The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Although clinical ethics consultation is a high-stakes endeavor with an increasing prominence in health care systems, progress in developing standards for quality is challenging. In this article, we describe the results of a pilot project utilizing portfolios as an evaluation tool. We found that this approach is feasible and resulted in a reasonably wide distribution of scores among the 23 submitted portfolios that we evaluated. We discuss limitations and implications of these results, and suggest that this is a significant step (...) on the pathway to an eventual certification process for clinical ethics consultants. (shrink)

Previous work suggests that relative increases in socially evaluative threat modulate the psychobiological stress response. However, few studies have compared stressors which manipulate the level of socially evaluative threat to which the participant is exposed. Here we present two studies. In the first, we assessed the integrity of an ecologically valid, laboratory stressor and its effects on acute psychobiological reactivity and ability to evoke an anticipatory response prior to participation. Specifically, we assessed whether the expectation and experience of direct social (...) evaluation evokes greater reactivity than indirect evaluation. In the second study, we sought to replicate the findings regarding acute stress reactivity whilst extending the assessment window to assess the extent to which the stressor evokes anticipatory responses. As hypothesized, greater reactivity was observed following direct social evaluation compared with indirect observation. Increases in anxiety, heart rate and blood pressure were demonstrated across both studies and the paradigm therefore provides an ecologically valid technique for the activation of psychological and cardiovascular stress responding. Additionally, anticipation of experiencing socially evaluated multitasking led to increases in anxiety, tension, and worry prior to the event itself, supporting previous suggestions that threat anticipation may prolong the activation of stress mechanisms. In the present studies we assessed whether the expectation and experience of direct social evaluation evokes greater reactivity than indirect evaluation. The findings have demonstrated that direct social evaluation of multitasking is a more potent stressor than multitasking with indirect evaluation. Furthermore, our findings indicate that the period of anticipation of stressful events may be critical to understanding the process of stress regulation, and as such we recommend extending the sampling window to allow for the investigation of these processes. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, (...) Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Clinical ethics consultation is largely outside the scope of regulation and oversight, despite its importance. For decades, the bioethics community has been unable to reach a consensus on whether there should be accountability in this work, as there is for other clinical activities that influence the care of patients. The American Society for Bioethics and Humanities, the primary society of bioethicists and scholars in the medical humanities and the organizational home for individuals who perform CEC in the United States, has (...) initiated a two‐step quality attestation process as a means to assess clinical ethics consultants and help identify individuals who are qualified to perform this role. This article describes the process. (shrink)

The World Health Organization has declared a world pandemic due to COVID-19. In response, most affected countries have enacted measures involving compulsory confinement and restrictions on free movement, which likely influence citizens' lifestyles. This study investigates changes in health risk behaviors with duration of confinement. An online cross-sectional survey served to collect data about the Spanish adult population regarding health behaviors during the first 3 weeks of confinement. A large sample of participants from all Spanish regions completed the survey. Binomial (...) logistic regressions adjusted for socioeconomic characteristics, body mass index, previous HRBs, and confinement context were conducted to investigate associations between the number of weeks confined and a set of six HRBs. When adjusted, we observed significantly lower odds of experiencing a higher number of HRBs than before confinement overall in a time-dependent fashion: OR 0.63; 95% CI: 0.49–0.81 for the second and OR 0.47; 95% CI: 0.36–0.61 for the third week of confinement. These results were equally consistent in all age and gender subgroup analyses. The present study indicates that changes toward a higher number of HRBs than before confinement, as well as the prevalence of each HRB except screen exposure, decreased during the first 3 weeks of COVID-19 confinement, and thus the Spanish adult population may have adapted to the new situational context by gradually improving their health behaviors. (shrink)

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

Huston Smith has argued that the universal source of wholeness, which he refers to as the primordial tradition, is essential to a meaningful life. Indeed embracing this tradition is, said Smith, an act of rejoining the human race. Our current forms of organized religion offer us ritualized expressions of this tradition, yet often fail to provide us with transpersonal growth; it is this transpersonal growth that reconnects us with the source of religion. This essay differentiates mainstream religion from (...) a way that we can begin to construct a physical theory of the primordial tradition–a necessary first step toward reclaiming the source of religion. (shrink)

Huston Smith has argued that the universal source of wholeness, which he refers to as the primordial tradition, is essential to a meaningful life. Indeed embracing this tradition is, said Smith, an act of rejoining the human race. Our current forms of organized religion offer us ritualized expressions of this tradition, yet often fail to provide us with transpersonal growth; it is this transpersonal growth that reconnects us with the source of religion. This essay differentiates mainstream religion from (...) a way that we can begin to construct a physical theory of the primordial tradition–a necessary first step toward reclaiming the source of religion. (shrink)

Cultural influences are pervasive throughout human behaviour, and as human–robot interactions become more common, roboticists are increasingly focusing attention on how to build robots that are culturally competent and culturally sustainable. The current treatment of culture in robotics, however, is largely limited to the definition of culture as national culture. This is problematic for three reasons: it ignores subcultures, it loses specificity and hides the nuances in cultures, and it excludes refugees and stateless persons. We propose to shift the focus (...) of cultural robotics to redefine culture as an emergent phenomenon. We make use of three research programmes in the social and cognitive sciences to justify this definition. Consequently, cultural behaviour cannot be explicitly programmed into a robot, rather, a robot must be designed with the capability to participate in the interactions that lead to the arising of cultural behaviour. In the final part of the paper, we explore which capacities and abilities are the most salient for a robot to do this. (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)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (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)

Those interested in the relationship betw een environment structure and behavior — the topic of this special issue of Adaptive Behavior — w ill find much of value in Peter Godfrey-Smith's new book, Complexity and the Function of Mind in Nature (hereafter CFMN; all page citations are to CFMN unless otherw ise indicated). The w riting is clear and concise, aptly balancing precision and breadth, and a host of relevant issues are raised and advanced. Although my comments here w (...) ill focus only on the book's fundamental conceptual framew ork for how organisms relate to their environments, I enthusiastically recommend the entire book. (shrink)

Huston Smith has argued that the universal source of wholeness, which he refers to as the primordial tradition, is essential to a meaningful life. Indeed embracing this tradition is, said Smith, an act of rejoining the human race. Our current forms of organized religion offer us ritualized expressions of this tradition, yet often fail to provide us with transpersonal growth; it is this transpersonal growth that reconnects us with the source of religion. This essay differentiates mainstream religion from (...) a way that we can begin to construct a physical theory of the primordial tradition–a necessary first step toward reclaiming the source of religion. (shrink)

The medium surrounding cells either in culture or in tissues contains a chemical mix varying with cell state. As solutes move in and out of the cytoplasmic compartment they set up characteristic signatures in the cellular boundary layers. These layers are complex physical and chemical environments the profiles of which reflect cell physiology and provide conduits for intercellular messaging. Here we review some of the most relevant characteristics of the extracellular/intercellular space. Our initial focus is primarily on cultured cells but (...) we extend our consideration to the far more complex environment of tissues, and discuss how chemical signatures in the boundary layer can or may affect cell function. Critical to the entire essay are the methods used, or being developed, to monitor chemical profiles in the boundary layers. We review recent developments in ultramicro electrochemical sensors and tailored optical reporters suitable for the task in hand. (shrink)

Written by the 11th-century Spanish Arab, Abh Muhammad ibn MucnOn Twilight and the Rising of Cloudsdh's value of around 52 miles remained standard until the 17th century, when it was revised sharply downward in consideration of atmospheric refraction and barometric studies. The treatise itself survives in a single Hebrew exemplar, 25 Latin exemplars, and an Italian exemplar derived from the Latin. At the heart of this present study is a critical text based on a fullscale comparative transcription of 22 of (...) the Latin manuscripts, ranging in date from the 13th to the 17th century. (shrink)

“Although up to now the [visual] image has been [understood as] a construct of reason,” Kepler observes in the fifth chapter of his Ad Vitellionem Paralipomena, “henceforth the [visible] representations of objects should be considered as paintings [ picturae ] that are actual[ly projected] on paper or some other screen.” While not intended as a historical generalization, this claim nonetheless reflects historical reality. Virtually all visual theorists before Kepler did, in fact, conceive of optical images as subjective, not objective constructs (...) – or, to put it in modern terms, as virtual rather than real entities. By current lights, of course, the distinction between virtual and real images is both obvious and common-place: whereas the latter can be physically projected upon a screen, the former cannot. (shrink)

A. Mark Smith - Seeing and Being Seen in the Later Medieval World: Optics, Theology, and Religious Life - Journal of the History of Philosophy 44:3 Journal of the History of Philosophy 44.3 473-474 Dallas G. Denery, II. Seeing and Being Seen in the Later Medieval World: Optics, Theology, and Religious Life. Cambridge Studies in Medieval Life and Thought , 63. Cambridge-New York: Cambridge University Press, 2005. Pp. x + 202. Cloth, $75.00. Among the metaphors we live by (...) , visual metaphors figure prominently in our common discourse about cognition. We are well aware, of course, that in claiming to "see" meanings or "view" ideas in certain lights, we are speaking figuratively. Yet the analogy between thinking and seeing is more than a linguistic artifact. Until the seventeenth century,.. (shrink)

In the first section I outline the theory of abstraction, discussing first its con- ceptual basis, then its psychological-epistemological basis, and last its causal basis. My purpose throughout is to show how these bases, and thus the theory itself, were not only paramountly Aristotelian, but also eminently sensible. In the second section I draw the perspectivist account of vision within the bounds of the theory of abstraction and show stage by stage how that account unfolds coherently within those bounds. This (...) procedure should make clear that what the perspecti- vists actually offered was less a scientific theory of light or vision than a scientifi- cally justified world view. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

One problem facing Hockney and Falco is the lack of evidence among optical sources to support their claim that artists used image-projection by the early 1400s. After all, if quattrocento artists knew about image-projection, they must have learned about it from experts in the field, and no one was more expert at the time than Perspectivist opticians. As I argue in this paper, however, Perspectivist reflection-analysis posed certain theoretical and conceptual constraints that would have prevented Perspectivist opticians from recognizing, much (...) less understanding, image-projection. Their silence on this matter is therefore not evidence against the Hockney-Falco thesis. (shrink)

In the fifth book of his De aspectibus, the medieval Latin version of Ibn al-Haythamb al-Manir, Alhacen undertakes to determine precisely where a given ray of light will reflect to a given center of sight from a variety of convex and concave mirrors based on circular sections. As applied specifically to convex and concave spherical mirrors, this problem exercised several seventeenth-century thinkers, Christiaan Huygens foremost among them, and in that context it soon became known as Alhazens solution (or solutions) of (...) this problem is deficient in comparison to that of Huygens and later mathematicians. It is my purpose in this paper to show by reconstruction that in fact, far from deficient in any absolute sense, Alhacen’s approach to this problem was remarkably ingenious and elegant in its conceptual simplicity. (shrink)

From the late thirteenth to the early seventeenth century, the process of visual imaging was understood in the Latin West as an essentially subjective act initiated by the eye and completed by the brain. The crystalline lens took center stage in this act, its role determined by its peculiar physical and sensitive capacities. As a physical body, on the one hand, it was disposed to accept the physical impressions of light and color radiating to it from external objects. As a (...) sensitive body, on the other hand, it was enabled by the visual spirit flowing to it from the brain to feel those impressions visually. Acting as a sentient selector of visual information, the lens transformed the brute physical impressions of light and color into visual impressions. These, in turn, gave rise to perceptual “depictions” that were passed back along the stream of visual spirits to the brain. Known in Scholastic parlance as “intentional species,” these depictions served as virtual representations of their generating objects. As such, they provided the wherewithal not only for perception, but also for conception and cognition. (shrink)

That the medieval Latin version of Ibn al-Haytham's Kitāb al-Manā[zdotu]ir was translated into Italian in the fourteenth century has been known for well over a century. Recent studies have shown that this translation, which is contained in Vat. Lat. 4595, was instrumental in the composition of Lorenzo Ghiberti's Commentario terzo on art. Some eight years ago, the author of the present article tentatively identified the actual manuscript-source of that translation as MS Royal 12.G.7, which is currently held in the British (...) Library. This study establishes beyond reasonable doubt that his tentative identification was correct: MS Royal 12.G.7 is indeed the Latin source for the Italian translation in Vat. Lat. 4595. (shrink)

The 1920s and 30s were key decades for the history of American social science. The success of such quantitative disciplines as economics and psychology during World War I forced social scientists to reexamine their methods and practices and to consider recasting their field as a more objective science separated from its historical foundation in social reform. The debate that ensued, fiercely conducted in books, articles, correspondence, and even presidential addresses, made its way into every aspect of social science thought of (...) the period and is the subject of this book. Mark C. Smith first provides a historical overview of the controversy over the nature and future of the social sciences in early twentieth-century America and, then through a series of intellectual biographies, offers an intensive study of the work and lives of major figures who participated in this debate. Using an extensive range of materials, from published sources to manuscript collections, Smith examines "objectivists"--economist Wesley Mitchell and political scientist Charles Merriam--and the more "purposive thinkers"--historian Charles Beard, sociologist Robert Lynd, and political scientist and neo-Freudian Harold Lasswell. He shows how the debate over objectivity and social purpose was central to their professional and personal lives as well as to an understanding of American social science between the two world wars. These biographies bring to vivid life a contentious moment in American intellectual history and reveal its significance in the shaping of social science in this country. (shrink)

Since the 1960s, many artists have incorporated ecological concerns into their work, an endeavor that has required new strategies in art-making. To explore recent American manifestations of these interests, the David and Alfred Smart Museum commissioned new projects from artists Mark Dion, Peter Fend, and Dan Peterman, each focusing on interrelationships between particular organisms—human beings-and a specific group of sites—a museum building, a river landscape, and a university campus. The results, exhibited at the Smart Museum during the summer of (...) 2000, evoke the varied scales, from the microscopic to the global, at which human actions affect the environment. This catalog documents each of the artists' projects through an array of images and words: Smart Museum Associate Curator Stephanie Smith provides an introduction and brief overviews of the three projects, each of the artists contribute statements, and photographers Susan Anderson and Tom van Eynde document—in over 100 images—the processes and projects that comprise the exhibition. (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review (...) the paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

Plato's Republic has proven to be of astounding influence and importance. Justly celebrated as Plato's central text, it brings together all of his prior works, unifying them into a comprehensive vision that is at once theological, philosophical, political and moral. The essays in this volume provide a picture of the most interesting aspects of the Republic, and address questions that continue to puzzle and provoke, such as: Does Plato succeed in his argument that the life of justice is the most (...) attractive one? Is his tripartite analysis of the soul coherent and plausible? Why does Plato seem to have to force his philosopher-guardians to rule when they know this is something that they ought to do? What is the point of the strange and complicated closing Myth of Er? This volume will be essential to those looking for thoughtful and detailed excursions into the problems posed by Plato's text and ideas. (shrink)