Results for 'Peter D���Eustachio'

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  1. 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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  2. 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 (PRO) 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 (...)
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  3. 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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  4.  81
    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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  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. 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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  7.  30
    Belief, Truth and Knowledge.Peter D. Klein - 1976 - Philosophical Review 85 (2):225.
  8. Human Knowledge and the Infinite Regress of Reasons.Peter D. Klein - 1999 - Philosophical Perspectives 13:297-325.
  9. Certainty, a Refutation of Scepticism.Peter D. Klein - 1981 - University of Minnesota Press.
    Rich with historical and cultural value, these works are published unaltered from the original University of Minnesota Press editions.
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  10. Useful False Beliefs.Peter D. Klein - 2008 - In Quentin Smith (ed.), Epistemology: New Essays. Oxford University Press. pp. 25--63.
  11. Listening to Prozac.Peter D. Kramer - 1994 - Perspectives in Biology and Medicine 37 (3):460.
  12. A Proposed Definition of Propositional Knowledge.Peter D. Klein - 1971 - Journal of Philosophy 68 (16):471-482.
  13.  40
    Human Knowledge and the Infinite Regress of Reasons.Peter D. Klein - 1999 - Noûs 33 (s13):297-325.
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  14.  71
    Quantum Cognition: A New Theoretical Approach to Psychology.Peter D. Bruza, Zheng Wang & Jerome R. Busemeyer - 2015 - Trends in Cognitive Sciences 19 (7):383-393.
  15.  13
    Coordinate Transformations or Dynamic Models?Peter D. Neilson - 1992 - Behavioral and Brain Sciences 15 (2):348-348.
  16.  16
    Refiguring the Subaltern.Peter D. Thomas - 2018 - Political Theory 46 (6):861-884.
    The subaltern has frequently been understood as a figure of exclusion ever since it was first highlighted by the early Subaltern Studies collective’s creative reading of Antonio Gramsci’s carceral writings. In this article, I argue that a contextualist and diachronic study of the development of the notion of subaltern classes throughout Gramsci’s full Prison Notebooks reveals new resources for “refiguring” the subaltern. I propose three alternative figures to comprehend specific dimensions of Gramsci’s theorizations: the “irrepressible subaltern,” the “hegemonic subaltern,” and (...)
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  17. Knowledge, Causality, and Defeasibility.Peter D. Klein - 1976 - Journal of Philosophy 73 (20):792-812.
  18. Certainty.Peter D. Klein - 1998 - In Dancy Jonathan & Sosa Ernest (eds.), Routledge Encyclopedia of Philosophy. Routledge.
     
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  19. Reply to Ginet.Peter D. Klein - 2005 - In Steup Matthias & Sosa Ernest (eds.), Contemporary Debates in Epistemology. Blackwell.
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  20. 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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  21. How a Pyrrhonian Skeptic Might Respond to Academic Skepticism.Peter D. Klein - 2003 - In Luper Steven (ed.), The Skeptics: Contemporary Essays. Ashgate Press. pp. 75--94.
     
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  22.  5
    Epistemology.Peter D. Klein - 1998 - In Craig Edward (ed.), Routledge Encyclopedia of Philosophy. 1998.
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  23.  21
    Jurisdictions of Sexual Assault: Reforming the Texts and Testimony of Rape in Australia. [REVIEW]Peter D. Rush - 2011 - Feminist Legal Studies 19 (1):47-73.
    The reform of rape law remains a vexed enterprise. The wager of this article is that the plural traditions and technologies of criminal law can provide the resources for a radical rethinking of rape law. Parts 1 and 2 return to the historical and structural forms of rape law reform in Australia. These forms of reform illustrate a variety of criminal jurisdictions, and a transformation in the way in which rape law reform is conducted now. Against this transformation, Part 3 (...)
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  24.  30
    Contextualism and the Real Nature of Academic Skepticism.Peter D. Klein - 2000 - Philosophical Issues 10 (1):108-116.
  25.  59
    A Third Version of Constructivism: Rethinking Spinoza’s Metaethics.Peter D. Zuk - 2015 - Philosophical Studies 172 (10):2565-2574.
    In this essay, I claim that certain passages in Book IV of Benedict de Spinoza’s Ethics suggest a novel version of what is known as metaethical constructivism. The constructivist interpretation emerges in the course of attempting to resolve a tension between Spinoza’s apparent ethical egoism and some remarks he makes about the efficacy of collaborating with the right partners when attempting to promote our individual self-interest . Though Spinoza maintains that individuals necessarily aim to promote their self-interest, I argue that (...)
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  26.  10
    Valuing Diversity: Buddhist Reflection on Realizing a More Equitable Global Future.Peter D. Hershock - 2012 - State University of New York Press.
    Uses Buddhist philosophy to discuss diversity as a value, one that can contribute to equity in a globalizing world.
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  27. Infinitism.Peter D. Klein - 2011 - In Sven Bernecker & Duncan Pritchard (eds.), Routledge Companion to Epistemology. Routledge. pp. 245-256.
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  28. 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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  29.  37
    How to Get Certain Knowledge From Fallible Justification.Peter D. Klein - 2019 - Episteme 16 (4):395-412.
    “Real knowledge,” as I use the term, is the most highly prized form of true belief sought by an epistemic agent. This paper argues that defeasible infinitism provides a good way to characterize real knowledge and it shows how real knowledge can arise from fallible justification. Then, I argue that there are two ways of interpreting Ernest Sosa's account of real knowledge as belief that is aptly formed and capable of being fully defended. On the one hand, if beliefs are (...)
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  30. Misleading Evidence and the Restoration of Justification.Peter D. Klein - 1980 - Philosophical Studies 37 (1):81 - 89.
  31.  9
    Public Health and Health Care: Integration, Disintegration, or Eclipse.Peter D. Jacobson & Wendy E. Parmet - 2018 - Journal of Law, Medicine and Ethics 46 (4):940-951.
    Many observers have argued that the US health care system could be more efficient, and achieve better outcomes if providers focused more on improving the community's health, not just the welfare of individual patients. The passage of the Affordable Care Act in 2010 seemed to herald the promise of such reforms, and greater integration of the health care and public systems. In this article, we reassess the quest for integration, a quest we call the “integration project.” After examining the modest (...)
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  32.  83
    Infinitism's Take on Justification, Knowledge, Certainty and Skepticism.Peter D. Klein - 2005 - Veritas – Revista de Filosofia da Pucrs 50 (4):153-172.
    O propósito deste artigo é mostrar como podem ser desenvolvidas explicações robustas de justificação e de certeza no interior do infinitismo. Primeiro, eu explico como a concepção infinitista de justificação epistêmica difere das concepções fundacionista e coerentista. Em segundo lugar, explico como o infinitista pode oferecer uma solução ao problema do regresso epistêmico. Em terceiro lugar, explico como o infinitismo, per se, é compatível com as teorias daqueles que sustentam 1) que o conhecimento requer certeza e que uma tal forma (...)
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  33. Radical Interpretation and Global Skepticism.Peter D. Klein - 1986 - In Truth and Interpretation: Perspectives on the Philosophy of Donald Davidson. Cambridge: Blackwell.
  34.  1
    "Chatter": Language and History in Kierkegaard.Peter D. Fenves - 1993 - Stanford University Press.
    'Chatter' cannot always be taken lightly, for its insignificance and insubstantiality challenge the very notions of substance and significance through which rational discourses seek justification. This book shows that in 'chatter' Kierkegaard uncovered a specifically linguistic mode of negativity. The author examines in detail those writings of Kierkegaard in which he undertook complex negotiations with the threat - and also the promise - of 'chatter', which cuts across the distinctions in which the relation of language to reality - and above (...)
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  35.  13
    Gramsci's Revolutions: Passive and Permanent.Peter D. Thomas - 2020 - Modern Intellectual History 17 (1):117-146.
    Antonio Gramsci's notion of “passive revolution” has often been understood as a distinctive historical narrative, political concept, or theory of state formation. This article proposes to consider it instead as a “heuristic formula” within the “lexical architecture” of thePrison Notebooks. Based upon a diachronic and contextualist analysis of the usage of the formula, I argue that Gramsci's research on passive revolution emerged as a critical element within the development of his own distinctive conception of the “sublation” and “actualization” of the (...)
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  36. Misleading "Misleading Defeaters".Peter D. Klein - 1979 - Journal of Philosophy 76 (7):382-386.
  37. Infinitism is the Solution to the Epistemic Regress Problem.Peter D. Klein - 2005 - In Steup Matthias & Sosa Ernest (eds.), Contemporary Debates in Epistemology. Blackwell.
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  38.  16
    Co-Opting the Health and Human Rights Movement.Peter D. Jacobson & Soheil Soliman - 2002 - Journal of Law, Medicine and Ethics 30 (4):705-715.
    Public health is concerned with how to improve the population’s health. At times, though, actions to improve the community’s health may collide with individual civil rights. For example, a public health response to a bioterrorism attack, such as smallpox, may require relaxing an individual’s due process protections to prevent the smallpox from spreading. This tension lies at the heart of public health policy. It also must be considered in discussing the concept of human rights in health.Proponents of incorporating the concept (...)
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  39. The Failures of Dogmatism and a New Pyrrhonism.Peter D. Klein - 2000 - Acta Analytica 15 (24):7-24.
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  40.  38
    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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  41.  14
    Categorization in Early Infancy and the Continuity of Development.Peter D. Eimas - 1994 - Cognition 50 (1-3):83-93.
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  42.  63
    Hegemony, Passive Revolution and the Modern Prince.Peter D. Thomas - 2013 - Thesis Eleven 117 (1):20-39.
    Gramsci’s concept of hegemony has been interpreted in a wide variety of ways, including a theory of consent, of political unity, of ‘anti-politics’, and of geopolitical competition. These interpretations are united in regarding hegemony as a general theory of political power and domination, and as deriving from a particular interpretation of the concept of passive revolution. Building upon the recent intense season of philological research on the Prison Notebooks, this article argues that the concept of hegemony is better understood as (...)
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  43.  12
    Co-Opting the Health and Human Rights Movement.Peter D. Jacobson & Soheil Soliman - 2002 - Journal of Law, Medicine and Ethics 30 (4):705-715.
    Public health is concerned with how to improve the population’s health. At times, though, actions to improve the community’s health may collide with individual civil rights. For example, a public health response to a bioterrorism attack, such as smallpox, may require relaxing an individual’s due process protections to prevent the smallpox from spreading. This tension lies at the heart of public health policy. It also must be considered in discussing the concept of human rights in health.Proponents of incorporating the concept (...)
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  44.  24
    Non‐Genomic Transgenerational Inheritance of Disease Risk.Peter D. Gluckman, Mark A. Hanson & Alan S. Beedle - 2007 - Bioessays 29 (2):145-154.
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  45.  52
    Epistemic Justification and the Limits of Pyrrhonism.Peter D. Klein - 2011 - In Diego Machuca (ed.), Pyrrhonism in Ancient, Modern, and Contemporary Philosophy. Springer.
  46.  6
    Does Blue Uniform Color Enhance Winning Probability in Judo Contests?Peter D. Dijkstra, Paul T. Y. Preenen & Hans van Essen - 2018 - Frontiers in Psychology 9.
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  47.  29
    Interiority, Exteriority and the Realm of Intentionality.Peter D. Ashworth - 2017 - Journal of Phenomenological Psychology 48 (1):39-62.
    The realm of intentionality is definitive of phenomenology as a reflective methodology. Yet it is precisely the focus on the intentional given that has been condemned recently. Speculative realism argues that phenomenology is unsatisfactory since the reduction to the intentional realm excludes the ‘external’, i.e. reality independent of consciousness. This criticism allows me to clarify the nature of intentionality. Material phenomenology finds, in contrast, that the intentional realm excludes the ‘inner’. This criticism allows me to discuss the way in which (...)
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  48.  92
    Contextualism and the Real Nature of Academic Skepticism.Peter D. Klein - 2000 - Noûs 34 (s1):108 - 116.
  49.  21
    Litigation as Public Health Policy: Theory or Reality?Peter D. Jacobson & Soheil Soliman - 2002 - Journal of Law, Medicine and Ethics 30 (2):224-238.
    An ongoing debate among legal scholars and public health advocates is the role of litigation in shaping public policy. For the most part, the debate has been waged at a conceptual level, with opponents and proponents arguing within fairly well-defined boundaries. The debate has been based either on speculation of what litigation could achieve or on ideological grounds as to why litigation should or should not be used this way. With the exception of Rosenberg's study of how litigation shaped policy (...)
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  50.  22
    The Valorization of Sadness Alienation and the Melancholic Temperament.Peter D. Kramer - 2000 - Hastings Center Report 30 (2):13-18.
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