Results for 'Peter D���Eustachio'

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  1. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    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 (...)
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  2. The Representation of Protein Complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...)
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  3. Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...)
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  4. Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    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.
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  5.  16
    The Small Nuclear GTPase Ran: How Much Does It Run?Mark G. Rush, George Drivas & Peter D'eustachio - 1996 - Bioessays 18 (2):103-112.
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  6. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    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 (...)
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  7.  23
    Thomas, Peter D., The Gramscian Moment. Philosophy, Hegemony and Marxism Leiden: Brill, 2009.Peter Mayo - 2013 - Educational Philosophy and Theory 45 (7):804-810.
  8.  7
    Peter D. Mosses, Action Semantics[REVIEW]Varol Akman - 1993 - Journal of Logic and Computation 3 (4):442-444.
    This is a review of Action Semantics, by Peter D. Mosses, Cambridge Tracts in Theoretical Computer Science 26, Cambridge University Press, 1992.
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  9.  1
    Book Reviews : Fairness and Competence in Citizen Participation: Evaluating Methods of Environmental Discourse, Edited by Ortwin Renn, Thomas Webler, and Peter Wiedemenn. Dordrecht, The Netherlands: Kluwer Academic Publishers, 1995, 381 + Xix Pp. £60.00. [REVIEW]Peter D. Bailey - 1997 - Science, Technology and Human Values 22 (3):386-388.
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  10.  10
    Oedipus the King and Antigone.Peter D. Arnott (ed.) - 1960 - Wiley-Blackwell.
    Translated and edited by Peter D. Arnott, this classic and highly popular edition contains two essential plays in the development of Greek tragedy-_Oedipus the King and Antigone_-for performance and study. The editor's introduction contains a brief biography of the playwright and a description of Greek theater. Also included are a list of principal dates in the life of Sophocles and a bibliography.
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  11.  17
    Mary C. Flannery and Katie L. Walter, Eds., The Culture of Inquisition in Medieval England. Cambridge, UK, and Rochester, NY: D. S. Brewer, 2013. Pp. Viii, 194; 1 Black-and-White Figure. $99. ISBN: 978-1-84384-336-8. [REVIEW]Peter D. Clarke - 2015 - Speculum 90 (2):535-537.
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  12.  10
    II. The Theory of E. D. Hirsch.Peter D. Juhl - 1986 - In Interpretation: An Essay in the Philosophy of Literary Criticism. Princeton University Press. pp. 16-44.
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  13. The Evil of the Isolated Intellect: Hilda in "The Marble Faun".Peter D. Zivkovic - 1962 - Pacific Philosophical Quarterly 43 (2):202.
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  14.  41
    A Historical Perspective on the Future of the Car: William J. Mitchell, Christopher E. Borroni-Bird, and Lawrence D. Burns: Reinventing the Automobile: Personal Urban Mobility for the 21st Century. Cambridge, MA: MIT Press, 2010, 240 Pp, $21.95 HB.Peter D. Norton - 2011 - Metascience 20 (3):593-595.
    A historical perspective on the future of the car Content Type Journal Article Pages 1-3 DOI 10.1007/s11016-010-9479-z Authors Peter D. Norton, Department of Science, Technology and Society, University of Virginia, Charlottesville, VA 22904-4744, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.
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  15.  24
    Valuing Intelligence: Buddhist Reflection on the Attention Economy and Artificial Intelligence.Peter D. Hershock - unknown
    This talk by Dr. Peter D. Hershock makes use of Buddhist conceptual resources to assess how the emerging global attention economy and the confluence of big data, machine learning, and artificial intelligence are reshaping the human experience. Like the Copernican revolution, which de-centered humanity in the cosmos, the intelligence revolution is dissolving once-foundational certainties and opening new realms of opportunity. The results are almost sure to be mixed. Smart cities will be more efficient and more livable; smart health care (...)
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  16. The Experiential Therapist: Phenomenology, Trauma-Informed Care, and Mental Health.Peter D. Ladd - 2020 - Lexington Books.
    The Experiential Therapist steps outside of the medical model to explore alternative ways of thinking about mental health disorders. Peter D. Ladd argues that successful treatment results from an informed understanding of a patient’s experience, not an ability to name and categorize difficult experiences as classical disorders.
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  17.  11
    Climate and Compassion: Buddhist Contribution to an Ethics of Intergenerational Justice.Peter D. Hershock - unknown
    Over the last century, the world's urban population increased from 224 million to over 3.5 billion, and advances in manufacturing, transportation, and communication technologies brought virtually limitless lifestyle and identity options, as well as the greatest inequalities of wealth, risk, and opportunity in history. Yet, as momentous as these changes are, they are dwarfed by the fact that human activity is now affecting planetary processes like climate. Justice concerns about future generations are no longer academic curiosities; they are global ethical (...)
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  18. Public Zen, Personal Zen: A Buddhist Introduction.Peter D. Hershock - 2014 - Rowman & Littlefield Publishers.
    This deeply informed book introduces the basic teachings and practices of Buddhism and their spread across Asia. Peter D. Hershock explores the history of the enduring Japanese tradition of Zen—from its beginnings as a form of Buddhist thought and practice imported from China to its reinvention in medieval Japan as a force for religious, political, and cultural change to its role in Japan’s embrace of modernity. He deftly blends historical detail with the felt experiences of Zen practitioners grappling with (...)
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  19. Recovering Subalternity in the Humanities and Social Sciences.Peter D. Thomas - 2023 - In Didier Fassin & George Steinmetz (eds.), The Social Sciences in the Looking Glass: Studies in the Production of Knowledge. Duke University Press.
     
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  20. PSA 1978.Peter D. Asquith & Ian Hacking (eds.) - 1978 - University of Chicago Press.
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  21.  4
    Current Research in Philosophy of Science: Proceedings of the P.S.A. Critical Research Problems Conference.Peter D. Asquith & Henry Ely Kyburg (eds.) - 1979 - Philosophy of Science Association.
  22. Radical Interpretation and Global Skepticism.Peter D. Klein - 1986 - In Truth and Interpretation: Perspectives on the Philosophy of Donald Davidson. Cambridge: Blackwell.
  23. The Elderly and High Technology Medicine: A Case for Individualized, Autonomous Allocation.Peter D. Mott - 1990 - Theoretical Medicine and Bioethics 11 (2).
    The issues involved in decision making about the aggressiveness of future medical care for older persons are explored. They are related to population trends, the heterogeneity of older persons and a variety of factors involved in individual preferences. Case studies are presented to illustrate these points, as well as a review of pertinent literature. The argument is offered that, considering these many factors, a system of flexible, individualized care by informed patient preference, is more rational than the rationing of technological (...)
     
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  24.  45
    A Quantum Logic of Down Below.Peter D. Bruza, Dominic Widdows & John Woods - unknown
    This chapter is offered as a contribution to the logic of down below. We attempt to demonstrate that the nature of human agency necessitates that there actually be such a logic. The ensuing sections develop the suggestion that cognition down below has a structure strikingly similar to the physical structure of quantum states. In its general form, this is not an idea that originates with the present authors. It is known that there exist mathematical models from the cognitive science of (...)
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  25.  22
    Personal View: Withdrawal of Consent by Sperm Donors.Peter D. Sozou, Sally Sheldon & Geraldine M. Hartshorne - unknown
    Since 1991, sperm donors in the UK have had the legal right to withdraw consent for the use of their sperm in fertility treatment. This has the potential to adversely affect patients. It may mean that previous recipients of a donor’s sperm cannot have further children who are full biological siblings to an existing child, and that embryos created from the donor’s sperm and a patient’s eggs must be destroyed.
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  26. A Grammar of Visual Composition and its Biological Origin.Peter D. Stebbing - 2003 - Communication and Cognition: An Interdisciplinary Quarterly Journal 36:353-390.
     
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  27.  59
    The Place of Perception in Plato’s Tripartite Soul.Peter D. Larsen - 2017 - Proceedings of the Boston Area Colloquium of Ancient Philosophy 32 (1):69-99.
    This paper considers the place of the capacity for sense perception in Plato's tripartite soul. It argues, against a common recent interpretation, that despite being a capacity of the soul's appetitive part, sense perception is not independent of the soul's rational capacities. On the contrary, the soul's ability to recognize the content that it receives through sense perception depends upon the objects and the activity of its rational capacities. Defending a position of this sort requires one to suppose that despite (...)
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  28.  20
    Are There Forms of Sensible Qualities in Plato?Peter D. Larsen - 2018 - Journal of the American Philosophical Association 4 (2):225-242.
    This paper addresses the question of whether, according to Plato, there are forms of sensible qualities; it is also addressed to the wider question of whether there are forms of physical and material things more generally. In particular, it considers the tension raised by the following theses: (1) a Platonic form is the essence of some thing; (2) for Plato, those essences that are forms are imperceptible and are knowable through reasoning alone; (3) knowing the essence of a particular color (...)
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  29.  4
    “A Notion of the True System of the World”: Berkeley and His Use of Plato in Siris.Peter D. Larsen - 2022 - Archiv für Geschichte der Philosophie 104 (3):539-565.
    This paper considers Berkeley’s use of Plato in Siris. Berkeley’s engagement with ancient thinkers in Siris has been a source of puzzlement for many readers. In this paper I focus on Siris § 266. In particular, I consider why Berkeley says of the Platonists that they “distinguished the primary qualities in bodies from the secondary” and why, given his own well-known misgivings about the distinction, he characterizes this as part of a “notion of the true system of the world.” I (...)
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  30. Alive and Clicking : Reification and the Political Economy of Ipods.Peter D. Schaefer - 2008 - In D. E. Wittkower (ed.), Ipod and Philosophy. Open Court.
  31.  9
    Arresting Language: From Leibniz to Benjamin.Peter D. Fenves - 2001 - Stanford University Press.
    Speech act theory has taught us 'how to do things with words'. Arresting Language turns its attention in the opposite direction - toward the surprising things that language can undo and leave undone. In the eight essays of this volume, arresting language is seen as language at rest, words no longer in service to the project of establishing conventions or instituting legal regimes. Concentrating on both widely-known and seldom-read texts from a variety of philosophers, writers, and critics - from Leibniz (...)
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  32. Inventing the AIDS Virus.Peter D. Friedmann - 1997 - Perspectives in Biology and Medicine 40 (3):455.
  33. Warrant, Proper Function, Reliabilism and Defeasibility.Peter D. Klein - 1996 - In Kvanvig Jonathan (ed.), Warrant and Contemporary Epistemology. Rowman & Littlefield.
     
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  34. Why Not Infinitism?Peter D. Klein - 2000 - Epistemology 5:199-208.
    As the Pyrrhonians made clear, reasons that adequately justify beliefs can have only three possible structures: foundationalism, coherentism, and infinitism. Infinitism—the view that adequate reasons for our beliefs are infinite and non-repeating—has never been developed carefully, much less advocated. In this paper, I will argue that only infinitism can satisfy two intuitively plausible constraints on good reasoning: the avoidance of circular reasoning and the avoidance of arbitrariness. Further, I will argue that infinitism requires serious, but salutary, revisions in our evaluation (...)
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  35.  43
    Why Not Infinitism?Peter D. Klein - 2000 - The Proceedings of the Twentieth World Congress of Philosophy 5:199-208.
    As the Pyrrhonians made clear, reasons that adequately justify beliefs can have only three possible structures: foundationalism, coherentism, and infinitism. Infinitism—the view that adequate reasons for our beliefs are infinite and non-repeating—has never been developed carefully, much less advocated. In this paper, I will argue that only infinitism can satisfy two intuitively plausible constraints on good reasoning: the avoidance of circular reasoning and the avoidance of arbitrariness. Further, I will argue that infinitism requires serious, but salutary, revisions in our evaluation (...)
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  36. What Makes Knowledge the Most Highly Prized Form of True Belief?Peter D. Klein - 2012 - In Tim Black & Kelly Becker (eds.), The Sensitivity Principle in Epistemology.
    This chapter provides grounds for thinking that it is the quality of the reasons for the propositional content of our belief-states with true propositional contents, rather than the etiology of those belief-states, that determines whether the belief-state qualifies as knowledge. Normative epistemology rather than naturalized epistemology holds the key to understanding knowledge. This chapter delineates some important features of epistemic luck. It explores the etiology view and presents reasons for concluding that it cannot adequately account for epistemic luck. The chapter (...)
     
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  37. What IS Wrong with Foundationalism is That It Cannot Solve the Epistemic Regress Problem.Peter D. Klein - 2004 - Philosophy and Phenomenological Research 68 (1):166-171.
    There are many things that could be wrong with foundationalism. For example, some have claimed that a so-called basic belief cannot be both 1) a reason for non-basic beliefs and 2) such that it cannot be provided with at least prima facie justification. If something is a reason, they say, then that something has to be a proposition and if it is a proposition, then it is the kind of thing that requires a reason in order to be even prima (...)
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  38. Useful False Beliefs.Peter D. Klein - 2008 - In Quentin Smith (ed.), Epistemology: New Essays. Oxford University Press. pp. 25--63.
  39.  33
    Coherence, Knowledge and Skepticism.Peter D. Klein - 2003 - In Olsson Erik (ed.), The Epistemology of Keith Lehrer. Kluwer Academic Publishers. pp. 281--297.
  40. Certainty.Peter D. Klein - 1998 - In Dancy Jonathan & Sosa Ernest (eds.), Routledge Encyclopedia of Philosophy. Routledge.
     
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  41. Closure.Peter D. Klein - 1995 - In Audi Robert (ed.), The Cambridge Dictionary of Philosophy. Cambridge University Press.
     
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  42. 30. There is No Good Reason to Be an Academic Skeptic.Peter D. Klein - 2003 - In Steven Luper (ed.), Essential Knowledge: Readings in Epistemology. Longman. pp. 299.
  43. The Failures of Dogmatism and a New Pyrrhonism.Peter D. Klein - 2000 - Acta Analytica 15 (24):7-24.
     
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  44. Truth and Interpretation: Perspectives on the Philosophy of Donald Davidson.Peter D. Klein - 1986 - Cambridge: Blackwell.
  45. Scepticism.Peter D. Klein - 1992, 2010 - In Dancy Jonathan & Sosa Ernest (eds.), A Companiion to Epistemology.
     
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  46. Self-Profile.Peter D. Klein - 2010 - Blackwell Companion to Epistemology.
     
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  47. Reply to Ginet.Peter D. Klein - 2005 - In Steup Matthias & Sosa Ernest (eds.), Contemporary Debates in Epistemology. Blackwell.
     
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  48. Recent Publications.Peter D. Klein - 1983 - Philosophy and Phenomenological Research 43 (3):421.
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  49. Review of Armstrong's Belief, Truth and Knowledge, Philosophical Review, 85.2 1976, 225-227. [REVIEW]Peter D. Klein - 1976 - Philosophical Review 82 (5):225-227.
     
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  50.  53
    Epistemic Justification and the Limits of Pyrrhonism.Peter D. Klein - 2011 - In Diego Machuca (ed.), Pyrrhonism in Ancient, Modern, and Contemporary Philosophy. Springer.
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