Results for 'Wu Xiaoyan'

99 found
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  1. The Dialectic of Consciousness and Unconsciousness in Spontaneity of Genius: A Comparison between Classical Chinese Aesthetics and Kantian Ideas.Xiaoyan Hu - 2017 - Proceedings of the European Society for Aesthetics 9:246–274.
    This paper explores the elusive dialectic between concentration and forgetfulness, consciousness and unconsciousness in spontaneous artistic creation favoured by artists and advocated by critics in Chinese art history, by examining texts on painting and tracing back to ancient Daoist philosophical ideas, in a comparison with Kantian and post-Kantian aesthetics. Although artistic spontaneity in classical Chinese aesthetics seems to share similarities with Kant’s account of spontaneity in the art of genius, the emphasis on unconsciousness is valued by classical Chinese artists and (...)
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  2. Collected Papers (on Neutrosophic Theory and Its Applications in Algebra), Volume IX.Florentin Smarandache - 2022 - Miami, FL, USA: Global Knowledge.
    This ninth volume of Collected Papers includes 87 papers comprising 982 pages on Neutrosophic Theory and its applications in Algebra, written between 2014-2022 by the author alone or in collaboration with the following 81 co-authors (alphabetically ordered) from 19 countries: E.O. Adeleke, A.A.A. Agboola, Ahmed B. Al-Nafee, Ahmed Mostafa Khalil, Akbar Rezaei, S.A. Akinleye, Ali Hassan, Mumtaz Ali, Rajab Ali Borzooei , Assia Bakali, Cenap Özel, Victor Christianto, Chunxin Bo, Rakhal Das, Bijan Davvaz, R. Dhavaseelan, B. Elavarasan, Fahad Alsharari, T. (...)
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  3. The Notion of 'Qi Yun' (Spirit Consonance) in Chinese Painting.Xiaoyan Hu - 2016 - Proceedings of the European Society for Aesthetics 8:247–268.
    ‘Spirit consonance engendering a sense of life’ (Qi Yun Sheng Dong) as the first law of Chinese painting, originally proposed by Xie He (active 500–535?) in his six laws of painting, has been commonly echoed by numerous later Chinese artists up to this day. Tracing back the meaning of each character of ‘Qi Yun Sheng Dong’ from Pre-Qin up to the Six Dynasties, along with a comparative analysis on the renderings of ‘Qi Yun Sheng Dong’ by experts in Western academia, (...)
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  4. (1 other version)The Moral Dimension of Qiyun Aesthetics and Some Resonances with Kant and Schiller.Xiaoyan Hu - 2021 - Estetika : The European Journal of Aesthetics 2 (LVIII/XIV):129-143.
    In this paper, I suggest that the notion of qiyun (qi: spirit; yun: consonance) in the context of landscape painting involves a moral dimension. The Confucian doctrine of sincerity involved in bringing the landscapist’s or audience’s mind in accord with the Dao underpins the moral dimension of spiritual communion between artist, object, audience, and work. By projecting Kant’s and Schiller’s conceptions of aesthetic autonomy and the moral relevance of art onto the qiyun-focused context, we see that the reflection on parallels (...)
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  5. Beyond Representation: Reconsidering Loehr's Periodisation of Chinese Painting.Xiaoyan Hu - 2017 - Proceedings of ICA 2016 ‘Aesthetics and Mass Culture’ (E-Book), 2016.
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  6. The Moral Dimension of Qiyun Aesthetics and Some Kantian Resonances.Xiaoyan Hu - 2019 - Proceedings of the European Society for Aesthetics 11:339–374.
    In this paper, I suggest that the notion of qiyun (spirit consonance) in the context of landscape painting involves a moral dimension. The Confucian doctrine of sincerity involved in bringing the landscapist’s or audience’s mind in accord with the Dao underpins the moral dimension of spiritual communion between artist, object, audience and work. By projecting Kant’s, and Schiller’s somewhat modified Kantian philosophy of aesthetic autonomy and the moral relevance of art into the qiyun-focused context, we shall see that reflection on (...)
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  7. Experts and Deviants: The Story of Agentive Control.Wayne Wu - 2016 - Philosophy and Phenomenological Research 93 (1):101-26.
    This essay argues that current theories of action fail to explain agentive control because they have left out a psychological capacity central to control: attention. This makes it impossible to give a complete account of the mental antecedents that generate action. By investigating attention, and in particular the intention-attention nexus, we can characterize the functional role of intention in an illuminating way, explicate agentive control so that we have a uniform explanation of basic cases of causal deviance in action as (...)
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  8. Attention as Selection for Action.Wayne Wu - 2011 - In Christopher Mole, Declan Smithies & Wayne Wu (eds.), Attention: Philosophical and Psychological Essays. New York: Oxford University Press. pp. 97--116.
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  9. Shaking Up the Mind’s Ground Floor: The Cognitive Penetration of Visual Attention.Wayne Wu - 2017 - Journal of Philosophy 114 (1):5-32.
    In this paper, I argue that visual attention is cognitively penetrated by intention. I present a detailed account of attention and its neural basis, drawing on a recent computational model of neural modulation during attention: divisive normalization. I argue that intention shifts computations during divisive normalization. The epistemic consequences of attentional bias are discussed.
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  10. Explaining Schizophrenia: Auditory Verbal Hallucination and Self‐Monitoring.Wayne Wu - 2012 - Mind and Language 27 (1):86-107.
    Do self‐monitoring accounts, a dominant account of the positive symptoms of schizophrenia, explain auditory verbal hallucination? In this essay, I argue that the account fails to answer crucial questions any explanation of auditory verbal hallucination must address. Where the account provides a plausible answer, I make the case for an alternative explanation: auditory verbal hallucination is not the result of a failed control mechanism, namely failed self‐monitoring, but, rather, of the persistent automaticity of auditory experience of a voice. My argument (...)
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  11. Against Division: Consciousness, Information and the Visual Streams.Wayne Wu - 2014 - Mind and Language 29 (4):383-406.
    Milner and Goodale's influential account of the primate cortical visual streams involves a division of consciousness between them, for it is the ventral stream that has the responsibility for visual consciousness. Hence, the dorsal visual stream is a ‘zombie’ stream. In this article, I argue that certain information carried by the dorsal stream likely plays a central role in the egocentric spatial content of experience, especially the experience of visual spatial constancy. Thus, the dorsal stream contributes to a pervasive feature (...)
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  12. Attention as Selection for Action Defended.Wayne Wu - forthcoming - Philosophy and Phenomenological Research.
    Attention has become an important focal point of recent work in ethics and epistemology, yet philosophers continue to be noncommittal about what attention is. In this paper, I defend attention as selection for action in a weak form, namely that selection for action is sufficient for attention. I show that selection for action in this form is part of how we, the folk, experience it and how the cognitive scientist studies it. That is, selection for action pulls empirical and folk-psychology (...)
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  13. Mental Action and the Threat of Automaticity.Wayne Wu - 2013 - In Andy Clark, Julian Kiverstein & Tillmann Vierkant (eds.), Decomposing the Will. , US: Oxford University Press USA. pp. 244-61.
    This paper considers the connection between automaticity, control and agency. Indeed, recent philosophical and psychological works play up the incompatibility of automaticity and agency. Specifically, there is a threat of automaticity, for automaticity eliminates agency. Such conclusions stem from a tension between two thoughts: that automaticity pervades agency and yet automaticity rules out control. I provide an analysis of the notions of automaticity and control that maintains a simple connection: automaticity entails the absence of control. An appropriate analysis, however, shows (...)
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  14. The Case for Zombie Agency.Wayne Wu - 2013 - Mind 122 (485):217-230.
    In response to Mole 2009, I present an argument for zombie action. The crucial question is not whether but rather to what extent we are zombie agents. I argue that current evidence supports only minimal zombie agency.
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  15. Epistemic Advantage on the Margin: A Network Standpoint Epistemology.Jingyi Wu - 2022 - Philosophy and Phenomenological Research (3):1-23.
    ​I use network models to simulate social learning situations in which the dominant group ignores or devalues testimony from the marginalized group. I find that the marginalized group ends up with several epistemic advantages due to testimonial ignoration and devaluation. The results provide one possible explanation for a key claim of standpoint epistemology, the inversion thesis, by casting it as a consequence of another key claim of the theory, the unidirectional failure of testimonial reciprocity. Moreover, the results complicate the understanding (...)
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  16. Précis of Movements of the Mind.Wayne Wu - 2024 - Journal of Consciousness Studies 31 (7):119-126.
    In Movements of the Mind (MoM; Wu, 2023a), I give a theory of agency that uncovers its internal psychological structure, revealing how creatures with minds do things. While my focus is on things we do 'in our heads', mental actions, the theory concerns all forms of agency. The book also provides a theory of attention and its essential connection to action. It characterizes intention in action as a type of memory for work, drawing on empirical theories of working memory. Further, (...)
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  17. Is Vision for Action Unconscious?Wayne Wu - 2020 - Journal of Philosophy 117 (8):413-433.
    Empirical work and philosophical analysis have led to widespread acceptance that vision for action, served by the cortical dorsal stream, is unconscious. I argue that the empirical argument for this claim is unsound. That argument relies on subjects’ introspective reports. Yet on biological grounds, in light of the theory of primate cortical vision, introspection has no access to dorsal stream mediated visual states. It is thus wrongly assumed that introspective reports speak to absent phenomenology in the dorsal stream. In light (...)
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  18. Is inner speech the basis of auditory verbal hallucination in schizophrenia?Wayne Wu & Raymond Cho - 2014 - Frontiers in Psychiatry 14:1-3.
    We respond to Moseley and Wilkinson's defense of inner speech models of AVH.
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  19. How should we promote transient diversity in science?Jingyi Wu & Cailin O’Connor - 2023 - Synthese 201 (2):1-24.
    Diversity of practice is widely recognized as crucial to scientific progress. If all scientists perform the same tests in their research, they might miss important insights that other tests would yield. If all scientists adhere to the same theories, they might fail to explore other options which, in turn, might be superior. But the mechanisms that lead to this sort of diversity can also generate epistemic harms when scientific communities fail to reach swift consensus on successful theories. In this paper, (...)
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  20. Explaining Universality: Infinite Limit Systems in the Renormalization Group Method.Jingyi Wu - 2021 - Synthese (5-6):14897-14930.
    I analyze the role of infinite idealizations used in the renormalization group (RG hereafter) method in explaining universality across microscopically different physical systems in critical phenomena. I argue that despite the reference to infinite limit systems such as systems with infinite correlation lengths during the RG process, the key to explaining universality in critical phenomena need not involve infinite limit systems. I develop my argument by introducing what I regard as the explanatorily relevant property in RG explanations: linearization* property; I (...)
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  21. Being in the workspace, from a neural point of view: comments on Peter Carruthers, 'On central cognition'.Wayne Wu - 2014 - Philosophical Studies 170 (1):163-174.
    In his rich and provocative paper, Peter Carruthers announces two related theses: (a) a positive thesis that “central cognition is sensory based, depending on the activation and deployment of sensory images of various sorts” (Carruthers 2013) and (b) a negative thesis that the “central mind does not contain any workspace within which goals, decisions, intentions, or non-sensory judgments can be active” (Carruthers 2013). These are striking claims suggesting that a natural view about cognition, namely that explicit theoretical reasoning involves direct (...)
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  22. A Dream of a Stone: The Ethics of De-anthropocentrism.Tsaiyi Wu - 2020 - Open Philosophy 3 (1):413-428.
    De-anthropocentrism is the leitmotif of philosophy in the twenty-first century, encouraging diverse and competing thoughts as to how this goal may be achieved. This article argues that the method by which we may achieve de-anthropocentrism is ethical rather than metaphysical – it must involve a creation of the self, rather than an interpretation of the given human conditions. Through engagements with the thought of Nietzsche, Levinas, and Foucault, and a close reading of Baudelaire’s poem “La Beauté,” I will illustrate three (...)
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  23. The relationship of ethical decision-making to business ethics and performance in taiwan.Chen-Fong Wu - 2002 - Journal of Business Ethics 35 (3):163-176.
    This paper examines the relationship of ethical decision-making by individuals to corporate business ethics and organizational performance of three groups: SMEs, Outstanding SMEs and Large Enterprises, in order to provide a reference for Taiwanese entrepreneurs to practice better business ethics. The survey method involved random sampling of 132 enterprises within three groups. Some 524 out of 1320 questionnaires were valid. The survey results demonstrated that ethical decision-making by individuals, corporate business ethics and organizational performance are highly related. In summary, then, (...)
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  24. A Defense of Impurist Permissivism.Jenny Yi-Chen Wu - 2023 - Episteme:1-21.
    One famous debate in contemporary epistemology considers whether there is always one unique, epistemically rational way to respond to a given body of evidence. Generally speaking, answering “yes” to this question makes one a proponent of the Uniqueness thesis, while those who answer “no” are called “permissivists”. Another influential recent debate concerns whether non-truth-related factors can be the basis of epistemic justification, knowledge, or rational belief. Traditional theories answer “no”, and are therefore considered “purists”. However, more recently many theorists have (...)
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  25. Aggregation and Reductio.Patrick Wu - 2021 - Ethics 132 (2):508-525.
    Joe Horton argues that partial aggregation yields unacceptable verdicts in cases with risk and multiple decisions. I begin by showing that Horton’s challenge does not depend on risk, since exactly similar arguments apply to riskless cases. The underlying conflict Horton exposes is between partial aggregation and certain principles of diachronic choice. I then provide two arguments against these diachronic principles: they conflict with intuitions about parity, prerogatives, and cyclical preferences, and they rely on an odd assumption about diachronic choice. Finally, (...)
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  26. Chinese Thing-Metaphor: Translating Material Qualities to Spiritual Ideals.Tsaiyi Wu - 2020 - Philosophy East and West 70 (2):522-542.
    This article compares the use of Romantic metaphor with the Chinese literary device xiang 象 (which I translate as “thing-metaphor”) in regard to how they embody different metaphysical relations between humans and things. Whereas Romantic metaphor transports a physical thing to the immaterial realm of imagination, xiang is a literary device in which the material qualities of the thing, while creatively interpreted to generate human meaning, retain ontologically a strong physical presence. Xiang therefore epitomizes a theory of creation that challenges (...)
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  27. Derrida's Open and Its Closure: The Aporia of Différance and the Only Logic of Thinking.Mengxue Wu - 2018 - Language, Literature, Interdisciplinary Studies 2 (1):76-98.
    Derrida’s thought on “trace,” “différance,” “writing,” and “supplement” is always thought the breaking of logocentrism, the essence, the positive meaning, and the closure of the metaphysics of presence; this thinking is accordingly regarded the thinking with the fundamental structure of difference and openness. By tracking back to Saussure, Husserl and Levinas, this fundamental difference breaks the myth of ideal meaning as well as the illusion of the absolute open; its lack of ideality and absoluteness contains the fundamental difference within itself (...)
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  28. Is Mohism really li-promotionalism?Yun Wu & Amin Ebrahimi Afrouzi - 2021 - Asian Philosophy 31 (4):430-440.
    A longstanding orthodoxy holds that the Mohists regard the promotion of li (benefit, 利) as their ultimate normative criterion, meaning that they measure what is yi (just, 義) or buyi (unjust, 不義) depending on whether it maximizes li or not. This orthodoxy dates back at least to Joseph Edkins (1859), who saw Mozi as a utilitarian and an ally of Bentham. In this paper, we will argue that this orthodoxy should be reconsidered because it does not square with several passages (...)
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  29. Better than Best: Epistemic Landscapes and Diversity of Practice in Science.Jingyi Wu - forthcoming - Philosophy of Science.
    When solving a complex problem in a group, should group members always choose the best available solution that they are aware of? In this paper, I build simulation models to show that, perhaps surprisingly, a group of agents who individually randomly follow a better available solution than their own can end up outperforming a group of agents who individually always follow the best available solution. This result has implications for the feminist philosophy of science and social epistemology.
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  30. Study on Logic Reasoning and Ideological Characteristic of “Equivalence of Life and Death” of Chuang-Tzu. Di Wu - 2017 - Theory Horizon 526 (6):46-51.
    The Concept of Life and Death of Chuang-tzu have inherited and developed Confucianism and Taoism thoughts, establishing Ontological foundation of "Life - Body", distinguishing the transcendental concept of "Dead Heart" and the empirical concept of "Death Body", as well as proposing the thought of "Equivalence of Life and Death" finally. The logic Reasoning of Chuang-tzu "Equivalence of Life and Death", start from constructing the equal status of "Life" and “Death" from ontological argument. Life and Death then are reduced to be (...)
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  31. Aristotelian Distributive Justice: Holism or Egalitarianism. Di Wu - 2017 - Journal of Huazhong University of Science and Technology(Social Science Edition), 31 (6):60-64.
    Different understanding on Aristotelian distributive justice results in two main factions: holism and egalitarianism. Dennis McKerlie, one of the representatives of holism, criticized Martha Nussbaum's interpretation as an egalitarian. McKerlie argued that Nussbaum did not attach enough importance to the Proportional equality and Aristotelian Common good, as well as a deviation in the understanding of the concept of distribution. The defense of egalitarianism is that Aristotle's emphasis on the rational equality of citizens and the ontological presupposition of primal equality show (...)
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  32. From “Modern Technology” Criticism to “Future-oriented” Responsibility Ethics: Hans Jonas's Theoretical construction of Responsibility Ethics. Di Wu - 2018 - Science Economy Society 36 (4):25-32.
    Hans Jonas 's responsibility ethics is an important achievement of modern technology criticism and ethical theory innovation. The maturity of Jonas's ethical thought has gone through three main stages, namely, the critique of modern technology, the reflection of traditional ethics and the construction of the " Future-oriented " Responsibility Ethics. Jonas's criticism of modern technology not only has a strong epochal character but also carries on the spirit of social criticism since Marx. His insight into the traditional ethics theory and (...)
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  33. Moral Courage: Classification and Interpretation. Di Wu - 2020 - Theory Monthly 461 (5):139-145.
    In the evolution of Chinese and Western literatures, the emphasis on the "strength" of "courage" is gradually given to the "mind" of "courage", that is the intention of the Agent. The connotation of Chinese and Western traditional thoughts of "courage" reflected in the distinction between the "physical courage" and "moral courage". Philosophers distinguish moral courage from physical courage, which does not seem to be clear and complete. Moral courage however as moral elements have been distinguished from "courage as a virtue". (...)
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  34. Desertification.A. Mirzabaev, J. Wu, J. Evans, F. Garcia-Oliva, I. A. G. Hussein, M. H. Iqbal, J. Kimutai, T. Knowles, F. Meza, D. Nedjroaoui, F. Tena, M. Türkeş, R. J. Vázquez & M. Weltz - 2019 - In P. R. Shukla, J. Skeg, E. Calvo Buendia, V. Masson-Delmotte, H.-O. Pörtner, D. C. Roberts, P. Zhai, R. Slade, S. Connors, S. van Diemen, M. Ferrat, E. Haughey, S. Luz, M. Pathak, J. Petzold, J. Portugal Pereira, P. Vyas, E. Huntley, K. Kissick, M. Belkacemi & J. Malley (eds.), Climate Change and Land: an IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.
    IPCC SPECIAL REPORT ON CLIMATE CHANGE AND LAND (SRCCL) -/- Chapter 3: Climate Change and Land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems.
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  35. On Ethical Basis of Sharing Economy: Contractual Ethics, Technical Ethics, and Universal Ethics. Di Wu - 2020 - Journal of Luoyang Normal University 39 (6):73-78.
    With the development of sharing economy, a consensus to study this area from the perspective of morality and ethics has been recently reached. The key point of this study is the ethical basis of sharing economy. It should be noticed that the conceptual framework of sharing economy must be grounded within the market economy, technological innovation, and the spirit of "rational cooperation". It is, therefore, necessary to realize that the sharing economy is based on the Contractual Ethics internally rooted in (...)
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  36. Cognitive Science Research on The Relationship Between Personality and Emotion.Wu Wei & Keqin Kong - 2019 - Journal of Human Cognition 3 (1):5-12.
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  37. Priority, Ethical Principle, and Allocation of Scarce Medical Resources. Di Wu - 2021 - Studies in Dialectics of Nature 11 (37):62-68.
    Aiming at the allocation of scarce medical resources, Immanuel and other scholars have put forward a set of influential ethical values and guiding principles. It assigns the priority of resource allocation to those whose lives can be saved and maximized, those who can bring the greatest instrumental value, and those who are the worse off. For other members of society, random selection under the same conditions is adopted. Following the Rawlsian "lexical order, lexicographical" rule, this priority arrangement requires that the (...)
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  38. The Conscious Brain: How Attention Engenders Experience, by Jesse Prinz. [REVIEW]Wayne Wu - 2013 - Mind 122 (488):1174-1180.
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  39. (1 other version)In Defense of Platonic Essentialism About Numbers.Wu Megan - 2021 - Stance 14:102-114.
    In defense of anti-essentialism, pragmatist Richard Rorty holds that we may think of all objects as if they were numbers. I find that Rorty’s metaphysics hinges on two rather weak arguments against the essences of numbers. In contrast, Plato’s metaphysics offers a plausible definition of essentiality by which numbers do have essential properties. Further, I argue that Rorty’s argumentative mistake is mischaracterizing Plato’s definition. I conclude that Plato’s definition of “essential” is a robust one which implies that many properties, beyond (...)
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  40. Perspectival shapes are viewpoint-dependent relational properties.Tony Cheng, Yi Lin & Chen-Wei Wu - 2022 - Psychological Review (1):307-310.
    Recently, there is a renewed debate concerning the role of perspective in vision. Morales et al. (2020) present evidence that, in the case of viewing a rotated coin, the visual system is sensitive to what has often been called “perspectival shapes.” It has generated vigorous discussions, including an online symposium by Morales and Cohen, an exchange between Linton (2021) and Morales et al. (2021), and most recently, a fierce critique by Burge and Burge (2022), in which they launch various conceptual (...)
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    The impact of independent director interlocks on corporate green innovation: evidence from Chinese listed companies.Jalal Khan, Wu Fengyun & Arshad Fawad - forthcoming - International Journal of Business Governance and Ethics.
    Green innovation plays a critical role in mitigating environmental issues and balancing the interaction between economic growth and the natural environment. Drawing on social network and resource-dependence theory, this article scrutinises the relationship between independent director interlocks and corporate green innovation. Using the data from listed Chinese companies from 2010 to 2022, this study finds that independent director interlocks can significantly promote corporate green processes and product innovation. This research further finds that internal corporate contexts can also influence the relationship (...)
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  42. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
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  43. Perplexities of Consciousness, by Eric Schwitzgebel. [REVIEW]Sebastian Watzl & Wayne Wu - 2012 - Mind 121 (482):524-529.
    In this review of Eric Schwitzgebel's "Perplexities of Consciousness", we discuss the book's arguments in light of the role of attention in introspection.
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  44. Minimal Turing Test and Children's Education.Duan Zhang, Xiaoan Wu & Jijun He - 2022 - Journal of Human Cognition 6 (1):47-58.
    Considerable evidence proves that causal learning and causal understanding greatly enhance our ability to manipulate the physical world and are major factors that distinguish humans from other primates. How do we enable unintelligent robots to think causally, answer the questions raised with "why" and even understand the meaning of such questions? The solution is one of the keys to realizing artificial intelligence. Judea Pearl believes that to achieve human-like intelligence, researchers must start by imitating the intelligence of children, so he (...)
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  45. The effect of subliminal priming on team trust: The mediating role of perceived trustworthiness.Jie Cai, Rongxiu Wu, Jingyu Zhang & Xianghong Sun - 2023 - Frontiers in Psychology 14:1099267.
    The present study aimed to explore the effect of subliminal priming on team trust and the mechanism through the mediating role of perceived trustworthiness. A total of 144 participants were asked to complete a lexical decision task that was embedded with the “trust” or “suspicion” Chinese words as the subliminal stimuli. Then, they played a public good game and evaluated the perceived trustworthiness of the team. The results of the study showed that subliminal stimuli had a significant effect on team (...)
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  46. 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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  47. 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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  48. 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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  49. TGF-beta signaling proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...)
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  50. The development of non-coding RNA ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...)
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