study examined associations between common EF and general vs. specific symptom dimensions using structural equation modeling in adolescents and young adults with varying severity of mood symptoms. A General Depression factor capturing shared variance across symptoms statistically predicted lower Common EF. Additionally, a factor specific to physiological arousal was associated with lower Common EF. Anhedonia-specific and Mania-specific factors were not significantly related to Common EF. Altogether, these results indicate that deficits in common EF are driven by, or reflect, general features of mood pathology that are shared across symptom dimensions but are also specifically associated with physiological arousal. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:A Search for Unity in Diversity: The "Permanent Hegelian Deposit" in the Philosophy of John DeweyFrank X. RyanJames A. Good A Search for Unity in Diversity: The "Permanent Hegelian Deposit" in the Philosophy of John Dewey Lanham, MD: Lexington Books, 2006. xxx + 288 pp.Among the revelations of Dewey's rare moments of autobiographical reflection, none has generated more curiosity and investigative zeal than his 1930 claim to have (...) "drifted" from Hegel in the decade following his move from Michigan to Chicago in 1894. Beginning with Morton White's Origin of Dewey's Instrumentalism (1943), biographers have divided on the question of whether Dewey's later philosophy was more strongly influenced by William James's experimental psychology or F. J. E. Woodbridge's Aristotelian naturalism. Despite their differences, both approaches are essentially empirical and realistic, and thus the majority of sympathetic commentators have agreed that Dewey was a realist, albeit of a decidedly unorthodox stripe. For them the notion that Dewey retained any significant commitment to idealism, given its virtual eradication at the beginning of the twentieth century, would damage his influence and legacy.It has been something of a puzzle, accordingly, that in the same autobiographical essay Dewey alludes to a "permanent Hegelian deposit." For years Richard Rorty has claimed this differentiates a "good" Dewey committed to "social flourishing" from a "bad" Dewey prone to metaphysical dalliance. But the first systematic inquiry into Dewey's enduring Hegelianism is John R. Shook's Dewey's Empirical Theory of Knowledge and Reality (2000). Shook argues convincingly that Dewey never abandoned idealism, but rather transformed it into an experimental naturalism by doing away with both "mind-stuff" and equally noxious "things-in-themselves." In many ways James Good's A Search for Unity in Diversity is a bookend to Shook's project, though Good further differentiates Anglo-American Neo-Hegelianism from Hegel himself. According to Good, Dewey endorsed a Humanistic/Historicist interpretation of Hegel rooted in the reciprocal engagement of individuals and societies, rather than the supernatural and architectonic absolute championed by Neo-Hegelians such as T. H. Green, and F. H. Bradley. With [End Page 216] top-notch scholarship and scrupulous attention to detail, A Search for Unity in Diversity is both an excellent intellectual biography and a penetrating plea for a radical reinterpretation of Dewey's contribution to philosophy. I'll briefly sketch the historical account before addressing the more controversial claims about the "permanent Hegelian deposit."Even readers familiar with the half-dozen book-length treatments of Dewey's development will find this account refreshing and informative. Good's professional credentials as a historian shine as he recreates the rough and bustling Burlington of Dewey's youth. In the 1870s, German idealism was considered the epitome of political liberalism and progressive education, and Dewey's journey toward the "inclusive philosophical idea" of the social began in an environment swirling with the crosscurrents of Kant, Hegel, and Schelling. At the White Street Congregational Church, Lewis Barstow preached a liberal orthodoxy that was essentially "man-building" (102), and Good presents a convincing case for the likelihood that even in boyhood Dewey never viewed God as an aloof law-giver or cosmic architect, but as a process unifying the individual and the social within a natural world of unlimited potential. At the University of Vermont Dewey encountered a struggling rural college transformed into the first bastion of American transcendentalism by James Marsh, who inspired a "Burlington philosophy" that rejected atomistic empiricism for a holistic integrity of knowing and doing, facts and values, and pure and practical reasons (57–59).In noting the influence of the "St. Louis Hegelians" upon Dewey, most biographers have focused on W. T. Harris, the prominent founder of The Journal of Speculative Philosophy who published Dewey's earliest submissions and offered encouragement that led to his pursuit of graduate work at Johns Hopkins. Good augments this familiar tale with fascinating depictions of equally influential yet lesser-known Hegelians such as H. C. Brokmeyer, Denton Snider, and Thomas Davidson. At a time when European Hegelianism was polarized between, on the one hand, reactionary apologists for traditional Christianity and Prussian militarism and, on the other, radical... (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:A Search for Unity in Diversity: The "Permanent Hegelian Deposit" in the Philosophy of John DeweyFrank X. RyanJames A. Good A Search for Unity in Diversity: The "Permanent Hegelian Deposit" in the Philosophy of John Dewey Lanham, MD: Lexington Books, 2006. xxx + 288 pp.Among the revelations of Dewey's rare moments of autobiographical reflection, none has generated more curiosity and investigative zeal than his 1930 claim to have (...) "drifted" from Hegel in the decade following his move from Michigan to Chicago in 1894. Beginning with Morton White's Origin of Dewey's Instrumentalism (1943), biographers have divided on the question of whether Dewey's later philosophy was more strongly influenced by William James's experimental psychology or F. J. E. Woodbridge's Aristotelian naturalism. Despite their differences, both approaches are essentially empirical and realistic, and thus the majority of sympathetic commentators have agreed that Dewey was a realist, albeit of a decidedly unorthodox stripe. For them the notion that Dewey retained any significant commitment to idealism, given its virtual eradication at the beginning of the twentieth century, would damage his influence and legacy.It has been something of a puzzle, accordingly, that in the same autobiographical essay Dewey alludes to a "permanent Hegelian deposit." For years Richard Rorty has claimed this differentiates a "good" Dewey committed to "social flourishing" from a "bad" Dewey prone to metaphysical dalliance. But the first systematic inquiry into Dewey's enduring Hegelianism is John R. Shook's Dewey's Empirical Theory of Knowledge and Reality (2000). Shook argues convincingly that Dewey never abandoned idealism, but rather transformed it into an experimental naturalism by doing away with both "mind-stuff" and equally noxious "things-in-themselves." In many ways James Good's A Search for Unity in Diversity is a bookend to Shook's project, though Good further differentiates Anglo-American Neo-Hegelianism from Hegel himself. According to Good, Dewey endorsed a Humanistic/Historicist interpretation of Hegel rooted in the reciprocal engagement of individuals and societies, rather than the supernatural and architectonic absolute championed by Neo-Hegelians such as T. H. Green, and F. H. Bradley. With [End Page 216] top-notch scholarship and scrupulous attention to detail, A Search for Unity in Diversity is both an excellent intellectual biography and a penetrating plea for a radical reinterpretation of Dewey's contribution to philosophy. I'll briefly sketch the historical account before addressing the more controversial claims about the "permanent Hegelian deposit."Even readers familiar with the half-dozen book-length treatments of Dewey's development will find this account refreshing and informative. Good's professional credentials as a historian shine as he recreates the rough and bustling Burlington of Dewey's youth. In the 1870s, German idealism was considered the epitome of political liberalism and progressive education, and Dewey's journey toward the "inclusive philosophical idea" of the social began in an environment swirling with the crosscurrents of Kant, Hegel, and Schelling. At the White Street Congregational Church, Lewis Barstow preached a liberal orthodoxy that was essentially "man-building" (102), and Good presents a convincing case for the likelihood that even in boyhood Dewey never viewed God as an aloof law-giver or cosmic architect, but as a process unifying the individual and the social within a natural world of unlimited potential. At the University of Vermont Dewey encountered a struggling rural college transformed into the first bastion of American transcendentalism by James Marsh, who inspired a "Burlington philosophy" that rejected atomistic empiricism for a holistic integrity of knowing and doing, facts and values, and pure and practical reasons (57–59).In noting the influence of the "St. Louis Hegelians" upon Dewey, most biographers have focused on W. T. Harris, the prominent founder of The Journal of Speculative Philosophy who published Dewey's earliest submissions and offered encouragement that led to his pursuit of graduate work at Johns Hopkins. Good augments this familiar tale with fascinating depictions of equally influential yet lesser-known Hegelians such as H. C. Brokmeyer, Denton Snider, and Thomas Davidson. At a time when European Hegelianism was polarized between, on the one hand, reactionary apologists for traditional Christianity and Prussian militarism and, on the other, radical... (shrink)

In describing the flawless regularity of developmental processes and the correlation between changes at certain genetic loci and changes in morphology, biologists frequently employ two metaphors: that genes ‘control’ development, and that genomes embody ‘programs’ for development. Although these metaphors have an admirable sharpness and punch, they lead, when taken literally, to highly distorted pictures of developmental processes. A more balanced, and useful, view of the role of genes in development is that they act as suppliers of the material needs (...) of development and, in some instances, as context‐dependent catalysts of cellular changes, rather than as ‘controllers’ of developmental progress and direction. The consequences of adopting this alternative view of development are discussed. (shrink)

How should clinical ethicists be trained? Scholars have stated that clinical ethics fellowships create well-trained, competent ethicists. While this appears intuitive, few features of fellowship programs have been publicly discussed, let alone debated. In this paper, we examine how fellowships can foster effective mentoring relationships. These relationships provide the foundation for the fellow’s transition from novice to competent professional. In this essay, we begin by discussing our pedagogical commitments. Next, we describe the structures our program has created to assist our (...) fellows in becoming competent ethicists. We then outline the kinds of knowledge, skills, and professional attributes mentors should possess. Following this, we focus on the knowledge, skills, and professional attributes that fellows develop as they co-create effective mentoring relationships. We will not prescribe a single approach to fellowship training; instead, our perspective will, we hope, become a catalyst for further conversation on training and mentoring clinical ethics fellows. (shrink)

This book is intended for the use of the candid student, devised as a monitory preparation for deeper study of the philosophy of Spinoza. By its means it is hoped that the student may avoid the chief pitfalls of Spinoza-interpretation, and be carried past many of the difficulties encountered by the modern mind in the study of his writings. To this end perhaps the greatest hindrance to be met by the beginner is the ‘popular' exposition that attempts to expound the (...) thought of one age in terms of the favoured categories of another. By providing the necessary safeguards against misinterpretations arising from such causes, the author has sought to awaken interest in the closely knit fabric of Spinoza's doctrine of man and nature and God, and its practical import - and thus to revivify a specimen too long deprived of its native air. (shrink)

Purpose: Understanding the place of Ernst von Glasersfeld's Radical Constructivism (RC), and some of its implications, in the development of epistemology. Design: Characterization of two main options for the content of "knowledge" (without and with belief in mind-independent structures), sketch of their history in occidental thought; comparison of their properties concerning subjectivity, objectivity, second-order cybernetics, reliability of mental tools, and the needs and mechanisms for certainty and overall structures. Findings: Awareness that we structure mental working tools can, as RC suggests, (...) replace belief in mind-independent reality, and this change dissolves the conceptual problem of metaphysics-ontology, but also eliminates the certainty expected from it, which raises the possibility of relativism. Working-concepts cannot be deconstructed because they imply no ontological claims. Subject(s) are necessarily included in all knowledge (which does not mean solipsism): because subjective experience encompasses all mental tools, including those of objectivity and mathematics, while in contrast the subject itself cannot become an objective system. Practical reliability of mental tools differs from subjective certainty, which requires an ontological leap of faith to positive beliefs: for specific tools including automata, and for positive holistic structures. However, in agreement with the constructivist view, holistic views can instead have an unstructured center, with reliability = viability, which prevents relativism. In sum, belief in mid-independent reality is needed for certainty if desired; for all other purposes constructivism is more helpful. Implications: The change in view suggested by von Glasersfeld's work is of relevance for a number of fields of study with conceptual problems (such as the mind-brain relation). However, due to their generality, the implications will need evaluation in specific instances. The question of certainty needs attention for practical reasons. (shrink)

A trait is robust to a genetic or environmental variable if its variation is weakly correlated with variation in that variable. The source of robustness lies in the fact that the developmental processes that give rise to complex traits are nonlinear. A consequence of this nonlinearity is that not all genes are equally correlated with the trait whose ontogeny they control. Here we explore how developmental mechanisms determine and alter the correlation structure between genes and the traits that they control. (...) A formula is developed by which the correlation of a gene or environmental variable with a trait can be calculated if the mechanism that gives rise to the trait is known. The nature of robustness and the ways in which robustness can evolve are discussed in the context of the problems that arise in the analysis of inherently nonlinear systems. BioEssays 24:553–563, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Individuals with major depressive disorder (MDD) often ruminate about past experiences, especially those with negative content. These repetitive thoughts may interfere with cognitive processes related to attention and conflict monitoring. However, the temporal nature of these processes as reflected in event-related potentials (ERPs) has not been well-described. We examined behavioral and ERP indices of conflict monitoring during a modified flanker task and the allocation of attention during an attentional blink (AB) task in 33 individuals with MDD and 36 healthy controls, (...) and whether their behavioral performance and ERPs varied with level of rumination. N2 amplitude elicited by the flanker task was significantly reduced in participants with MDD compared to healthy controls. Level of self-reported rumination was also correlated with N2 amplitude. In contrast, P3 amplitude during the AB task was not significantly different between groups, nor was it correlated with rumination. No significant differences were found in behavioral task performance measures between groups or by rumination levels. These findings suggest that rumination in MDD is associated with select deficits in cognitive control, particularly related to conflict monitoring. (shrink)

The subject on which I am to address you this evening is one which, though it is of fundamental importance both for philosophy and for practice, cannot but present the gravest difficulties for such treatment as falls within the limits of this occasion. Philosophical problems are always difficult, but those of ultimate metaphysics are in this respect egregious. For the simplifications that are open to the scientific phenomenologist who can rest content with a spatiotemporal world, or to the analyst who (...) concentrates on the objective content with which the human understanding most conspicuously concerns itself, are not open to the metaphysician. He must meet the full complexity of things: not limiting himself to their appearances as objects within human experience, nor to a reflective analysis of their objective content, but taking them as they must be in themselves in order that they may appear as they empirically and reflectively do appear for the special cognitive faculties of man. I ask, therefore, for your patience and attention as I try first of all to lead you into, and then, as I hope, out of, the metaphysical labyrinth. For what I have to describe is something of a metaphysical adventure, or, if you like, a metaphysical ghoststory, in which the ghosts assume such reality as to make the solid things “give up the ghost”—which is just as it should be in a good ghost-story! (shrink)